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Balam S, Miura K, Ayadi I, Konaté D, Incandela NC, Agnolon V, Guindo MA, Diakité SA, Olugbile S, Nebie I, Herrera SM, Long C, Kajava AV, Diakité M, Corradin G, Herrera S, Herrera MA. Cross-reactivity of r Pvs48/45, a recombinant Plasmodium vivax protein, with sera from Plasmodium falciparum endemic areas of Africa. bioRxiv 2024:2024.04.10.588966. [PMID: 38659832 PMCID: PMC11042229 DOI: 10.1101/2024.04.10.588966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Background Ps48/45, a Plasmodium gametocyte surface protein, is a promising candidate for malaria transmission-blocking (TB) vaccine. Due to its relevance for a multispecies vaccine, we explored the cross-reactivity and TB activity of a recombinant P. vivax Ps48/45 protein (rPvs48/45) with sera from P. falciparum-exposed African donors. Methods rPvs48/45 was produced in Chinese hamster ovary cell lines and tested by ELISA for its cross-reactivity with sera from Burkina Faso, Tanzania, Mali, and Nigeria - In addition, BALB/c mice were immunized with the rPvs48/45 protein formulated in Montanide ISA-51 and inoculated with a crude extract of P. falciparum NF-54 gametocytes to evaluate the parasite-boosting effect on rPvs48/45 antibody titers. Specific anti-rPvs48/45 IgG purified from African sera was used to evaluate the ex vivo TB activity on P. falciparum, using standard mosquito membrane feeding assays (SMFA). Results rPvs48/45 protein showed cross-reactivity with sera of individuals from all four African countries, in proportions ranging from 94% (Tanzania) to 40% (Nigeria). Also, the level of cross-reactive antibodies varied significantly between countries (p<0.0001), with a higher antibody level in Mali and the lowest in Nigeria. In addition, antibody levels were higher in adults (≥ 17 years) than young children (≤ 5 years) in both Mali and Tanzania, with a higher proportion of responders in adults (90%) than in children (61%) (p<0.0001) in Mali, where male (75%) and female (80%) displayed similar antibody responses. Furthermore, immunization of mice with P. falciparum gametocytes boosted anti-Pvs48/45 antibody responses, recognizing P. falciparum gametocytes in indirect immunofluorescence antibody test. Notably, rPvs48/45 affinity-purified African IgG exhibited a TB activity of 61% against P. falciparum in SMFA. Conclusion African sera (exposed only to P. falciparum) cross-recognized the rPvs48/45 protein. This, together with the functional activity of IgG, warrants further studies for the potential development of a P. vivax and P. falciparum cross-protective TB vaccine.
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Affiliation(s)
- Saidou Balam
- International Center for Excellence in Research (ICER-Mali), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Imen Ayadi
- Immunobiology Department, University of Lausanne, Lausanne, Switzerland
| | - Drissa Konaté
- International Center for Excellence in Research (ICER-Mali), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Valentina Agnolon
- Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland aaaa
| | - Merepen A Guindo
- International Center for Excellence in Research (ICER-Mali), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seidina A.S. Diakité
- International Center for Excellence in Research (ICER-Mali), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Sope Olugbile
- Immunobiology Department, University of Lausanne, Lausanne, Switzerland
| | - Issa Nebie
- Groupe de Recherche Action Santé (GRAS), Burkina Faso, West Africa
| | | | - Carole Long
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Andrey V. Kajava
- Montpellier Cell Biology Research Center (CRBM), University of Montpellier, CNRS, France
| | - Mahamadou Diakité
- International Center for Excellence in Research (ICER-Mali), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Socrates Herrera
- Caucaseco Scientific Research Center, Cali, Colombia
- Malaria Vaccine and Drug Development Center, Cali, Colombia
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Bondarev SA, Uspenskaya MV, Leclercq J, Falgarone T, Zhouravleva GA, Kajava AV. AmyloComp: A Bioinformatic Tool for Prediction of Amyloid Co-aggregation. J Mol Biol 2024:168437. [PMID: 38185324 DOI: 10.1016/j.jmb.2024.168437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
Typically, amyloid fibrils consist of multiple copies of the same protein. In these fibrils, each polypeptide chain adopts the same β-arc-containing conformation and these chains are stacked in a parallel and in-register manner. In the last few years, however, a considerable body of data has been accumulated about co-aggregation of different amyloid-forming proteins. Among known examples of the co-aggregation are heteroaggregates of different yeast prions and human proteins Rip1 and Rip3. Since the co-aggregation is linked to such important phenomena as infectivity of amyloids and molecular mechanisms of functional amyloids, we analyzed its structural aspects in more details. An axial stacking of different proteins within the same amyloid fibril is one of the most common type of co-aggregation. By using an approach based on structural similarity of the growing tips of amyloids, we developed a computational method to predict amyloidogenic β-arch structures that are able to interact with each other by the axial stacking. Furthermore, we compiled a dataset consisting of 26 experimentally known pairs of proteins capable or incapable to co-aggregate. We utilized this dataset to test and refine our algorithm. The developed method opens a way for a number of applications, including the identification of microbial proteins capable triggering amyloidosis in humans. AmyloComp is available on the website: https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=30.
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Affiliation(s)
- Stanislav A Bondarev
- Department of Genetics and Biotechnology and Laboratory of Amyloid Biology, St. Petersburg State University, Saint Petersburg 199034, Russian Federation.
| | - Mayya V Uspenskaya
- Institute of Bioengineering, ITMO University, St. Petersburg 197101, Russian Federation
| | - Jérémy Leclercq
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France
| | - Théo Falgarone
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology and Laboratory of Amyloid Biology, St. Petersburg State University, Saint Petersburg 199034, Russian Federation
| | - Andrey V Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France.
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3
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Monzon AM, Arrías PN, Elofsson A, Mier P, Andrade-Navarro MA, Bevilacqua M, Clementel D, Bateman A, Hirsh L, Fornasari MS, Parisi G, Piovesan D, Kajava AV, Tosatto SCE. A STRP-ed definition of Structured Tandem Repeats in Proteins. J Struct Biol 2023; 215:108023. [PMID: 37652396 DOI: 10.1016/j.jsb.2023.108023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/31/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
Tandem Repeat Proteins (TRPs) are a class of proteins with repetitive amino acid sequences that have been studied extensively for over two decades. Different features at the level of sequence, structure, function and evolution have been attributed to them by various authors. And yet many of its salient features appear only when looking at specific subclasses of protein tandem repeats. Here, we attempt to rationalize the existing knowledge on Tandem Repeat Proteins (TRPs) by pointing out several dichotomies. The emerging picture is more nuanced than generally assumed and allows us to draw some boundaries of what is not a "proper" TRP. We conclude with an operational definition of a specific subset, which we have denominated STRPs (Structural Tandem Repeat Proteins), which separates a subclass of tandem repeats with distinctive features from several other less well-defined types of repeats. We believe that this definition will help researchers in the field to better characterize the biological meaning of this large yet largely understudied group of proteins.
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Affiliation(s)
- Alexander Miguel Monzon
- Dept. of Information Engineering, University of Padova, via Giovanni Gradenigo 6/B, 35131 Padova, Italy
| | - Paula Nazarena Arrías
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Arne Elofsson
- Dept. of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Tomtebodavägen 23, 171 21 Solna, Sweden
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Martina Bevilacqua
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Damiano Clementel
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Layla Hirsh
- Dept. of Engineering, Faculty of Science and Engineering, Pontifical Catholic University of Peru, Av. Universitaria 1801 San Miguel, Lima 32, Lima, Peru
| | - Maria Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | - Damiano Piovesan
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, 34293 Montpellier, France
| | - Silvio C E Tosatto
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy.
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4
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Arrías PN, Monzon AM, Clementel D, Mozaffari S, Piovesan D, Kajava AV, Tosatto SCE. The repetitive structure of DNA clamps: An overlooked protein tandem repeat. J Struct Biol 2023; 215:108001. [PMID: 37467824 DOI: 10.1016/j.jsb.2023.108001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Structured tandem repeats proteins (STRPs) are a specific kind of tandem repeat proteins characterized by a modular and repetitive three-dimensional structure arrangement. The majority of STRPs adopt solenoid structures, but with the increasing availability of experimental structures and high-quality predicted structural models, more STRP folds can be characterized. Here, we describe "Box repeats", an overlooked STRP fold present in the DNA sliding clamp processivity factors, which has eluded classification although structural data has been available since the late 1990s. Each Box repeat is a β⍺βββ module of about 60 residues, which forms a class V "beads-on-a-string" type STRP. The number of repeats present in processivity factors is organism dependent. Monomers of PCNA proteins in both Archaea and Eukarya have 4 repeats, while the monomers of bacterial beta-sliding clamps have 6 repeats. This new repeat fold has been added to the RepeatsDB database, which now provides structural annotation for 66 Box repeat proteins belonging to different organisms, including viruses.
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Affiliation(s)
- Paula Nazarena Arrías
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Alexander Miguel Monzon
- Department of Information Engineering, University of Padova, via Giovanni Gradenigo 6/B, 35131 Padova, Italy
| | - Damiano Clementel
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Soroush Mozaffari
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, 34293 Montpellier, France
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy.
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5
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Manasra S, Kajava AV. Why does the first protein repeat often become the only one? J Struct Biol 2023; 215:108014. [PMID: 37567371 DOI: 10.1016/j.jsb.2023.108014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/06/2023] [Accepted: 08/09/2023] [Indexed: 08/13/2023]
Abstract
Proteins with two similar motifs in tandem are one of the most common cases of tandem repeat proteins. The question arises: why is the first emerged repeat frequently fixed in the process of evolution, despite the ample opportunities to continue its multiplication at the DNA level? To answer this question, we systematically analyzed the structure and function of these proteins. Our analysis showed that, in the vast majority of cases, the structural repetitive units have a two-fold (C2) internal symmetry. These closed structures provide an internal structural limitation for the subsequent growth of the repeat number. Frequently, the units "swap" their secondary structure elements with each other. Moreover, the duplicated domains, in contrast to other tandem repeat proteins, form binding sites for small molecules around the axis of C2 symmetry. Thus, the closure of the C2 structures and the emergence of new functional sites around the axis of C2 symmetry provide plausible explanations for why a repeat, once appeared, becomes fixed in the evolutionary process. We have placed these structures within the general structural classification of tandem repeat proteins, classifying them as either Class IV or V depending on the size of the repetitive unit.
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Affiliation(s)
- Simona Manasra
- Institute of Bioengineering, ITMO University, Kronverksky Pr. 49, 197101 Saint Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, 34293 Montpellier, France.
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6
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Falgarone T, Villain E, Richard F, Osmanli Z, Kajava AV. Census of exposed aggregation-prone regions in proteomes. Brief Bioinform 2023; 24:bbad183. [PMID: 37200152 DOI: 10.1093/bib/bbad183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/30/2023] [Accepted: 04/21/2023] [Indexed: 05/20/2023] Open
Abstract
Loss of solubility usually leads to the detrimental elimination of protein function. In some cases, the protein aggregation is also required for beneficial functions. Given the duality of this phenomenon, it remains a fundamental question how natural selection controls the aggregation. The exponential growth of genomic sequence data and recent progress with in silico predictors of the aggregation allows approaching this problem by a large-scale bioinformatics analysis. Most of the aggregation-prone regions are hidden within the 3D structure, rendering them inaccessible for the intermolecular interactions responsible for aggregation. Thus, the most realistic census of the aggregation-prone regions requires crossing aggregation prediction with information about the location of the natively unfolded regions. This allows us to detect so-called 'exposed aggregation-prone regions' (EARs). Here, we analyzed the occurrence and distribution of the EARs in 76 reference proteomes from the three kingdoms of life. For this purpose, we used a bioinformatics pipeline, which provides a consensual result based on several predictors of aggregation. Our analysis revealed a number of new statistically significant correlations about the presence of EARs in different organisms, their dependence on protein length, cellular localizations, co-occurrence with short linear motifs and the level of protein expression. We also obtained a list of proteins with the conserved aggregation-prone sequences for further experimental tests. Insights gained from this work led to a deeper understanding of the relationship between protein evolution and aggregation.
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Affiliation(s)
- Théo Falgarone
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
| | - Etienne Villain
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
| | - Francois Richard
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
| | - Zarifa Osmanli
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
- Biophysics Institute, Ministry of Science and Education of Azerbaijan Republic, Az1141, Baku, Azerbaijan
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
- Institut de Biologie Computationnelle, Université Montpellier, 34095 Montpellier, France
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7
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Karas BY, Sitnikova VE, Nosenko TN, Dedkov VG, Arsentieva NA, Gavrilenko NV, Moiseev IS, Totolian AA, Kajava AV, Uspenskaya MV. ATR-FTIR spectrum analysis of plasma samples for rapid identification of recovered COVID-19 individuals. J Biophotonics 2023:e202200166. [PMID: 36869427 DOI: 10.1002/jbio.202200166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 01/08/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The development of fast, cheap and reliable methods to determine seroconversion against infectious agents is of great practical importance. In the context of the COVID-19 pandemic, an important issue is to study the rate of formation of the immune layer in the population of different regions, as well as the study of the formation of post-vaccination immunity in individuals after vaccination. Currently, the main method for this kind of research is enzyme immunoassay (ELISA, enzyme-linked immunosorbent assay). This technique is sufficiently sensitive and specific, but it requires significant time and material costs. We investigated the applicability of attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy associated with machine learning in blood plasma to detect seroconversion against SARS-CoV-2. The study included samples of 60 patients. Clear spectral differences in plasma samples from recovered COVID-19 patients and conditionally healthy donors were identified using multivariate and statistical analysis. The results showed that ATR-FTIR spectroscopy, combined with principal components analysis (PCA) and linear discriminant analysis (LDA) or artificial neural network (ANN), made it possible to efficiently identify specimens from recovered COVID-19 patients. We built classification models based on PCA associated with LDA and ANN. Our analysis led to 87% accuracy for PCA-LDA model and 91% accuracy for ANN, respectively. Based on this proof-of-concept study, we believe this method could offer a simple, label-free, cost-effective tool for detecting seroconversion against SARS-CoV-2. This approach could be used as an alternative to ELISA.
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Affiliation(s)
- Boris Y Karas
- Institute BioEngineering, ITMO University, St. Petersburg, Russia
| | - Vera E Sitnikova
- Institute BioEngineering, ITMO University, St. Petersburg, Russia
| | | | - Vladimir G Dedkov
- Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, St. Petersburg, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Natalia A Arsentieva
- Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, St. Petersburg, Russia
| | - Natalia V Gavrilenko
- Raisa Gorbacheva memorial Research Institute for Pediatric Oncology, Hematology and Transplantation, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Ivan S Moiseev
- Raisa Gorbacheva memorial Research Institute for Pediatric Oncology, Hematology and Transplantation, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Areg A Totolian
- Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, St. Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, Université Montpellier, Montpellier, France
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Bonnet M, Roche F, Fagotto-Kaufmann C, Gazdagh G, Truong I, Comunale F, Barbosa S, Bonhomme M, Nafati N, Hunt D, Rodriguez MP, Chaudhry A, Shears D, Madruga M, Vansenne F, Curie A, Kajava AV, Baralle D, Fassier C, Debant A, Schmidt S. Pathogenic TRIO variants associated with neurodevelopmental disorders perturb the molecular regulation of TRIO and axon pathfinding in vivo. Mol Psychiatry 2023; 28:1527-1544. [PMID: 36717740 DOI: 10.1038/s41380-023-01963-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 12/26/2022] [Accepted: 01/13/2023] [Indexed: 01/31/2023]
Abstract
The RhoGEF TRIO is known to play a major role in neuronal development by controlling actin cytoskeleton remodeling, primarily through the activation of the RAC1 GTPase. Numerous de novo mutations in the TRIO gene have been identified in individuals with neurodevelopmental disorders (NDDs). We have previously established the first phenotype/genotype correlation in TRIO-associated diseases, with striking correlation between the clinical features of the individuals and the opposite modulation of RAC1 activity by TRIO variants targeting different domains. The mutations hyperactivating RAC1 are of particular interest, as they are recurrently found in patients and are associated with a severe form of NDD and macrocephaly, indicating their importance in the etiology of the disease. Yet, it remains unknown how these pathogenic TRIO variants disrupt TRIO activity at a molecular level and how they affect neurodevelopmental processes such as axon outgrowth or guidance. Here we report an additional cohort of individuals carrying a pathogenic TRIO variant that reinforces our initial phenotype/genotype correlation. More importantly, by performing conformation predictions coupled to biochemical validation, we propose a model whereby TRIO is inhibited by an intramolecular fold and NDD-associated variants relieve this inhibition, leading to RAC1 hyperactivation. Moreover, we show that in cultured primary neurons and in the zebrafish developmental model, these gain-of-function variants differentially affect axon outgrowth and branching in vitro and in vivo, as compared to loss-of-function TRIO variants. In summary, by combining clinical, molecular, cellular and in vivo data, we provide compelling new evidence for the pathogenicity of novel genetic variants targeting the TRIO gene in NDDs. We report a novel mechanism whereby the fine-tuned regulation of TRIO activity is critical for proper neuronal development and is disrupted by pathogenic mutations.
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Affiliation(s)
- Maxime Bonnet
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), University of Montpellier, CNRS, Montpellier, France
| | - Fiona Roche
- Institut de la Vision, Sorbonne University, CNRS, INSERM, Paris, France
| | - Christine Fagotto-Kaufmann
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), University of Montpellier, CNRS, Montpellier, France
| | - Gabriella Gazdagh
- Faculty of Medicine, University of Southampton, Southampton, SO16 5YA, UK.,Wessex Clinical Genetics Service, University Hospital Southampton National Health Service Foundation Trust, Southampton, SO16 5YA, UK
| | - Iona Truong
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), University of Montpellier, CNRS, Montpellier, France.,Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Franck Comunale
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), University of Montpellier, CNRS, Montpellier, France
| | - Sonia Barbosa
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), University of Montpellier, CNRS, Montpellier, France
| | - Marion Bonhomme
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), University of Montpellier, CNRS, Montpellier, France
| | - Nicolas Nafati
- Montpellier Ressources Imagerie, BioCampus, University of Montpellier, CNRS, INSERM, 34293, Montpellier, France
| | - David Hunt
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, SO16 5YA, UK
| | | | - Ayeshah Chaudhry
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Deborah Shears
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Marcos Madruga
- Hospital Viamed Santa Ángela De la Cruz, Sevilla, 41014, Spain
| | - Fleur Vansenne
- Department of Clinical Genetics, University Medical Center, Groningen, 9713 GZ, Groningen, The Netherlands
| | - Aurore Curie
- Reference Center for Intellectual Disability from rare causes, Department of Child Neurology, Woman Mother and Child Hospital, Hospices Civils de Lyon, Lyon Neuroscience Research Centre, CNRS UMR5292, INSERM U1028, Université de Lyon, Bron, France
| | - Andrey V Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), University of Montpellier, CNRS, Montpellier, France
| | - Diana Baralle
- Faculty of Medicine, University of Southampton, Southampton, SO16 5YA, UK
| | - Coralie Fassier
- Institut de la Vision, Sorbonne University, CNRS, INSERM, Paris, France
| | - Anne Debant
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), University of Montpellier, CNRS, Montpellier, France.
| | - Susanne Schmidt
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), University of Montpellier, CNRS, Montpellier, France.
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Osmanli Z, Falgarone T, Samadova T, Aldrian G, Leclercq J, Shahmuradov I, Kajava AV. The Difference in Structural States between Canonical Proteins and Their Isoforms Established by Proteome-Wide Bioinformatics Analysis. Biomolecules 2022; 12:1610. [PMID: 36358962 PMCID: PMC9687161 DOI: 10.3390/biom12111610] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 09/02/2023] Open
Abstract
Alternative splicing is an important means of generating the protein diversity necessary for cellular functions. Hence, there is a growing interest in assessing the structural and functional impact of alternative protein isoforms. Typically, experimental studies are used to determine the structures of the canonical proteins ignoring the other isoforms. Therefore, there is still a large gap between abundant sequence information and meager structural data on these isoforms. During the last decade, significant progress has been achieved in the development of bioinformatics tools for structural and functional annotations of proteins. Moreover, the appearance of the AlphaFold program opened up the possibility to model a large number of high-confidence structures of the isoforms. In this study, using state-of-the-art tools, we performed in silico analysis of 58 eukaryotic proteomes. The evaluated structural states included structured domains, intrinsically disordered regions, aggregation-prone regions, and tandem repeats. Among other things, we found that the isoforms have fewer signal peptides, transmembrane regions, or tandem repeat regions in comparison with their canonical counterparts. This could change protein function and/or cellular localization. The AlphaFold modeling demonstrated that frequently isoforms, having differences with the canonical sequences, still can fold in similar structures though with significant structural rearrangements which can lead to changes of their functions. Based on the modeling, we suggested classification of the structural differences between canonical proteins and isoforms. Altogether, we can conclude that a majority of isoforms, similarly to the canonical proteins are under selective pressure for the functional roles.
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Affiliation(s)
- Zarifa Osmanli
- CRBM, Université de Montpellier, CNRS, 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France
- Institute of Biophysics, ANAS, Baku AZ1141, Azerbaijan
| | - Theo Falgarone
- CRBM, Université de Montpellier, CNRS, 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France
| | | | - Gudrun Aldrian
- CRBM, Université de Montpellier, CNRS, 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France
| | - Jeremy Leclercq
- CRBM, Université de Montpellier, CNRS, 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France
| | | | - Andrey V. Kajava
- CRBM, Université de Montpellier, CNRS, 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France
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10
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Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Basquin J, Lindorff-Larsen K, Bateman A, Kajava AV, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P. A structural biology community assessment of AlphaFold2 applications. Nat Struct Mol Biol 2022; 29:1056-1067. [PMID: 36344848 PMCID: PMC9663297 DOI: 10.1038/s41594-022-00849-w] [Citation(s) in RCA: 179] [Impact Index Per Article: 89.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 09/20/2022] [Indexed: 11/09/2022]
Abstract
Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have reached the accuracy of experimentally determined models. Although this has been independently verified, the implementation of these methods across structural-biology applications remains to be tested. Here, we evaluate the use of AlphaFold2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modeling of interactions; and modeling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modeled when compared with homology modeling, identifying structural features rarely seen in the Protein Data Bank. AF2-based predictions of protein disorder and complexes surpass dedicated tools, and AF2 models can be used across diverse applications equally well compared with experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life-science research.
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Affiliation(s)
- Mehmet Akdel
- Bioinformatics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, the Netherlands
| | - Douglas E V Pires
- School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Eduard Porta Pardo
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Jürgen Jänes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Arthur O Zalevsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Patrick Bryant
- Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden
| | - Lydia L Good
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Roman A Laskowski
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Gabriele Pozzati
- Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden
| | - Aditi Shenoy
- Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden
| | - Wensi Zhu
- Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden
| | - Petras Kundrotas
- Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden
| | | | - Carlos H M Rodrigues
- School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Alistair S Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - David Burke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Neera Borkakoti
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Adam Frost
- Department of Biochemistry and Biophysics University of California, San Francisco, CA, USA
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Andrey V Kajava
- Université de Montpellier, Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM) CNRS, Montpellier, France
| | | | - Sergey Ovchinnikov
- Faculty of Arts and Sciences, Division of Science, Harvard University, Cambridge, MA, USA.
| | | | - David B Ascher
- School of Chemistry and Molecular Biology, University of Queensland, Brisbane, Queensland, Australia.
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
| | | | - Amelie Stein
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Arne Elofsson
- Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden.
| | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, The University of Cambridge, Cambridge, UK.
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.
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11
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Pratesi F, Errante F, Pacini L, Peña-Moreno IC, Quiceno S, Carotenuto A, Balam S, Konaté D, Diakité MM, Arévalo-Herrera M, Kajava AV, Rovero P, Corradin G, Migliorini P, Papini AM, Herrera S. A SARS-CoV-2 Spike Receptor Binding Motif Peptide Induces Anti-Spike Antibodies in Mice andIs Recognized by COVID-19 Patients. Front Immunol 2022; 13:879946. [PMID: 35693806 PMCID: PMC9178084 DOI: 10.3389/fimmu.2022.879946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
The currently devastating pandemic of severe acute respiratory syndrome known as coronavirus disease 2019 or COVID-19 is caused by the coronavirus SARS-CoV-2. Both the virus and the disease have been extensively studied worldwide. A trimeric spike (S) protein expressed on the virus outer bilayer leaflet has been identified as a ligand that allows the virus to penetrate human host cells and cause infection. Its receptor-binding domain (RBD) interacts with the angiotensin-converting enzyme 2 (ACE2), the host-cell viral receptor, and is, therefore, the subject of intense research for the development of virus control means, particularly vaccines. In this work, we search for smaller fragments of the S protein able to elicit virus-neutralizing antibodies, suitable for production by peptide synthesis technology. Based on the analysis of available data, we selected a 72 aa long receptor binding motif (RBM436-507) of RBD. We used ELISA to study the antibody response to each of the three antigens (S protein, its RBD domain and the RBM436-507 synthetic peptide) in humans exposed to the infection and in immunized mice. The seroreactivity analysis showed that anti-RBM antibodies are produced in COVID-19 patients and immunized mice and may exert neutralizing function, although with a frequency lower than anti-S and -RBD. These results provide a basis for further studies towards the development of vaccines or treatments focused on specific regions of the S virus protein, which can benefit from the absence of folding problems, conformational constraints and other advantages of the peptide synthesis production.
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Affiliation(s)
- Federico Pratesi
- Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Fosca Errante
- Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino, Italy
| | - Lorenzo Pacini
- Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | | | - Sebastian Quiceno
- Department of Immunology, Caucaseco Scientific Research Center, Cali, Colombia
| | | | - Saidou Balam
- Immunogenetic Laboratory and Parasitology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Drissa Konaté
- Immunogenetic Laboratory and Parasitology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mahamadou M. Diakité
- Immunogenetic Laboratory and Parasitology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | | | - Paolo Rovero
- Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino, Italy
| | | | - Paola Migliorini
- Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Anna M. Papini
- Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Sócrates Herrera
- Department of Immunology, Caucaseco Scientific Research Center, Cali, Colombia
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12
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Traoré A, Guindo MA, Konaté D, Traoré B, Diakité SA, Kanté S, Dembélé A, Cissé A, Incandela NC, Kodio M, Coulibaly YI, Faye O, Kajava AV, Pratesi F, Migliorini P, Papini AM, Pacini L, Rovero P, Errante F, Diakité M, Arevalo-Herrera M, Herrera S, Corradin G, Balam S. Seroreactivity of the Severe Acute Respiratory Syndrome Coronavirus 2 Recombinant S Protein, Receptor-Binding Domain, and Its Receptor-Binding Motif in COVID-19 Patients and Their Cross-Reactivity With Pre-COVID-19 Samples From Malaria-Endemic Areas. Front Immunol 2022; 13:856033. [PMID: 35585976 PMCID: PMC9109707 DOI: 10.3389/fimmu.2022.856033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/28/2022] [Indexed: 12/23/2022] Open
Abstract
Despite the global interest and the unprecedented number of scientific studies triggered by the COVID-19 pandemic, few data are available from developing and low-income countries. In these regions, communities live under the threat of various transmissible diseases aside from COVID-19, including malaria. This study aims to determine the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroreactivity of antibodies from COVID-19 and pre-COVID-19 samples of individuals in Mali (West Africa). Blood samples from COVID-19 patients (n = 266) at Bamako Dermatology Hospital (HDB) and pre-COVID-19 donors (n = 283) from a previous malaria survey conducted in Dangassa village were tested by ELISA to assess IgG antibodies specific to the full-length spike (S) protein, the receptor-binding domain (RBD), and the receptor-binding motif (RBM436-507). Study participants were categorized by age, gender, treatment duration for COVID-19, and comorbidities. In addition, the cross-seroreactivity of samples from pre-COVID-19, malaria-positive patients against the three antigens was assessed. Recognition of the SARS-CoV-2 proteins by sera from COVID-19 patients was 80.5% for S, 71.1% for RBD, and 31.9% for RBM (p < 0.001). While antibody responses to S and RBD tended to be age-dependent, responses to RBM were not. Responses were not gender-dependent for any of the antigens. Higher antibody levels to S, RBD, and RBM at hospital entry were associated with shorter treatment durations, particularly for RBD (p < 0.01). In contrast, higher body weights negatively influenced the anti-S antibody response, and asthma and diabetes weakened the anti-RBM antibody responses. Although lower, a significant cross-reactive antibody response to S (21.9%), RBD (6.7%), and RBM (8.8%) was detected in the pre-COVID-19 and malaria samples. Cross-reactive antibody responses to RBM were mostly associated (p < 0.01) with the absence of current Plasmodium falciparum infection, warranting further study.
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Affiliation(s)
- Abdouramane Traoré
- Immunogenetic Laboratory and Parasitology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Merepen A. Guindo
- Immunogenetic Laboratory and Parasitology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Drissa Konaté
- Immunogenetic Laboratory and Parasitology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bourama Traoré
- Department of Ministry of Health and Social Development, Hopital de Dermatologie de Bamako (HDB), Bamako, Mali
| | - Seidina A. Diakité
- Immunogenetic Laboratory and Parasitology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Salimata Kanté
- Immunogenetic Laboratory and Parasitology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Assitan Dembélé
- Immunogenetic Laboratory and Parasitology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Abdourhamane Cissé
- Immunogenetic Laboratory and Parasitology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Nathan C. Incandela
- Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, United States
| | - Mamoudou Kodio
- Department of Ministry of Health and Social Development, Hopital de Dermatologie de Bamako (HDB), Bamako, Mali
| | - Yaya I. Coulibaly
- Department of Ministry of Health and Social Development, Hopital de Dermatologie de Bamako (HDB), Bamako, Mali
| | - Ousmane Faye
- Department of Ministry of Health and Social Development, Hopital de Dermatologie de Bamako (HDB), Bamako, Mali
| | - Andrey V. Kajava
- Montpellier Cell Biology Research Center (CRBM), University of Montpellier, CNRS, Montpellier, France
| | - Federico Pratesi
- Immuno-Allergology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Paola Migliorini
- Immuno-Allergology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Florence, Italy
| | - Lorenzo Pacini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Florence, Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Neurosciences, Psychology, Drug Research and Child Health, Section of Pharmaceutical Sciences and Nutraceutics, University of Florence, Florence, Italy
| | - Fosca Errante
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Neurosciences, Psychology, Drug Research and Child Health, Section of Pharmaceutical Sciences and Nutraceutics, University of Florence, Florence, Italy
| | - Mahamadou Diakité
- Immunogenetic Laboratory and Parasitology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Myriam Arevalo-Herrera
- Department of Immunology, Malaria Vaccine and Drug Development Center, Cali, Colombia
- Department of Immunology, Caucaseco Scientific Research Center, Cali, Colombia
| | - Socrates Herrera
- Department of Immunology, Malaria Vaccine and Drug Development Center, Cali, Colombia
- Department of Immunology, Caucaseco Scientific Research Center, Cali, Colombia
| | | | - Saidou Balam
- Immunogenetic Laboratory and Parasitology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
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13
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Falgarone T, Villain É, Guettaf A, Leclercq J, Kajava AV. TAPASS: Tool for Annotation of Protein Amyloidogenicity in the context of other Structural States. J Struct Biol 2022; 214:107840. [PMID: 35149212 DOI: 10.1016/j.jsb.2022.107840] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/03/2022] [Accepted: 02/04/2022] [Indexed: 12/28/2022]
Abstract
Numerous studies have demonstrated that the propensity of a protein to form amyloids or amorphous aggregates is encoded by its amino acid sequence. This led to the emergence of several computational programs to predict amyloidogenicity from amino acid sequences. However, a growing number of studies indicate that an accurate prediction of the protein aggregation can only be achieved when also accounting for the overall structural context of the protein, and the likelihood of transition between the initial state and the aggregate. Here, we describe a computational pipeline called TAPASS, which was designed to do just that. The pipeline assigns each residue of a protein as belonging to a structured region or an intrinsically disordered region (IDR). For this purpose, TAPASS uses either several state-of-the-art programs for prediction of IDRs, of transmembrane regions and of structured domains or the artificial intelligence program AlphaFold. In the next step, this assignment is crossed with amyloidogenicity prediction. As a result, TAPASS allows the detection of Exposed Amyloidogenic Regions (EARs) located within intrinsically disordered regions (IDRs) and carrying high amyloidogenic potential. TAPASS can substantially improve the prediction of amyloids and be used in proteome-wide analysis to discover new amyloid-forming proteins. Its results, combined with clinical data, can create individual risk profiles for different amyloidoses, opening up new opportunities for personalised medicine. The architecture of the pipeline is designed so that it makes it easy to add new individual predictors as they become available. TAPASS can be used through the web interface (https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=32).
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Affiliation(s)
- Théo Falgarone
- CRBM, Université de Montpellier, CNRS, Montpellier, France
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14
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Tamburrini KC, Pesce G, Nilsson J, Gondelaud F, Kajava AV, Berrin JG, Longhi S. Predicting Protein Conformational Disorder and Disordered Binding Sites. Methods Mol Biol 2022; 2449:95-147. [PMID: 35507260 DOI: 10.1007/978-1-0716-2095-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In the last two decades it has become increasingly evident that a large number of proteins adopt either a fully or a partially disordered conformation. Intrinsically disordered proteins are ubiquitous proteins that fulfill essential biological functions while lacking a stable 3D structure. Their conformational heterogeneity is encoded by the amino acid sequence, thereby allowing intrinsically disordered proteins or regions to be recognized based on their sequence properties. The identification of disordered regions facilitates the functional annotation of proteins and is instrumental for delineating boundaries of protein domains amenable to crystallization. This chapter focuses on the methods currently employed for predicting protein disorder and identifying intrinsically disordered binding sites.
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Affiliation(s)
- Ketty C Tamburrini
- Aix Marseille Univ, CNRS, Architecture et Fonction des Macromolécules Biologiques, AFMB, UMR 7257, Marseille, France
- INRAE, Aix Marseille Univ, Biodiversité et Biotechnologie Fongiques (BBF), UMR 1163, Marseille, France
| | - Giulia Pesce
- Aix Marseille Univ, CNRS, Architecture et Fonction des Macromolécules Biologiques, AFMB, UMR 7257, Marseille, France
| | - Juliet Nilsson
- Aix Marseille Univ, CNRS, Architecture et Fonction des Macromolécules Biologiques, AFMB, UMR 7257, Marseille, France
| | - Frank Gondelaud
- Aix Marseille Univ, CNRS, Architecture et Fonction des Macromolécules Biologiques, AFMB, UMR 7257, Marseille, France
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237, CNRS, Université Montpellier, Montpellier, France
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ, Biodiversité et Biotechnologie Fongiques (BBF), UMR 1163, Marseille, France
| | - Sonia Longhi
- Aix Marseille Univ, CNRS, Architecture et Fonction des Macromolécules Biologiques, AFMB, UMR 7257, Marseille, France.
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15
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Singh P, Samanta K, Kebe NM, Michel G, Legrand B, Sitnikova VE, Kajava AV, Pagès M, Bastien P, Pomares C, Coux O, Hernandez JF. The C-terminal segment of Leishmania major HslU: Toward potential inhibitors of LmHslVU activity. Bioorg Chem 2021; 119:105539. [PMID: 34894575 DOI: 10.1016/j.bioorg.2021.105539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/08/2021] [Accepted: 12/01/2021] [Indexed: 01/23/2023]
Abstract
It is urgent to develop less toxic and more efficient treatments for leishmaniases and trypanosomiases. We explore the possibility to target the parasite mitochondrial HslVU protease, which is essential for growth and has no analogue in the human host. For this, we develop compounds potentially inhibiting the complex assembly by mimicking the C-terminal (C-ter) segment of the ATPase HslU. We previously showed that a dodecapeptide derived from Leishmania major HslU C-ter segment (LmC12-U2, Cpd 1) was able to bind to and activate the digestion of a fluorogenic substrate by LmHslV. Here, we present the study of its structure-activity relationships. By replacing each essential residue with related non-proteinogenic residues, we obtained more potent analogues. In particular, a cyclohexylglycine residue at position 11 (cpd 24) allowed a more than three-fold gain in potency while reducing the size of compound 24 from twelve to six residues (cpd 50) without significant loss of potency, opening the way toward short HslU C-ter peptidomimetics as potential inhibitors of HslV proteolytic function. Finally, conjugates constituted of LmC6-U2 analogues and a mitochondrial penetrating peptide were found to penetrate into the promastigote form of L. infantum and to inhibit the parasite growth without showing toxicity toward human THP-1 cells at the same concentration (i.e. 30 μM).
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Affiliation(s)
- Priyanka Singh
- IBMM, CNRS, Univ Montpellier, ENSCM, Montpellier, France
| | | | - Ndeye Mathy Kebe
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), UMR5237, CNRS, Univ Montpellier, 1919, route de Mende, 34000 Montpellier, France
| | - Grégory Michel
- Centre Méditerranéen de Médecine Moléculaire (C3M), U1065, Université Côte d'Azur, Inserm, Archimed Building, 151 route Saint Antoine de Ginestière, 06000 Nice, France
| | | | - Vera E Sitnikova
- International Research Institute of Bioengineering, ITMO University, Kronverksky Pr. 49, 197101 Saint Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), UMR5237, CNRS, Univ Montpellier, 1919, route de Mende, 34000 Montpellier, France
| | - Michel Pagès
- MIVEGEC, Univ Montpellier, CNRS, IRD, CHU, 191 avenue du Doyen Giraud, 34000 Montpellier, France
| | - Patrick Bastien
- MIVEGEC, Univ Montpellier, CNRS, IRD, CHU, 191 avenue du Doyen Giraud, 34000 Montpellier, France
| | - Christelle Pomares
- Centre Méditerranéen de Médecine Moléculaire (C3M), U1065, Université Côte d'Azur, Inserm, Archimed Building, 151 route Saint Antoine de Ginestière, 06000 Nice, France
| | - Olivier Coux
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), UMR5237, CNRS, Univ Montpellier, 1919, route de Mende, 34000 Montpellier, France.
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16
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Villain E, Fort P, Kajava AV. Aspartate-phobia of thermophiles as a reaction to deleterious chemical transformations. Bioessays 2021; 44:e2100213. [PMID: 34791689 DOI: 10.1002/bies.202100213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/08/2022]
Abstract
Prokaryotes growing at high temperatures have a high proportion of charged residues in their proteins to stabilize their 3D structure. By mining 175 disparate bacterial and archaeal proteomes we found that, against the general trend for charged residues, the frequency of aspartic acid residues decreases strongly as natural growth temperature increases. In search of the explanation, we hypothesized that the reason for such unusual correlation is the deleterious consequences of spontaneous chemical transformations of aspartate at high temperatures. Our subsequent statistical analysis supported this hypothesis. This finding reveals that organisms have likely adapted to high temperatures by minimizing the harmful consequences of spontaneous chemical transformations.
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Affiliation(s)
- Etienne Villain
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université de Montpellier 1919 Route de Mende, Montpellier, France
| | - Philippe Fort
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université de Montpellier 1919 Route de Mende, Montpellier, France
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université de Montpellier 1919 Route de Mende, Montpellier, France
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17
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Salladini E, Gondelaud F, Nilsson JF, Pesce G, Bignon C, Murrali MG, Fabre R, Pierattelli R, Kajava AV, Horvat B, Gerlier D, Mathieu C, Longhi S. Identification of a Region in the Common Amino-terminal Domain of Hendra Virus P, V, and W Proteins Responsible for Phase Transition and Amyloid Formation. Biomolecules 2021; 11:1324. [PMID: 34572537 PMCID: PMC8471210 DOI: 10.3390/biom11091324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022] Open
Abstract
Henipaviruses are BSL-4 zoonotic pathogens responsible in humans for severe encephalitis. Their V protein is a key player in the evasion of the host innate immune response. We previously showed that the Henipavirus V proteins consist of a long intrinsically disordered N-terminal domain (NTD) and a β-enriched C-terminal domain (CTD). These terminals are critical for V binding to DDB1, which is a cellular protein that is a component of the ubiquitin ligase E3 complex, as well as binding to MDA5 and LGP2, which are two host sensors of viral RNA. Here, we serendipitously discovered that the Hendra virus V protein undergoes a liquid-to-hydrogel phase transition and identified the V region responsible for this phenomenon. This region, referred to as PNT3 and encompassing residues 200-310, was further investigated using a combination of biophysical and structural approaches. Congo red binding assays, together with negative-staining transmisison electron microscopy (TEM) studies, show that PNT3 forms amyloid-like fibrils. Fibrillation abilities are dramatically reduced in a rationally designed PNT3 variant in which a stretch of three contiguous tyrosines, falling within an amyloidogenic motif, were replaced by three alanines. Worthy to note, Congo red staining experiments provided hints that these amyloid-like fibrils form not only in vitro but also in cellula after transfection or infection. The present results set the stage for further investigations aimed at assessing the functional role of phase separation and fibrillation by the Henipavirus V proteins.
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Affiliation(s)
- Edoardo Salladini
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Frank Gondelaud
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Juliet F. Nilsson
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Giulia Pesce
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Christophe Bignon
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Maria Grazia Murrali
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy; (M.G.M.); (R.P.)
| | - Roxane Fabre
- Centre d’Immunologie de Marseille-Luminy (CIML), CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Aix Marseille University, CEDEX 9, 13288 Marseille, France;
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy; (M.G.M.); (R.P.)
| | - Andrey V. Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier, UMR 5237, CNRS, Université Montpellier, 34293 Montpellier, France;
| | - Branka Horvat
- Team Immunobiology of the Viral Infections, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM, U1111, CNRS, UMR 5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France; (B.H.); (D.G.); (C.M.)
| | - Denis Gerlier
- Team Immunobiology of the Viral Infections, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM, U1111, CNRS, UMR 5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France; (B.H.); (D.G.); (C.M.)
| | - Cyrille Mathieu
- Team Immunobiology of the Viral Infections, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM, U1111, CNRS, UMR 5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France; (B.H.); (D.G.); (C.M.)
| | - Sonia Longhi
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
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18
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Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z, Ouzounis CA, Promponas VJ, Kajava AV, Hancock JM, Tosatto SCE, Dosztanyi Z, Andrade-Navarro MA. Disentangling the complexity of low complexity proteins. Brief Bioinform 2021; 21:458-472. [PMID: 30698641 PMCID: PMC7299295 DOI: 10.1093/bib/bbz007] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/19/2018] [Accepted: 01/07/2019] [Indexed: 12/31/2022] Open
Abstract
There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, and more generally the overlaps between different properties related to LCRs, using examples. We argue that statistical measures alone cannot capture all structural aspects of LCRs and recommend the combined usage of a variety of predictive tools and measurements. While the methodologies available to study LCRs are already very advanced, we foresee that a more comprehensive annotation of sequences in the databases will enable the improvement of predictions and a better understanding of the evolution and the connection between structure and function of LCRs. This will require the use of standards for the generation and exchange of data describing all aspects of LCRs. Short abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, plus overlaps between different properties related to LCRs, using examples.
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Affiliation(s)
- Pablo Mier
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Lisanna Paladin
- Department of Biomedical Science, University of Padova, Padova, Italy
| | - Stella Tamana
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Sophia Petrosian
- Biological Computation and Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
| | - Borbála Hajdu-Soltész
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Annika Urbanek
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Aleksandra Gruca
- Institute of Informatics, Silesian University of Technology, Gliwice, Poland
| | - Dariusz Plewczynski
- Center of New Technologies, University of Warsaw, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Christos A Ouzounis
- Biological Computation and Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Andrey V Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS-UMR, Institut de Biologie Computationnelle, Universite de Montpellier, Montpellier, France.,Institute of Bioengineering, University ITMO, St. Petersburg, Russia
| | - John M Hancock
- Earlham Institute, Norwich, UK.,ELIXIR Hub, Welcome Genome Campus, Hinxton, UK
| | - Silvio C E Tosatto
- Department of Biomedical Science, University of Padova, Padova, Italy.,CNR Institute of Neuroscience, Padova, Italy
| | - Zsuzsanna Dosztanyi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Mainz, Germany
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19
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Arévalo-Herrera M, Miura K, Cespedes N, Echeverry C, Solano E, Castellanos A, Ramirez JS, Miranda A, Kajava AV, Long C, Corradin G, Herrera S. Immunoreactivity of Sera From Low to Moderate Malaria-Endemic Areas Against Plasmodium vivax r Pvs48/45 Proteins Produced in Escherichia coli and Chinese Hamster Ovary Systems. Front Immunol 2021; 12:634738. [PMID: 34248932 PMCID: PMC8264144 DOI: 10.3389/fimmu.2021.634738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
P48/45 is a conserved gametocyte antigen involved in Plasmodium parasite fertilization. A recombinant Plasmodium vivax P48/45 (Pvs48/45) protein expressed in Escherichia coli (E. coli) was highly antigenic and immunogenic in experimental animals and elicited specific transmission-blocking (TB) antibodies in a previous pilot study. Here, a similar Pvs48/45 gene was expressed in Chinese Hamster Ovary (CHO) cells and we compared its immunoreactivity with the E. coli product. Specific antibody titers were determined using plasma from Colombian individuals (n=227) living in endemic areas where both P. vivax and P. falciparum are prevalent and from Guatemala (n=54) where P. vivax is highly prevalent. In Colombia, plasma seroprevalence to CHO-rPvs48/45 protein was 46.3%, while for E. coli-rPvs48/45 protein was 36.1% (p<0.001). In Guatemala, the sero prevalence was 24.1% and 14.8% (p<0.001), respectively. Reactivity index (RI) against both proteins showed an age-dependent increase. IgG2 was the predominant subclass and the antibody avidity index evaluated by ELISA ranged between 4-6 mol/L. Ex vivo P. vivax mosquito direct membrane feeding assays (DMFA) performed in presence of study plasmas, displayed significant parasite transmission-blocking (TB), however, there was no direct correlation between antibody titers and oocysts transmission reduction activity (%TRA). Nevertheless, DMFA with CHO rPvs48/45 affinity purified IgG showed a dose response; 90.2% TRA at 100 μg/mL and 71.8% inhibition at 10 μg/mL. In conclusion, the CHO-rPvs48/45 protein was more immunoreactive in most of the malaria endemic places studied, and CHO-rPvs48/45 specific IgG showed functional activity, supporting further testing of the protein vaccine potential.
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Affiliation(s)
- Myriam Arévalo-Herrera
- Immunology Department, Malaria Vaccine and Drug Development Center, Cali, Colombia
- Immunology Department, Caucaseco Scientific Research Center, Cali, Colombia
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Nora Cespedes
- Immunology Department, Malaria Vaccine and Drug Development Center, Cali, Colombia
| | - Carlos Echeverry
- Immunology Department, Malaria Vaccine and Drug Development Center, Cali, Colombia
| | - Eduardo Solano
- Immunology Department, Caucaseco Scientific Research Center, Cali, Colombia
| | - Angélica Castellanos
- Immunology Department, Malaria Vaccine and Drug Development Center, Cali, Colombia
| | | | - Adolfo Miranda
- Parasitology Department, Centro Nacional de Epidemiología (CNE), Guatemala City, Guatemala
| | - Andrey V. Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier, Université Montpellier, Montpellier, France
| | - Carole Long
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | | | - Sócrates Herrera
- Immunology Department, Malaria Vaccine and Drug Development Center, Cali, Colombia
- Immunology Department, Caucaseco Scientific Research Center, Cali, Colombia
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20
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Paladin L, Bevilacqua M, Errigo S, Piovesan D, Mičetić I, Necci M, Monzon AM, Fabre ML, Lopez JL, Nilsson JF, Rios J, Menna PL, Cabrera M, Buitron MG, Kulik MG, Fernandez-Alberti S, Fornasari MS, Parisi G, Lagares A, Hirsh L, Andrade-Navarro MA, Kajava AV, Tosatto SCE. RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures. Nucleic Acids Res 2021; 49:D452-D457. [PMID: 33237313 PMCID: PMC7778985 DOI: 10.1093/nar/gkaa1097] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/17/2020] [Accepted: 11/19/2020] [Indexed: 11/21/2022] Open
Abstract
The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class > Topology > Fold) with two new levels (Clan > Family) requiring sequence similarity and describing repeat motifs in collaboration with Pfam. Data growth has been addressed with improved mechanisms for browsing the classification hierarchy. A new UniProt-centric view unifies the increasingly frequent annotation of structures from identical or similar sequences. This update of RepeatsDB aligns with our commitment to develop a resource that extracts, organizes and distributes specialized information on tandem repeat protein structures.
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Affiliation(s)
- Lisanna Paladin
- Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy
| | - Martina Bevilacqua
- Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy
| | - Sara Errigo
- Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy
| | - Damiano Piovesan
- Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy
| | - Ivan Mičetić
- Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy
| | - Marco Necci
- Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy
| | | | - Maria Laura Fabre
- IBBM-CONICET, Dept. of Biological Sciences, La Plata National University, 49 y 115, 1900 La Plata, Argentina
| | - Jose Luis Lopez
- IBBM-CONICET, Dept. of Biological Sciences, La Plata National University, 49 y 115, 1900 La Plata, Argentina
| | - Juliet F Nilsson
- IBBM-CONICET, Dept. of Biological Sciences, La Plata National University, 49 y 115, 1900 La Plata, Argentina
| | - Javier Rios
- Dept. of Science and Technology, National University of Quilmes, Roque Sáenz Peña 352, Bernal, Buenos Aires, Argentina
| | - Pablo Lorenzano Menna
- Dept. of Science and Technology, National University of Quilmes, Roque Sáenz Peña 352, Bernal, Buenos Aires, Argentina
| | - Maia Cabrera
- Dept. of Science and Technology, National University of Quilmes, Roque Sáenz Peña 352, Bernal, Buenos Aires, Argentina
| | - Martin Gonzalez Buitron
- Dept. of Science and Technology, National University of Quilmes, Roque Sáenz Peña 352, Bernal, Buenos Aires, Argentina
| | - Mariane Gonçalves Kulik
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Sebastian Fernandez-Alberti
- Dept. of Science and Technology, National University of Quilmes, Roque Sáenz Peña 352, Bernal, Buenos Aires, Argentina
| | - Maria Silvina Fornasari
- Dept. of Science and Technology, National University of Quilmes, Roque Sáenz Peña 352, Bernal, Buenos Aires, Argentina
| | - Gustavo Parisi
- Dept. of Science and Technology, National University of Quilmes, Roque Sáenz Peña 352, Bernal, Buenos Aires, Argentina
| | - Antonio Lagares
- IBBM-CONICET, Dept. of Biological Sciences, La Plata National University, 49 y 115, 1900 La Plata, Argentina
| | - Layla Hirsh
- Dept. of Engineering, Faculty of Science and Engineering, Pontifical Catholic University of Peru, Av. Universitaria 1801 San Miguel, Lima 32, Lima, Peru
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237, CNRS, Univ. Montpellier, Montpellier, France
| | - Silvio C E Tosatto
- Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy
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21
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Perovic V, Leclercq JY, Sumonja N, Richard FD, Veljkovic N, Kajava AV. Tally-2.0: upgraded validator of tandem repeat detection in protein sequences. Bioinformatics 2020; 36:3260-3262. [PMID: 32096820 DOI: 10.1093/bioinformatics/btaa121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/02/2020] [Accepted: 02/18/2020] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Proteins containing tandem repeats (TRs) are abundant, frequently fold in elongated non-globular structures and perform vital functions. A number of computational tools have been developed to detect TRs in protein sequences. A blurred boundary between imperfect TR motifs and non-repetitive sequences gave rise to necessity to validate the detected TRs. RESULTS Tally-2.0 is a scoring tool based on a machine learning (ML) approach, which allows to validate the results of TR detection. It was upgraded by using improved training datasets and additional ML features. Tally-2.0 performs at a level of 93% sensitivity, 83% specificity and an area under the receiver operating characteristic curve of 95%. AVAILABILITY AND IMPLEMENTATION Tally-2.0 is available, as a web tool and as a standalone application published under Apache License 2.0, on the URL https://bioinfo.crbm.cnrs.fr/index.php? route=tools&tool=27. It is supported on Linux. Source code is available upon request. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Vladimir Perovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade 11001, Serbia
| | - Jeremy Y Leclercq
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université de Montpellier, Montpellier 34293, France
| | - Neven Sumonja
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade 11001, Serbia
| | - Francois D Richard
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université de Montpellier, Montpellier 34293, France.,Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven 3000, Belgium
| | - Nevena Veljkovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade 11001, Serbia
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université de Montpellier, Montpellier 34293, France
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22
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Wang W, Azizyan RA, Garro A, Kajava AV, Ventura S. Multifunctional Amyloid Oligomeric Nanoparticles for Specific Cell Targeting and Drug Delivery. Biomacromolecules 2020; 21:4302-4312. [PMID: 32885960 DOI: 10.1021/acs.biomac.0c01103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural selection has endorsed proteins with amazing structures and functionalities that cannot be matched by synthetic means, explaining the exponential interest in developing protein-based materials. Protein self-assembly allows fabricating complex supramolecular structures from relatively simple building blocks, a bottom-up strategy naturally employed by amyloid fibrils. However, the design of amyloid-inspired materials with biological activity is inherently difficult. Here, we exploit a modular procedure to generate functional amyloid nanostructures with tight control of their mesoscopic properties. The soft amyloid core of a yeast prion was fused to dihydrofolate reductase through flexible linkers of different sizes. This enabled us to produce, for the first time, biocompatible protein-only amyloid-like oligomeric nanoparticles with defined dimensions in which the embedded enzyme remained highly active, as assessed by biophysical and enzymatic assays. The modular design allowed one to obtain multifunctional nanoparticles by incorporating the antibody-binding Z-domain to the protein fusion. We show how these assemblies can be exploited for antibody-directed targeting of specific cell types and the localized delivery of methotrexate, resulting in the intracellular uptake of the drug by cancer cells and their death. Overall, the novel protein particles we describe in this work might find applications in areas as diverse as biocatalysis, bioimaging, or targeted therapies.
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Affiliation(s)
- Weiqiang Wang
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Rafayel A Azizyan
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université Montpellier, Montpellier 34090, France.,Institut de Biologie Computationnelle, Université Montpellier, Montpellier 34090, France
| | - Adriana Garro
- Universidad Nacional de San Luis IMASL-CONICET, San Luis D5702, Argentina
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université Montpellier, Montpellier 34090, France.,Institut de Biologie Computationnelle, Université Montpellier, Montpellier 34090, France
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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23
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Azizyan RA, Wang W, Anikeenko A, Radkova Z, Bakulina A, Garro A, Charlier L, Dumas C, Ventura S, Kajava AV. Amyloidogenicity as a driving force for the formation of functional oligomers. J Struct Biol 2020; 212:107604. [PMID: 32805411 DOI: 10.1016/j.jsb.2020.107604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 11/28/2022]
Abstract
Insoluble amyloid fibrils formed by self-assembly of amyloidogenic regions of proteins have a cross-β-structure. In this work, by using targeted molecular dynamics and rigid body simulation, we demonstrate that if a protein consists of an amyloidogenic region and a globular domain(s) and if the linker between them is short enough, such molecules cannot assemble into amyloid fibrils, instead, they form oligomers with a defined and limited number of β-strands in the cross-β core. We show that this blockage of the amyloid growth is due to the steric repulsion of the globular structures linked to amyloidogenic regions. Furthermore, we establish a relationship between the linker length and the number of monomers in such nanoparticles. We hypothesise that such oligomerisation can be a yet unrecognised way to form natural protein complexes involved in biological processes. Our results can also be used in protein engineering for designing soluble nanoparticles carrying different functional domains.
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Affiliation(s)
- Rafayel A Azizyan
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237, CNRS, Université Montpellier, Montpellier, France; Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France
| | - Weiqiang Wang
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193-Bellaterra, Spain
| | | | | | | | - Adriana Garro
- Universidad Nacional de San Luis IMASL-CONICET, San Luis, Argentina
| | - Landry Charlier
- Institut des Biomolécules Max Mousseron, Montpellier, France
| | - Christian Dumas
- Centre de Biochimie Structurale, CNRS, UMR5048, INSERM, U1054, Université de Montpellier, Montpellier, France
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193-Bellaterra, Spain
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237, CNRS, Université Montpellier, Montpellier, France; Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.
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24
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Sleiman Y, Souidi M, Kumar R, Yang E, Jaffré F, Zhou T, Bernardin A, Reiken S, Cazorla O, Kajava AV, Moreau A, Pasquié JL, Marks AR, Lerman BB, Chen S, Cheung JW, Evans T, Lacampagne A, Meli AC. Modeling polymorphic ventricular tachycardia at rest using patient-specific induced pluripotent stem cell-derived cardiomyocytes. EBioMedicine 2020; 60:103024. [PMID: 32980690 PMCID: PMC7519379 DOI: 10.1016/j.ebiom.2020.103024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/27/2020] [Accepted: 09/09/2020] [Indexed: 12/21/2022] Open
Abstract
Background While mutations in the cardiac type 2 ryanodine receptor (RyR2) have been linked to exercise-induced or catecholaminergic polymorphic ventricular tachycardia (CPVT), its association with polymorphic ventricular tachycardia (PMVT) occurring at rest is unclear. We aimed at constructing a patient-specific human-induced pluripotent stem cell (hiPSC) model of PMVT occurring at rest linked to a single point mutation in RyR2. Methods Blood samples were obtained from a patient with PMVT at rest due to a heterozygous RyR2-H29D mutation. Patient-specific hiPSCs were generated from the blood samples, and the hiPSC-derived cardiomyocytes (CMs) were generated via directed differentiation. Using CRIPSR/Cas9 technology, isogenic controls were generated by correcting the RyR2-H29D mutation. Using patch-clamp, fluorescent confocal microscopy and video-image-based analysis, the molecular and functional properties of RyR2-H29D hiPSC—CMs and control hiPSC—CMs were compared. Findings RyR2-H29D hiPSC—CMs exhibit intracellular sarcoplasmic reticulum (SR) Ca2+ leak through RyR2 under physiological pacing. RyR2-H29D enhances the contribution of inositol 1,4,5-trisphosphate receptors to excitation-contraction coupling (ECC) that exacerbates abnormal Ca2+ release in RyR2-H29D hiPSC—CMs. RyR2-H29D hiPSC—CMs exhibit shorter action potentials, delayed afterdepolarizations, arrhythmias and aberrant contractile properties compared to isogenic controls. The RyR2-H29D mutation causes post-translational remodeling that is fully reversed with isogenic controls. Interpretation To conclude, in a model based on a RyR2 point mutation that is associated with short-coupled PMVT at rest, RyR2-H29D hiPSC—CMs exhibited aberrant intracellular Ca2+ homeostasis, shortened action potentials, arrhythmias and abnormal contractile properties. Funding French Muscular Dystrophy Association (AFM; project 16,073, MNM2 2012 and 20,225), “Fondation de la Recherche Médicale” (FRM; SPF20130526710), “Institut National pour la Santé et la Recherche Médicale” (INSERM), National Institutes of Health (ARM; R01 HL145473) and New York State Department of Health (NYSTEM C029156).
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Affiliation(s)
- Yvonne Sleiman
- PhyMedExp, Inserm, CNRS, University of Montpellier, Montpellier, France
| | - Monia Souidi
- PhyMedExp, Inserm, CNRS, University of Montpellier, Montpellier, France
| | - Ritu Kumar
- Department of Surgery, Weill Cornell Medical College, New York, NY, United States
| | - Ellen Yang
- Department of Surgery, Weill Cornell Medical College, New York, NY, United States
| | - Fabrice Jaffré
- Department of Surgery, Weill Cornell Medical College, New York, NY, United States
| | - Ting Zhou
- Department of Surgery, Weill Cornell Medical College, New York, NY, United States
| | - Albin Bernardin
- PhyMedExp, Inserm, CNRS, University of Montpellier, Montpellier, France
| | - Steve Reiken
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Columbia University College of Physicians and Surgeons, New York, NY, United States
| | - Olivier Cazorla
- PhyMedExp, Inserm, CNRS, University of Montpellier, Montpellier, France
| | | | - Adrien Moreau
- PhyMedExp, Inserm, CNRS, University of Montpellier, Montpellier, France
| | - Jean-Luc Pasquié
- PhyMedExp, Inserm, CNRS, University of Montpellier, Montpellier, France; Department of Cardiology, CHU of Montpellier, Montpellier, France
| | - Andrew R Marks
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Columbia University College of Physicians and Surgeons, New York, NY, United States
| | - Bruce B Lerman
- Division of Cardiology, Weill Cornell Medical College, New York, NY, United States
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, New York, NY, United States
| | - Jim W Cheung
- Division of Cardiology, Weill Cornell Medical College, New York, NY, United States
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, New York, NY, United States
| | - Alain Lacampagne
- PhyMedExp, Inserm, CNRS, University of Montpellier, Montpellier, France
| | - Albano C Meli
- PhyMedExp, Inserm, CNRS, University of Montpellier, Montpellier, France.
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Sulatskaya AI, Bondarev SA, Sulatsky MI, Trubitsina NP, Belousov MV, Zhouravleva GA, Llanos MA, Kajava AV, Kuznetsova IM, Turoverov KK. Point mutations affecting yeast prion propagation change the structure of its amyloid fibrils. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, Iglesias V, Kajava AV, Kovacs OP, Lamb J, Lambrughi M, Lazar T, Leclercq JY, Leonardi E, Macedo-Ribeiro S, Macossay-Castillo M, Maiani E, Manso JA, Marino-Buslje C, Martínez-Pérez E, Mészáros B, Mičetić I, Minervini G, Murvai N, Necci M, Ouzounis CA, Pajkos M, Paladin L, Pancsa R, Papaleo E, Parisi G, Pasche E, Barbosa Pereira PJ, Promponas VJ, Pujols J, Quaglia F, Ruch P, Salvatore M, Schad E, Szabo B, Szaniszló T, Tamana S, Tantos A, Veljkovic N, Ventura S, Vranken W, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D. DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res 2020; 48:D269-D276. [PMID: 31713636 PMCID: PMC7145575 DOI: 10.1093/nar/gkz975] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/11/2019] [Accepted: 10/12/2019] [Indexed: 11/29/2022] Open
Abstract
The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the ‘dark’ proteome.
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Affiliation(s)
- András Hatos
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Borbála Hajdu-Soltész
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Alexander M Monzon
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina
| | - Lucía Álvarez
- Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Burcu Aykac-Fas
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Claudio Bassot
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden
| | - Guillermo I Benítez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina
| | - Martina Bevilacqua
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Anastasia Chasapi
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica GR-57500, Greece
| | - Lucia Chemes
- Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina.,Departamento de Fisiología y Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, Chelsea, London SW3 6BJ, UK
| | - Radoslav Davidović
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade 11001, Serbia
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN 46202, USA
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden
| | - Julien Gobeill
- Swiss Institute of Bioinformatics and HES-SO \ HEG, Geneva 1200, Switzerland
| | - Nicolás S González Foutel
- Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Govindarajan Sudha
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden
| | - Mainak Guharoy
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Tamas Horvath
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Valentin Iglesias
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, Montpellier 34293, France.,Institut de Biologie Computationnelle(IBC), Montpellier 34095, France
| | - Orsolya P Kovacs
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - John Lamb
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Tamas Lazar
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Jeremy Y Leclercq
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, Montpellier 34293, France
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padova, Padova 35127, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova 35127, Italy
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal
| | - Mauricio Macossay-Castillo
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Emiliano Maiani
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - José A Manso
- Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal
| | - Cristina Marino-Buslje
- Bioinformatics Unit. Fundación Instituto Leloir, Ciudad de Buenos Aires C1405BWE, Argentina
| | | | - Bálint Mészáros
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Ivan Mičetić
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Nikoletta Murvai
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Marco Necci
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Christos A Ouzounis
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica GR-57500, Greece
| | - Mátyás Pajkos
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Lisanna Paladin
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark.,Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina
| | - Emilie Pasche
- Swiss Institute of Bioinformatics and HES-SO \ HEG, Geneva 1200, Switzerland
| | - Pedro J Barbosa Pereira
- Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY 1678, Cyprus
| | - Jordi Pujols
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Patrick Ruch
- Swiss Institute of Bioinformatics and HES-SO \ HEG, Geneva 1200, Switzerland
| | - Marco Salvatore
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Beata Szabo
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Tamás Szaniszló
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Stella Tamana
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY 1678, Cyprus
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Nevena Veljkovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade 11001, Serbia
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels (IB2), ULB-VUB, Brussels 1050, Belgium
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Peter Tompa
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy.,CNR Institute of Neurosceince, Padova 35121, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
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27
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Skitchenko RK, Usoltsev D, Uspenskaya M, Kajava AV, Guskov A. Census of halide-binding sites in protein structures. Bioinformatics 2020; 36:3064-3071. [PMID: 32022861 PMCID: PMC7214031 DOI: 10.1093/bioinformatics/btaa079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 12/02/2022] Open
Abstract
Motivation Halides are negatively charged ions of halogens, forming fluorides (F−), chlorides (Cl−), bromides (Br−) and iodides (I−). These anions are quite reactive and interact both specifically and non-specifically with proteins. Despite their ubiquitous presence and important roles in protein function, little is known about the preferences of halides binding to proteins. To address this problem, we performed the analysis of halide–protein interactions, based on the entries in the Protein Data Bank. Results We have compiled a pipeline for the quick analysis of halide-binding sites in proteins using the available software. Our analysis revealed that all of halides are strongly attracted by the guanidinium moiety of arginine side chains, however, there are also certain preferences among halides for other partners. Furthermore, there is a certain preference for coordination numbers in the binding sites, with a correlation between coordination numbers and amino acid composition. This pipeline can be used as a tool for the analysis of specific halide–protein interactions and assist phasing experiments relying on halides as anomalous scatters. Availability and implementation All data described in this article can be reproduced via complied pipeline published at https://github.com/rostkick/Halide_sites/blob/master/README.md. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Dmitrii Usoltsev
- Institute BioEngineering, ITMO University, Saint-Petersburg 197101, Russia
| | - Mayya Uspenskaya
- Institute BioEngineering, ITMO University, Saint-Petersburg 197101, Russia
| | - Andrey V Kajava
- Institute BioEngineering, ITMO University, Saint-Petersburg 197101, Russia.,Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Universite Montpellier, Montpellier 34293, France
| | - Albert Guskov
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen 9747 AG, the Netherlands
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28
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Drozdova PB, Barbitoff YA, Belousov MV, Skitchenko RK, Rogoza TM, Leclercq JY, Kajava AV, Matveenko AG, Zhouravleva GA, Bondarev SA. Estimation of amyloid aggregate sizes with semi-denaturing detergent agarose gel electrophoresis and its limitations. Prion 2020; 14:118-128. [PMID: 32306832 PMCID: PMC7199750 DOI: 10.1080/19336896.2020.1751574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Semi-denaturing detergent agarose gel electrophoresis (SDD-AGE) was proposed by Vitaly V. Kushnirov in the Michael D. Ter-Avanesyan’s laboratory as a method to compare sizes of amyloid aggregates. Currently, this method is widely used for amyloid investigation, but mostly as a qualitative approach. In this work, we assessed the possibilities and limitations of the quantitative analysis of amyloid aggregate size distribution using SDD-AGE results. For this purpose, we used aggregates of two well-characterized yeast amyloid-forming proteins, Sup35 and Rnq1, and developed a protocol to standardize image analysis and process the result. A detailed investigation of factors that may affect the results of SDD-AGE revealed that both the cell lysis method and electrophoresis conditions can substantially affect the estimation of aggregate size. Despite this, quantitative analysis of SDD-AGE results is possible when one needs to estimate and compare the size of aggregates on the same gel, or even in different experiments, if the experimental conditions are tightly controlled and additional standards are used.
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Affiliation(s)
- Polina B Drozdova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Institute of Biology, Irkutsk State University, Irkutsk, Russia
| | - Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Rostislav K Skitchenko
- International Research Institute of Bioengineering, ITMO University, St. Petersburg, Russia
| | - Tatyana M Rogoza
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Vavilov Institute of General Genetics Russian Academy of Sciences, St. Petersburg Branch, St. Petersburg, Russia
| | - Jeremy Y Leclercq
- Centre de Recherche En Biologie Cellulaire De Montpellier, UMR 5237 CNRS, Montpellier, France
| | - Andrey V Kajava
- International Research Institute of Bioengineering, ITMO University, St. Petersburg, Russia.,Centre de Recherche En Biologie Cellulaire De Montpellier, UMR 5237 CNRS, Montpellier, France
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
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29
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Barbosa S, Greville-Heygate S, Bonnet M, Godwin A, Fagotto-Kaufmann C, Kajava AV, Laouteouet D, Mawby R, Wai HA, Dingemans AJ, Hehir-Kwa J, Willems M, Capri Y, Mehta SG, Cox H, Goudie D, Vansenne F, Turnpenny P, Vincent M, Cogné B, Lesca G, Hertecant J, Rodriguez D, Keren B, Burglen L, Gérard M, Putoux A, Cantagrel V, Siquier-Pernet K, Rio M, Banka S, Sarkar A, Steeves M, Parker M, Clement E, Moutton S, Tran Mau-Them F, Piton A, de Vries BB, Guille M, Debant A, Schmidt S, Baralle D, Baralle D. Opposite Modulation of RAC1 by Mutations in TRIO Is Associated with Distinct, Domain-Specific Neurodevelopmental Disorders. Am J Hum Genet 2020; 106:338-355. [PMID: 32109419 PMCID: PMC7058823 DOI: 10.1016/j.ajhg.2020.01.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022] Open
Abstract
The Rho-guanine nucleotide exchange factor (RhoGEF) TRIO acts as a key regulator of neuronal migration, axonal outgrowth, axon guidance, and synaptogenesis by activating the GTPase RAC1 and modulating actin cytoskeleton remodeling. Pathogenic variants in TRIO are associated with neurodevelopmental diseases, including intellectual disability (ID) and autism spectrum disorders (ASD). Here, we report the largest international cohort of 24 individuals with confirmed pathogenic missense or nonsense variants in TRIO. The nonsense mutations are spread along the TRIO sequence, and affected individuals show variable neurodevelopmental phenotypes. In contrast, missense variants cluster into two mutational hotspots in the TRIO sequence, one in the seventh spectrin repeat and one in the RAC1-activating GEFD1. Although all individuals in this cohort present with developmental delay and a neuro-behavioral phenotype, individuals with a pathogenic variant in the seventh spectrin repeat have a more severe ID associated with macrocephaly than do most individuals with GEFD1 variants, who display milder ID and microcephaly. Functional studies show that the spectrin and GEFD1 variants cause a TRIO-mediated hyper- or hypo-activation of RAC1, respectively, and we observe a striking correlation between RAC1 activation levels and the head size of the affected individuals. In addition, truncations in TRIO GEFD1 in the vertebrate model X. tropicalis induce defects that are concordant with the human phenotype. This work demonstrates distinct clinical and molecular disorders clustering in the GEFD1 and seventh spectrin repeat domains and highlights the importance of tight control of TRIO-RAC1 signaling in neuronal development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Diana Baralle
- Wessex Clinical Genetics, University Hospital Southampton National Health Service Foundation Trust, Southampton SO16 5YA, UK; Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK.
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30
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Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A, Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res 2019; 47:10994-11006. [PMID: 31584084 PMCID: PMC6868369 DOI: 10.1093/nar/gkz841] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/03/2019] [Accepted: 10/01/2019] [Indexed: 12/13/2022] Open
Abstract
The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with 'ready-to-use' deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and that may proliferate in public database repositories affecting all downstream analyses. As a case study, we provide examples of the Atlantic cod genome, whose sequencing and assembly were hindered by a particularly high prevalence of tandem repeats. We complement this case study with examples from other species, where mis-annotations and sequencing errors have propagated into protein databases. With this review, we aim to raise the awareness level within the community of database users, and alert scientists working in the underlying workflow of database creation that the data they omit or improperly assemble may well contain important biological information valuable to others.
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Affiliation(s)
- Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Pablo Mier
- Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Husch-Weg 15, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Husch-Weg 15, 55128 Mainz, Germany
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton. CB10 1SD, UK
| | - Patryk Jarnot
- Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Aleksandra Gruca
- Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Universite Montpellier 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France
- Institut de Biologie Computationnelle, 34095 Montpellier, France
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, PO Box 20537, CY 1678 Nicosia, Cyprus
| | - Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
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Danilov LG, Matveenko AG, Ryzhkova VE, Belousov MV, Poleshchuk OI, Likholetova DV, Sokolov PA, Kasyanenko NA, Kajava AV, Zhouravleva GA, Bondarev SA. Design of a New [ PSI +]-No-More Mutation in SUP35 With Strong Inhibitory Effect on the [ PSI +] Prion Propagation. Front Mol Neurosci 2019; 12:274. [PMID: 31803017 PMCID: PMC6877606 DOI: 10.3389/fnmol.2019.00274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/28/2019] [Indexed: 12/04/2022] Open
Abstract
A number of [PSI+]-no-more (PNM) mutations, eliminating [PSI+] prion, were previously described in SUP35. In this study, we designed and analyzed a new PNM mutation based on the parallel in-register β-structure of Sup35 prion fibrils suggested by the known experimental data. In such an arrangement, substitution of non-charged residues by charged ones may destabilize the fibril structure. We introduced Q33K/A34K amino acid substitutions into the Sup35 protein, corresponding allele was called sup35-M0. The mutagenized residues were chosen based on ArchCandy in silico prediction of high inhibitory effect on the amyloidogenic potential of Sup35. The experiments confirmed that Sup35-M0 leads to the elimination of [PSI+] with high efficiency. Our data suggested that the elimination of the [PSI+] prion is associated with the decreased aggregation properties of the protein. The new mutation can induce the prion with very low efficiency and is able to propagate only weak [PSI+] prion variants. We also showed that Sup35-M0 protein co-aggregates with the wild-type Sup35 in vivo. Moreover, our data confirmed the utility of the strategy of substitution of non-charged residues by charged ones to design new mutations to inhibit a prion formation.
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Affiliation(s)
- Lavrentii G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Varvara E Ryzhkova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
| | - Olga I Poleshchuk
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Daria V Likholetova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Petr A Sokolov
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University, St. Petersburg, Russia
| | - Nina A Kasyanenko
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University, St. Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, Montpellier, France.,Institut de Biologie Computationnelle (IBC), Universitè Montpellier, Montpellier, France
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
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Wang W, Navarro S, Azizyan RA, Baño-Polo M, Esperante SA, Kajava AV, Ventura S. Prion soft amyloid core driven self-assembly of globular proteins into bioactive nanofibrils. Nanoscale 2019; 11:12680-12694. [PMID: 31237592 DOI: 10.1039/c9nr01755k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Amyloids have been exploited to build amazing bioactive materials. In most cases, short synthetic peptides constitute the functional components of such materials. The controlled assembly of globular proteins into active amyloid nanofibrils is still challenging, because the formation of amyloids implies a conformational conversion towards a β-sheet-rich structure, with a concomitant loss of the native fold and the inactivation of the protein. There is, however, a remarkable exception to this rule: yeast prions. They are singular proteins able to switch between a soluble and an amyloid state. In both states, the structure of their globular domains remains essentially intact. The transit between these two conformations is encoded in prion domains (PrDs): long and disordered sequences to which the active globular domains are appended. PrDs are much larger than typical self-assembling peptides. This seriously limits their use for nanotechnological applications. We have recently shown that these domains contain soft amyloid cores (SACs) that suffice to nucleate their self-assembly reaction. Here we genetically fused a model SAC with different globular proteins. We demonstrate that this very short sequence acts as a minimalist PrD, driving the selective and slow assembly of the initially soluble fusion proteins into amyloid fibrils in which the globular proteins retain their native structure and display high activity. Overall, we provide here a novel, modular and straightforward strategy to build active protein-based nanomaterials at a preparative scale.
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Affiliation(s)
- Weiqiang Wang
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Rafayel A Azizyan
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, 34293 Montpellier, Cedex 5, France
| | - Manuel Baño-Polo
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Sebastian A Esperante
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, 34293 Montpellier, Cedex 5, France
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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Bondarev SA, Bondareva OV, Zhouravleva GA, Kajava AV. BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures. Bioinformatics 2018; 34:599-608. [PMID: 29444233 DOI: 10.1093/bioinformatics/btx629] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/03/2017] [Indexed: 11/12/2022] Open
Abstract
Motivation Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics. Results We developed a computer program BetaSerpentine that reconstructs β-serpentine arrangements from individual β-arches predicted by ArchCandy program and ranks them in order of preference. It was shown that the BetaSerpentine program in combination with the experimental data can be used to gain insight into the detailed 3D structure of amyloids. It opens avenues to the structure-based interpretation and design of the experiments. Availability and implementation BetaSerpentine webserver can be accessed through website: http://bioinfo.montp.cnrs.fr/b-serpentine. Source code is available in git.hub repository (github.com/stanislavspbgu/BetaSerpentine). Contact stanislavspbgu@gmail.com or andrey.kajava@crbm.cnrs.fr. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stanislav A Bondarev
- Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Olga V Bondareva
- Laboratory of Molecular Systematics, Zoological Institute RAS, Saint Petersburg 199034, Russia
| | - Galina A Zhouravleva
- Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Andrey V Kajava
- Structural Bioinformatics and Molecular Modeling, Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France.,Institut de Biologie Computationnelle, Montpellier 34095, France.,Bioengineering Department, University ITMO, Saint Petersburg, 197101, Russia
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34
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Villain E, Nikekhin AA, Kajava AV. Porins and Amyloids are Coded by Similar Sequence Motifs. Proteomics 2018; 19:e1800075. [DOI: 10.1002/pmic.201800075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/27/2018] [Indexed: 01/25/2023]
Affiliation(s)
- Etienne Villain
- Centre de Recherche en Biologie cellulaire de MontpellierUMR 5237 CNRSUniversité Montpellier 1919 Route de MendeCEDEX 5 34293 Montpellier France
- Institut de Biologie Computationnelle 34095 Montpellier France
| | | | - Andrey V. Kajava
- Centre de Recherche en Biologie cellulaire de MontpellierUMR 5237 CNRSUniversité Montpellier 1919 Route de MendeCEDEX 5 34293 Montpellier France
- Institut de Biologie Computationnelle 34095 Montpellier France
- Institute of BioengineeringITMO University St. Petersburg 197101 Russia
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35
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Acimovic I, Refaat MM, Moreau A, Salykin A, Reiken S, Sleiman Y, Souidi M, Přibyl J, Kajava AV, Richard S, Lu JT, Chevalier P, Skládal P, Dvořak P, Rotrekl V, Marks AR, Scheinman MM, Lacampagne A, Meli AC. Post-Translational Modifications and Diastolic Calcium Leak Associated to the Novel RyR2-D3638A Mutation Lead to CPVT in Patient-Specific hiPSC-Derived Cardiomyocytes. J Clin Med 2018; 7:jcm7110423. [PMID: 30413023 PMCID: PMC6262462 DOI: 10.3390/jcm7110423] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 10/31/2018] [Accepted: 11/04/2018] [Indexed: 12/14/2022] Open
Abstract
Background: Sarcoplasmic reticulum Ca2+ leak and post-translational modifications under stress have been implicated in catecholaminergic polymorphic ventricular tachycardia (CPVT), a highly lethal inherited arrhythmogenic disorder. Human induced pluripotent stem cells (hiPSCs) offer a unique opportunity for disease modeling. Objective: The aims were to obtain functional hiPSC-derived cardiomyocytes from a CPVT patient harboring a novel ryanodine receptor (RyR2) mutation and model the syndrome, drug responses and investigate the molecular mechanisms associated to the CPVT syndrome. Methods: Patient-specific cardiomyocytes were generated from a young athletic female diagnosed with CPVT. The contractile, intracellular Ca2+ handling and electrophysiological properties as well as the RyR2 macromolecular remodeling were studied. Results: Exercise stress electrocardiography revealed polymorphic ventricular tachycardia when treated with metoprolol and marked improvement with flecainide alone. We found abnormal stress-induced contractile and electrophysiological properties associated with sarcoplasmic reticulum Ca2+ leak in CPVT hiPSC-derived cardiomyocytes. We found inadequate response to metoprolol and a potent response of flecainide. Stabilizing RyR2 with a Rycal compound prevents those abnormalities specifically in CPVT hiPSC-derived cardiomyocytes. The RyR2-D3638A mutation is located in the conformational change inducing-central core domain and leads to RyR2 macromolecular remodeling including depletion of PP2A and Calstabin2. Conclusion: We identified a novel RyR2-D3638A mutation causing 3D conformational defects and aberrant biophysical properties associated to RyR2 macromolecular complex post-translational remodeling. The molecular remodeling is for the first time revealed using patient-specific hiPSC-derived cardiomyocytes which may explain the CPVT proband’s resistance. Our study promotes hiPSC-derived cardiomyocytes as a suitable model for disease modeling, testing new therapeutic compounds, personalized medicine and deciphering underlying molecular mechanisms.
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Affiliation(s)
- Ivana Acimovic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic.
| | - Marwan M Refaat
- Department of Internal Medicine, Cardiology Division/Cardiac Electrophysiology Section and Department of Biochemistry and Molecular Genetics, American University of Beirut Faculty of Medicine and Medical Center, Beirut 1107 2020, Lebanon.
| | - Adrien Moreau
- NeuroMyoGène Institute, University of Claude Bernard Lyon 1, 69100 Villeurbanne, France.
- PhyMedExp, INSERM, University of Montpellier, CNRS, 371 Avenue du Doyen G. Giraud, 34295 Montpellier CEDEX 5, France.
| | - Anton Salykin
- Department of Biology, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic.
| | - Steve Reiken
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Yvonne Sleiman
- PhyMedExp, INSERM, University of Montpellier, CNRS, 371 Avenue du Doyen G. Giraud, 34295 Montpellier CEDEX 5, France.
| | - Monia Souidi
- PhyMedExp, INSERM, University of Montpellier, CNRS, 371 Avenue du Doyen G. Giraud, 34295 Montpellier CEDEX 5, France.
| | - Jan Přibyl
- CEITEC, Masaryk University, Brno 62500, Czech Republic.
| | - Andrey V Kajava
- CRBM, CNRS, University of Montpellier, 34293 Montpellier, France and University ITMO, St Petersburg 197101, Russia.
| | - Sylvain Richard
- PhyMedExp, INSERM, University of Montpellier, CNRS, 371 Avenue du Doyen G. Giraud, 34295 Montpellier CEDEX 5, France.
| | - Jonathan T Lu
- Department of Cardiology, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA.
| | - Philippe Chevalier
- NeuroMyoGène Institute, University of Claude Bernard Lyon 1, 69100 Villeurbanne, France.
| | - Petr Skládal
- CEITEC, Masaryk University, Brno 62500, Czech Republic.
| | - Petr Dvořak
- Department of Biology, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic.
| | - Vladimir Rotrekl
- Department of Biology, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Brno 60200, Czech Republic.
| | - Andrew R Marks
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Melvin M Scheinman
- San Francisco Medical Center, University of California, San Francisco, CA 94115, USA.
| | - Alain Lacampagne
- PhyMedExp, INSERM, University of Montpellier, CNRS, 371 Avenue du Doyen G. Giraud, 34295 Montpellier CEDEX 5, France.
| | - Albano C Meli
- PhyMedExp, INSERM, University of Montpellier, CNRS, 371 Avenue du Doyen G. Giraud, 34295 Montpellier CEDEX 5, France.
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Bondarev SA, Antonets KS, Kajava AV, Nizhnikov AA, Zhouravleva GA. Protein Co-Aggregation Related to Amyloids: Methods of Investigation, Diversity, and Classification. Int J Mol Sci 2018; 19:ijms19082292. [PMID: 30081572 PMCID: PMC6121665 DOI: 10.3390/ijms19082292] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/29/2018] [Accepted: 08/02/2018] [Indexed: 01/04/2023] Open
Abstract
Amyloids are unbranched protein fibrils with a characteristic spatial structure. Although the amyloids were first described as protein deposits that are associated with the diseases, today it is becoming clear that these protein fibrils play multiple biological roles that are essential for different organisms, from archaea and bacteria to humans. The appearance of amyloid, first of all, causes changes in the intracellular quantity of the corresponding soluble protein(s), and at the same time the aggregate can include other proteins due to different molecular mechanisms. The co-aggregation may have different consequences even though usually this process leads to the depletion of a functional protein that may be associated with different diseases. The protein co-aggregation that is related to functional amyloids may mediate important biological processes and change of protein functions. In this review, we survey the known examples of the amyloid-related co-aggregation of proteins, discuss their pathogenic and functional roles, and analyze methods of their studies from bacteria and yeast to mammals. Such analysis allow for us to propose the following co-aggregation classes: (i) titration: deposition of soluble proteins on the amyloids formed by their functional partners, with such interactions mediated by a specific binding site; (ii) sequestration: interaction of amyloids with certain proteins lacking a specific binding site; (iii) axial co-aggregation of different proteins within the same amyloid fibril; and, (iv) lateral co-aggregation of amyloid fibrils, each formed by different proteins.
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Affiliation(s)
- Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
| | - Kirill S Antonets
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh., 3, Pushkin, St. Petersburg 196608, Russia.
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France.
- Institut de Biologie Computationnelle (IBC), 34095 Montpellier, France.
- University ITMO, Institute of Bioengineering, Kronverksky Pr. 49, St. Petersburg 197101, Russia.
| | - Anton A Nizhnikov
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh., 3, Pushkin, St. Petersburg 196608, Russia.
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
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37
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Rojas-Lopez M, Zorgani MA, Kelley LA, Bailly X, Kajava AV, Henderson IR, Polticelli F, Pizza M, Rosini R, Desvaux M. Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β-Helical Passenger. Front Microbiol 2018; 8:2607. [PMID: 29375499 PMCID: PMC5767081 DOI: 10.3389/fmicb.2017.02607] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/14/2017] [Indexed: 11/29/2022] Open
Abstract
Autotransporters (ATs) belong to a family of modular proteins secreted by the Type V, subtype a, secretion system (T5aSS) and considered as an important source of virulence factors in lipopolysaccharidic diderm bacteria (archetypical Gram-negative bacteria). While exported by the Sec pathway, the ATs are further secreted across the outer membrane via their own C-terminal translocator forming a β-barrel, through which the rest of the protein, namely the passenger, can pass. In several ATs, an autochaperone domain (AC) present at the C-terminal region of the passenger and upstream of the translocator was demonstrated as strictly required for proper secretion and folding. However, considering it was functionally characterised and identified only in a handful of ATs, wariness recently fells on the commonality and conservation of this structural element in the T5aSS. To circumvent the issue of sequence divergence and taking advantage of the resolved three-dimensional structure of some ACs, identification of this domain was performed following structural alignment among all AT passengers experimentally resolved by crystallography before searching in a dataset of 1523 ATs. While demonstrating that the AC is indeed a conserved structure found in numerous ATs, phylogenetic analysis further revealed a distribution into deeply rooted branches, from which emerge 20 main clusters. Sequence analysis revealed that an AC could be identified in the large majority of SAATs (self-associating ATs) but not in any LEATs (lipase/esterase ATs) nor in some PATs (protease autotransporters) and PHATs (phosphatase/hydrolase ATs). Structural analysis indicated that an AC was present in passengers exhibiting single-stranded right-handed parallel β-helix, whatever the type of β-solenoid, but not with α-helical globular fold. From this investigation, the AC of type 1 appears as a prevalent and conserved structural element exclusively associated to β-helical AT passenger and should promote further studies about the protein secretion and folding via the T5aSS, especially toward α-helical AT passengers.
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Affiliation(s)
- Maricarmen Rojas-Lopez
- Université Clermont Auvergne, INRA, UMR454 MEDiS, Clermont-Ferrand, France.,GSK, Siena, Italy
| | - Mohamed A Zorgani
- Université Clermont Auvergne, INRA, UMR454 MEDiS, Clermont-Ferrand, France
| | - Lawrence A Kelley
- Structural Bioinformatics Group, Imperial College London, London, United Kingdom
| | - Xavier Bailly
- Institut National de la Recherche Agronomique, UR346 Epidémiologie Animale, Saint Genès Champanelle, France
| | - Andrey V Kajava
- CRBM UMR5237 CNRS, Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Fabio Polticelli
- Department of Sciences, National Institute of Nuclear Physics, Roma Tre University, Rome, Italy
| | | | | | - Mickaël Desvaux
- Université Clermont Auvergne, INRA, UMR454 MEDiS, Clermont-Ferrand, France
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38
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Kajava AV, Tosatto SCE. Editorial for special issue "Proteins with tandem repeats: sequences, structures and functions"☆. J Struct Biol 2017; 201:86-87. [PMID: 29294402 DOI: 10.1016/j.jsb.2017.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 12/26/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, Montpellier 34293, France; Institut de Biologie Computationnelle, Montpellier, France.
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy; CNR Institute of Neuroscience, I-35121 Padova, Italy
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39
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Roche DB, Viet PD, Bakulina A, Hirsh L, Tosatto SCE, Kajava AV. Classification of β-hairpin repeat proteins. J Struct Biol 2017; 201:130-138. [PMID: 29017817 DOI: 10.1016/j.jsb.2017.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 12/11/2022]
Abstract
In recent years, a number of new protein structures that possess tandem repeats have emerged. Many of these proteins are comprised of tandem arrays of β-hairpins. Today, the amount and variety of the data on these β-hairpin repeat (BHR) structures have reached a level that requires detailed analysis and further classification. In this paper, we classified the BHR proteins, compared structures, sequences of repeat motifs, functions and distribution across the major taxonomic kingdoms of life and within organisms. As a result, we identified six different BHR folds in tandem repeat proteins of Class III (elongated structures) and one BHR fold (up-and-down β-barrel) in Class IV ("closed" structures). Our survey reveals the high incidence of the BHR proteins among bacteria and viruses and their possible relationship to the structures of amyloid fibrils. It indicates that BHR folds will be an attractive target for future structural studies, especially in the context of age-related amyloidosis and emerging infectious diseases. This work allowed us to update the RepeatsDB database, which contains annotated tandem repeat protein structures and to construct sequence profiles based on BHR structural alignments.
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Affiliation(s)
- Daniel B Roche
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, Montpellier 34293, France; Institut de Biologie Computationnelle, Montpellier, France
| | - Phuong Do Viet
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, Montpellier 34293, France; Institut de Biologie Computationnelle, Montpellier, France
| | - Anastasia Bakulina
- Novosibirsk State University, Pirogova str. 1, Novosibirsk 630090, Russia; State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Russia
| | - Layla Hirsh
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy; Engineering Department, Pontifical Catholic University of Peru, Lima 32, Peru
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, Montpellier 34293, France; Institut de Biologie Computationnelle, Montpellier, France.
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40
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Roche DB, Villain E, Kajava AV. Usage of a dataset of NMR resolved protein structures to test aggregation versus solubility prediction algorithms. Protein Sci 2017; 26:1864-1869. [PMID: 28685932 DOI: 10.1002/pro.3225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/21/2017] [Accepted: 06/29/2017] [Indexed: 01/08/2023]
Abstract
There has been an increased interest in computational methods for amyloid and (or) aggregate prediction, due to the prevalence of these aggregates in numerous diseases and their recently discovered functional importance. To evaluate these methods, several datasets have been compiled. Typically, aggregation-prone regions of proteins, which form aggregates or amyloids in vivo, are more than 15 residues long and intrinsically disordered. However, the number of such experimentally established amyloid forming and non-forming sequences are limited, not exceeding one hundred entries in existing databases. In this work, we parsed all available NMR-resolved protein structures from the PDB and assembled a new, sevenfold larger, dataset of unfolded sequences, soluble at high concentrations. We proposed to use these sequences as a negative set for evaluating methods for predicting aggregation in vivo. We also present the results of benchmarking cutting edge tools for the prediction of aggregation versus solubility propensity.
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Affiliation(s)
- Daniel B Roche
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS-UMR 5237, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
| | - Etienne Villain
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS-UMR 5237, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS-UMR 5237, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France.,University ITMO, 49 Kronverksky Pr, 197101, St. Petersburg, Russia
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41
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Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SCE. Corrigendum: DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res 2016; 45:D1123-D1124. [PMID: 27965415 PMCID: PMC5210598 DOI: 10.1093/nar/gkw1279] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Francesco Tabaro
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,Institute of Biosciences and Medical Technology, University of Tampere, Finland
| | - Ivan Mičetić
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Marco Necci
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | | | - Norman E Davey
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.,Ireland UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Radoslav Davidović
- Centre for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, 11001 Belgrade, Serbia
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, 1/c Pázmány Péter sétány, 1117 Budapest, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Alessandra Gasparini
- Department of Woman and Child Health, University of Padova, I-35128 Padova, Italy
| | - András Hatos
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, Cedex 5, Montpellier 34293, France.,Institut de Biologie Computationnelle (IBC), Montpellier 34095, France.,University ITMO, Institute of Bioengineering, St. Petersburg 197101, Russia
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary.,Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padova, I-35128 Padova, Italy
| | - Tamas Lazar
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Sandra Macedo-Ribeiro
- Biomolecular Structure and Function Group, Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Mauricio Macossay-Castillo
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Attila Meszaros
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Nikoletta Murvai
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Jordi Pujols
- Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Daniel B Roche
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, Cedex 5, Montpellier 34293, France.,Institut de Biologie Computationnelle (IBC), Montpellier 34095, France
| | | | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | | | - Beata Szabo
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Fiorella Tonello
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,CNR Institute of Neurosceince, I-35121 Padova, Italy
| | - Konstantinos D Tsirigos
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Nevena Veljković
- Centre for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, 11001 Belgrade, Serbia
| | - Salvador Ventura
- Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels (IB2), ULB-VUB, Brussels 1050, Belgium
| | - Per Warholm
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Vladimir N Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia.,Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | - Sonia Longhi
- Aix-Marseille Univ, CNRS, AFMB, UMR 7257, Marseille, France
| | - Peter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary .,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy .,CNR Institute of Neurosceince, I-35121 Padova, Italy
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42
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Paladin L, Hirsh L, Piovesan D, Andrade-Navarro MA, Kajava AV, Tosatto SCE. RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures. Nucleic Acids Res 2016; 45:3613. [PMID: 27928056 PMCID: PMC5389603 DOI: 10.1093/nar/gkw1268] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Lisanna Paladin
- Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy
| | - Layla Hirsh
- Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy.,Departamento de Ingeniería, Pontificia Universidad Católica del Perú, 32 Lima, Perú
| | - Damiano Piovesan
- Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology, Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire, CNRS, Université Montpellier, 34293 Montpellier, France.,Institut de Biologie Computationnelle (IBC), 34293 Montpellier, France.,Institute of Bioengineering, University ITMO, 197101 St. Petersburg, Russia
| | - Silvio C E Tosatto
- Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy.,CNR Institute of Neuroscience, 35121 Padova, Italy
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43
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Paladin L, Hirsh L, Piovesan D, Andrade-Navarro MA, Kajava AV, Tosatto SCE. RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures. Nucleic Acids Res 2016; 45:D308-D312. [PMID: 27899671 PMCID: PMC5210593 DOI: 10.1093/nar/gkw1136] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/20/2016] [Accepted: 10/31/2016] [Indexed: 12/19/2022] Open
Abstract
RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ∼5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method over the entire Protein Data Bank, with data quality is guaranteed by an extensive manual validation for >60% of the entries. The updated web interface includes a new search engine for complex queries and a fully re-designed entry page for a better overview of structural data. It is now possible to compare unit positions, together with secondary structure, fold information and Pfam domains. Moreover, a new classification level has been introduced on top of the existing scheme as an independent layer for sequence similarity relationships at 40%, 60% and 90% identity.
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Affiliation(s)
- Lisanna Paladin
- Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy
| | - Layla Hirsh
- Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy.,Departamento de Ingeniería, Pontificia Universidad Católica del Perú, 32 Lima, Perú
| | - Damiano Piovesan
- Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology, Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire, CNRS, Université Montpellier, 34293 Montpellier, France.,Institut de Biologie Computationnelle (IBC), 34293 Montpellier, France.,Institute of Bioengineering, University ITMO, 197101 St. Petersburg, Russia
| | - Silvio C E Tosatto
- Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy .,CNR Institute of Neuroscience, 35121 Padova, Italy
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44
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Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SCE. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res 2016; 45:D219-D227. [PMID: 27899601 PMCID: PMC5210544 DOI: 10.1093/nar/gkw1056] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 01/16/2023] Open
Abstract
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so. We define IDPs as proteins that are disordered along their entire sequence, i.e. entirely lack structural elements, and IDRs as regions that are at least five consecutive residues without well-defined structure. We base our assessment of disorder strictly on experimental evidence, such as X-ray crystallography and nuclear magnetic resonance (primary techniques) and a broad range of other experimental approaches (secondary techniques). Confident and ambiguous annotations are highlighted separately. DisProt 7.0 presents classified knowledge regarding the experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable resource for the research community for a better understanding structural disorder and for developing better computational tools for studying disordered proteins.
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Affiliation(s)
- Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Francesco Tabaro
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,Institute of Biosciences and Medical Technology, University of Tampere, Finland
| | - Ivan Mičetić
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Marco Necci
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | | | - Norman E Davey
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.,Ireland UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Radoslav Davidović
- Centre for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, 11001 Belgrade, Serbia
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, 1/c Pázmány Péter sétány, 1117 Budapest, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Alessandra Gasparini
- Department of Woman and Child Health, University of Padova, I-35128 Padova, Italy
| | - András Hatos
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, Cedex 5, Montpellier 34293, France.,Institut de Biologie Computationnelle (IBC), Montpellier 34095, France.,University ITMO, Institute of Bioengineering, St. Petersburg 197101, Russia
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary.,Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padova, I-35128 Padova, Italy
| | - Tamas Lazar
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Sandra Macedo-Ribeiro
- Biomolecular Structure and Function Group, Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Mauricio Macossay-Castillo
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Attila Meszaros
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Nikoletta Murvai
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Jordi Pujols
- Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Daniel B Roche
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, Cedex 5, Montpellier 34293, France.,Institut de Biologie Computationnelle (IBC), Montpellier 34095, France
| | | | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | | | - Beata Szabo
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Fiorella Tonello
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,CNR Institute of Neurosceince, I-35121 Padova, Italy
| | - Konstantinos D Tsirigos
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Nevena Veljković
- Centre for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, 11001 Belgrade, Serbia
| | - Salvador Ventura
- Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels (IB2), ULB-VUB, Brussels 1050, Belgium
| | - Per Warholm
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Vladimir N Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia.,Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | - Sonia Longhi
- Aix-Marseille Univ, CNRS, AFMB, UMR 7257, Marseille, France
| | - Peter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary .,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy .,CNR Institute of Neurosceince, I-35121 Padova, Italy
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45
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Richard FD, Alves R, Kajava AV. Tally: a scoring tool for boundary determination between repetitive and non-repetitive protein sequences. Bioinformatics 2016; 32:1952-8. [PMID: 27153701 DOI: 10.1093/bioinformatics/btw118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/25/2016] [Indexed: 12/23/2022] Open
Abstract
MOTIVATION Tandem Repeats (TRs) are abundant in proteins, having a variety of fundamental functions. In many cases, evolution has blurred their repetitive patterns. This leads to the problem of distinguishing between sequences that contain highly imperfect TRs, and the sequences without TRs. The 3D structure of proteins can be used as a benchmarking criterion for TR detection in sequences, because the vast majority of proteins having TRs in sequences are built of repetitive 3D structural blocks. According to our benchmark, none of the existing scoring methods are able to clearly distinguish, based on the sequence analysis, between structures with and without 3D TRs. RESULTS We developed a scoring tool called Tally, which is based on a machine learning approach. Tally is able to achieve a better separation between sequences with structural TRs and sequences of aperiodic structures, than existing scoring procedures. It performs at a level of 81% sensitivity, while achieving a high specificity of 74% and an Area Under the Receiver Operating Characteristic Curve of 86%. Tally can be used to select a set of structurally and functionally meaningful TRs from all TRs detected in proteomes. The generated dataset is available for benchmarking purposes. AVAILABILITY AND IMPLEMENTATION Source code is available upon request. Tool and dataset can be accessed through our website: http://bioinfo.montp.cnrs.fr/?r=Tally CONTACT andrey.kajava@crbm.cnrs.fr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- François D Richard
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, Cedex 5, Montpellier 34293, France Institut de Biologie Computationnelle (IBC), Montpellier 34095, France
| | - Ronnie Alves
- Institut de Biologie Computationnelle (IBC), Montpellier 34095, France Pós-Graduação em Ciência da Computação (PPGCC), Universidade Federal do Pará, Belém, Brazil
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, Cedex 5, Montpellier 34293, France Institut de Biologie Computationnelle (IBC), Montpellier 34095, France University ITMO, Institute of Bioengineering, St. Petersburg 197101, Russia
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Vallejo AF, Martinez NL, Tobon A, Alger J, Lacerda MV, Kajava AV, Arévalo-Herrera M, Herrera S. Global genetic diversity of the Plasmodium vivax transmission-blocking vaccine candidate Pvs48/45. Malar J 2016; 15:202. [PMID: 27067024 PMCID: PMC4828788 DOI: 10.1186/s12936-016-1263-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/31/2016] [Indexed: 12/17/2022] Open
Abstract
Background Plasmodium vivax 48/45 protein is expressed on the surface of gametocytes/gametes and plays a key role in gamete fusion during fertilization. This protein was recently expressed in Escherichia coli host as a recombinant product that was highly immunogenic in mice and monkeys and induced antibodies with high transmission-blocking activity, suggesting its potential as a P. vivax transmission-blocking vaccine candidate. To determine sequence polymorphism of natural parasite isolates and its potential influence on the protein structure, all pvs48/45 sequences reported in databases from around the world as well as those from low-transmission settings of Latin America were compared. Methods Plasmodium vivax parasite isolates from malaria-endemic regions of Colombia, Brazil and Honduras (n = 60) were used to sequence the Pvs48/45 gene, and compared to those previously reported to GenBank and PlasmoDB (n = 222). Pvs48/45 gene haplotypes were analysed to determine the functional significance of genetic variation in protein structure and vaccine potential. Results Nine non-synonymous substitutions (E35K, Y196H, H211N, K250N, D335Y, E353Q, A376T, K390T, K418R) and three synonymous substitutions (I73, T149, C156) that define seven different haplotypes were found among the 282 isolates from nine countries when compared with the Sal I reference sequence. Nucleotide diversity (π) was 0.00173 for worldwide samples (range 0.00033–0.00216), resulting in relatively high diversity in Myanmar and Colombia, and low diversity in Mexico, Peru and South Korea. The two most frequent substitutions (E353Q: 41.9 %, K250N: 39.5 %) were predicted to be located in antigenic regions without affecting putative B cell epitopes or the tertiary protein structure. Conclusions There is limited sequence polymorphism in pvs48/45 with noted geographical clustering among Asian and American isolates. The low genetic diversity of the protein does not influence the predicted antigenicity or protein structure and, therefore, supports its further development as transmission-blocking vaccine candidate.
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Affiliation(s)
| | | | | | - Jackeline Alger
- Facultad de Ciencias Médicas, Hospital Escuela Universitario, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Marcus V Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Andrey V Kajava
- Centre de Recherches Biochimie Macromoléculaire (CRBM), Institut de Biologie Computationnelle (IBC), CNRS, University of Montpellier, Montpellier, France.,Institute of Bioengineering, University ITMO, Saint Petersburg, Russia
| | - Myriam Arévalo-Herrera
- Caucaseco Scientific Research Center, Cali, Colombia.,School of Health, Universidad del Valle, Cali, Colombia
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Dearborn AD, Wall JS, Cheng N, Heymann JB, Kajava AV, Varkey J, Langen R, Steven AC. α-Synuclein Amyloid Fibrils with Two Entwined, Asymmetrically Associated Protofibrils. J Biol Chem 2015; 291:2310-8. [PMID: 26644467 DOI: 10.1074/jbc.m115.698787] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Indexed: 11/06/2022] Open
Abstract
Parkinson disease and other progressive neurodegenerative conditions are characterized by the intracerebral presence of Lewy bodies, containing amyloid fibrils of α-synuclein. We used cryo-electron microscopy and scanning transmission electron microscopy (STEM) to study in vitro-assembled fibrils. These fibrils are highly polymorphic. Focusing on twisting fibrils with an inter-crossover spacing of 77 nm, our reconstructions showed them to consist of paired protofibrils. STEM mass per length data gave one subunit per 0.47 nm axial rise per protofibril, consistent with a superpleated β-structure. The STEM images show two thread-like densities running along each of these fibrils, which we interpret as ladders of metal ions. These threads confirmed the two-protofibril architecture of the 77-nm twisting fibrils and allowed us to identify this morphotype in STEM micrographs. Some other, but not all, fibril morphotypes also exhibit dense threads, implying that they also present a putative metal binding site. We propose a molecular model for the protofibril and suggest that polymorphic variant fibrils have different numbers of protofibrils that are associated differently.
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Affiliation(s)
- Altaira D Dearborn
- From the Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Joseph S Wall
- the Department of Biology, Brookhaven National Laboratory, Upton, New York 19973
| | - Naiqian Cheng
- From the Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - J Bernard Heymann
- From the Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrey V Kajava
- the Centre de Recherches de Biochimie Macromoléculaire, CNRS, University of Montpellier, Montpellier 34172, France, the University ITMO, Institute of Bioengineering, 197101 St. Petersburg, Russia
| | - Jobin Varkey
- the Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90033, and Karunya University, Coimbatore, Tamil Nadu 641 114, India
| | - Ralf Langen
- the Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90033, and
| | - Alasdair C Steven
- From the Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892,
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48
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Kholod N, Sivogrivov D, Latypov O, Mayorov S, Kuznitsyn R, Kajava AV, Shlyapnikov M, Granovsky I. Single substitution in bacteriophage T4 RNase H alters the ratio between its exo- and endonuclease activities. Mutat Res 2015; 781:49-57. [PMID: 26432500 DOI: 10.1016/j.mrfmmm.2015.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/10/2015] [Accepted: 09/16/2015] [Indexed: 11/16/2022]
Abstract
The article describes substitutions in bacteriophage T4 RNase H which provide so called das-effect. Phage T4 DNA arrest suppression (das) mutations have been described to be capable of partially suppressing the phage DNA arrest phenotype caused by a dysfunction in genes 46 and/or 47 (also known as Mre11/Rad50 complex). Genetic mapping of das13 (one of the das mutations) has shown it to be in the region of the rnh gene encoding RNase H. Here we report that Das13 mutant of RNase H has substitutions of valine 43 and leucine 242 with isoleucines. To investigate the influence of these mutations on RNase H nuclease properties we have designed a novel in vitro assay that allows us to separate and quantify exo- or endonuclease activities of flap endonuclease. The nuclease assay in vitro showed that V43I substitution increased the ratio between exonuclease/endonuclease activities of RNase H whereas L242I substitution did not affect the nuclease activity of RNase H in vitro. However, both mutations were necessary for the full das effect in vivo. Molecular modelling of the nuclease structure suggests that V43I substitution may lead to disposition of H4 helix, responsible for the interaction with the first base pairs of 5'end of branched DNA. These structural changes may affect unwinding of the first base pairs of gapped or nicked DNA generating a short flap and therefore may stabilize the DNA-enzyme complex. L242I substitution did not affect the structure of RNase H and its role in providing das-effect remains unclear.
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Affiliation(s)
- Natalia Kholod
- Laboratory of Genetic Enzymology, Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, 5 Prospect Nauki, Pushchino, Moscow Region 142290, Russia
| | - Dmitry Sivogrivov
- Laboratory of Genetic Enzymology, Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, 5 Prospect Nauki, Pushchino, Moscow Region 142290, Russia
| | - Oleg Latypov
- Laboratory of Genetic Enzymology, Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, 5 Prospect Nauki, Pushchino, Moscow Region 142290, Russia
| | - Sergey Mayorov
- Laboratory of Genetic Enzymology, Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, 5 Prospect Nauki, Pushchino, Moscow Region 142290, Russia
| | - Rafail Kuznitsyn
- Laboratory of Genetic Enzymology, Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, 5 Prospect Nauki, Pushchino, Moscow Region 142290, Russia; Federal Government-financed Educational Institution of Higher Professional Education «Vyatka State University», 36 Moskovskaya street, Kirov 610000, Russia
| | - Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire, CNRS, Université Montpellier 1 et 2, 1919 Route de Mende, 34293 Montpellier Cédex 5, France; The Institut de Biologie Computationnelle, 95 rue de la Galéra, 34095 Montpellier, Cédex, France
| | - Mikhail Shlyapnikov
- Laboratory of Genetic Enzymology, Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, 5 Prospect Nauki, Pushchino, Moscow Region 142290, Russia
| | - Igor Granovsky
- Laboratory of Genetic Enzymology, Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, 5 Prospect Nauki, Pushchino, Moscow Region 142290, Russia.
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Do Viet P, Roche DB, Kajava AV. TAPO: A combined method for the identification of tandem repeats in protein structures. FEBS Lett 2015; 589:2611-9. [PMID: 26320412 DOI: 10.1016/j.febslet.2015.08.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 10/23/2022]
Abstract
In recent years, there has been an emergence of new 3D structures of proteins containing tandem repeats (TRs), as a result of improved expression and crystallization strategies. Databases focused on structure classifications (PDB, SCOP, CATH) do not provide an easy solution for selection of these structures from PDB. Several approaches have been developed, but no best approach exists to identify the whole range of 3D TRs. Here we describe the TAndem PrOtein detector (TAPO) that uses periodicities of atomic coordinates and other types of structural representation, including strings generated by conformational alphabets, residue contact maps, and arrangements of vectors of secondary structure elements. The benchmarking shows the superior performance of TAPO over the existing programs. In accordance with our analysis of PDB using TAPO, 19% of proteins contain 3D TRs. This analysis allowed us to identify new families of 3D TRs, suggesting that TAPO can be used to regularly update the collection and classification of existing repetitive structures.
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Affiliation(s)
- Phuong Do Viet
- Centre de Recherche de Biochimie Macromoléculaire, UMR 5237 CNRS, Université Montpellier, 1919, Route de Mende, 34293 Montpellier Cedex 5, France; Institut de Biologie Computationnelle, Université Montpellier, Bat. 5, 860, rue St Priest, 34095 Montpellier Cedex 5, France
| | - Daniel B Roche
- Centre de Recherche de Biochimie Macromoléculaire, UMR 5237 CNRS, Université Montpellier, 1919, Route de Mende, 34293 Montpellier Cedex 5, France; Institut de Biologie Computationnelle, Université Montpellier, Bat. 5, 860, rue St Priest, 34095 Montpellier Cedex 5, France
| | - Andrey V Kajava
- Centre de Recherche de Biochimie Macromoléculaire, UMR 5237 CNRS, Université Montpellier, 1919, Route de Mende, 34293 Montpellier Cedex 5, France; Institut de Biologie Computationnelle, Université Montpellier, Bat. 5, 860, rue St Priest, 34095 Montpellier Cedex 5, France.
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50
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Ramya L, Gautham N, Chaloin L, Kajava AV. Restricted mobility of side chains on concave surfaces of solenoid proteins may impart heightened potential for intermolecular interactions. Proteins 2015; 83:1654-64. [PMID: 26138156 DOI: 10.1002/prot.24851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 06/14/2015] [Accepted: 06/24/2015] [Indexed: 11/07/2022]
Abstract
Significant progress has been made in the determination of the protein structures with their number today passing over a hundred thousand structures. The next challenge is the understanding and prediction of protein-protein and protein-ligand interactions. In this work we address this problem by analyzing curved solenoid proteins. Many of these proteins are considered as "hub molecules" for their high potential to interact with many different molecules and to be a scaffold for multisubunit protein machineries. Our analysis of these structures through molecular dynamics simulations reveals that the mobility of the side-chains on the concave surfaces of the solenoids is lower than on the convex ones. This result provides an explanation to the observed preferential binding of the ligands, including small and flexible ligands, to the concave surface of the curved solenoid proteins. The relationship between the landscapes and dynamic properties of the protein surfaces can be further generalized to the other types of protein structures and eventually used in the computer algorithms, allowing prediction of protein-ligand interactions by analysis of protein surfaces.
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Affiliation(s)
- L Ramya
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600 025, India
| | - N Gautham
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600 025, India
| | - Laurent Chaloin
- Centre d'études d'agents Pathogènes et Biotechnologie pour la Santé, CNRS-FRE3689, 1919 Route de Mende, 34293 Montpellier, Cedex 5, France.,Institut de Biologie Computationnelle, 95 Rue de la Galéra, 34095, Montpellier, France
| | - Andrey V Kajava
- University ITMO, Institute of Bioengineering, 197101, St. Petersburg, Russia.,Centre de Recherches de Biochimie Macromoléculaire, UMR5237 CNRS, Université Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.,Institut de Biologie Computationnelle, 95 Rue de la Galéra, 34095, Montpellier, France
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