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Santos-Silva CAD, Vilela LMB, Oliveira-Silva RLD, Silva JBD, Machado AR, Bezerra-Neto JP, Crovella S, Benko-Iseppon AM. Cassava (Manihot esculenta) defensins: Prospection, structural analysis and tissue-specific expression under biotic/abiotic stresses. Biochimie 2021; 186:1-12. [PMID: 33789147 DOI: 10.1016/j.biochi.2021.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 03/10/2021] [Accepted: 03/18/2021] [Indexed: 11/26/2022]
Abstract
Defensins are a prominent family of antimicrobial peptides. They play sophisticated roles in the defense against pathogens in all living organisms, but few works address their expression under different conditions and plant tissues. The present work prospected defensins of Manihot esculenta Crantz, popularly known as cassava. Five defensin candidates (MeDefs) were retrieved from the genome sequences and characterized. Considering chromosome distribution, only MeDef1 and 2 occupy adjacent positions in the same chromosome arm. All 3D structures had antiparallel ß-sheets, an α-helix, and amphipathic residues distributed throughout the peptides with a predominance of cationic surface charge. MeDefs expression was validated by RT-qPCR, including two stress types (biotic: fungus Macrophomina pseudophaseolina, and abiotic: mechanical injury) and a combination of both stresses (fungus+injury) in three different tissues (root, stem, and leaf). For this purpose, ten reference genes (RGs) were tested, and three were chosen to characterize MeDef expression. MeDef3 was up-regulated at roots in all stress situations tested. MeDef1 and MeDef5 were induced in leaves under biotic and abiotic stresses, but not in both stress types simultaneously. Only MeDef2 was down-regulated in the stem tissue also with biotic/abiotic combined stresses. These results indicate that although defensins are known to be responsive to pathogen infection, they may act as preformed defense or, still, have tissue or stress specificities. Aspects of their structure, stability and evolution are also discussed.
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Affiliation(s)
- Carlos André Dos Santos-Silva
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - Lívia Maria Batista Vilela
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - Roberta Lane de Oliveira-Silva
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - Jéssica Barboza da Silva
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - Alexandre Reis Machado
- Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - João Pacífico Bezerra-Neto
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - Sergio Crovella
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil.
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102
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Hollin T, Jaroszewski L, Stajich JE, Godzik A, Le Roch KG. Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins. Microb Genom 2021; 7. [PMID: 33656416 PMCID: PMC8190603 DOI: 10.1099/mgen.0.000541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The RNA binding domain abundant in apicomplexans (RAP) is a protein domain identified in a diverse group of proteins, called RAP proteins, many of which have been shown to be involved in RNA binding. To understand the expansion and potential function of the RAP proteins, we conducted a hidden Markov model based screen among the proteomes of 54 eukaryotes, 17 bacteria and 12 archaea. We demonstrated that the domain is present in closely and distantly related organisms with particular expansions in Alveolata and Chlorophyta, and are not unique to Apicomplexa as previously believed. All RAP proteins identified can be decomposed into two parts. In the N-terminal region, the presence of variable helical repeats seems to participate in the specific targeting of diverse RNAs, while the RAP domain is mostly identified in the C-terminal region and is highly conserved across the different phylogenetic groups studied. Several conserved residues defining the signature motif could be crucial to ensure the function(s) of the RAP proteins. Modelling of RAP domains in apicomplexan parasites confirmed an ⍺/β structure of a restriction endonuclease-like fold. The phylogenetic trees generated from multiple alignment of RAP domains and full-length proteins from various distantly related eukaryotes indicated a complex evolutionary history of this family. We further discuss these results to assess the potential function of this protein family in apicomplexan parasites.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Lukasz Jaroszewski
- Department of Biomedical Sciences, University of California Riverside School of Medicine, 900 University Avenue, Riverside, CA 92521, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Adam Godzik
- Department of Biomedical Sciences, University of California Riverside School of Medicine, 900 University Avenue, Riverside, CA 92521, USA
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
- *Correspondence: Karine G. Le Roch,
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103
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Kreiter J, Rupprecht A, Škulj S, Brkljača Z, Žuna K, Knyazev DG, Bardakji S, Vazdar M, Pohl EE. ANT1 Activation and Inhibition Patterns Support the Fatty Acid Cycling Mechanism for Proton Transport. Int J Mol Sci 2021; 22:ijms22052490. [PMID: 33801254 PMCID: PMC7958136 DOI: 10.3390/ijms22052490] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 01/26/2023] Open
Abstract
Adenine nucleotide translocase (ANT) is a well-known mitochondrial exchanger of ATP against ADP. In contrast, few studies have shown that ANT also mediates proton transport across the inner mitochondrial membrane. The results of these studies are controversial and lead to different hypotheses about molecular transport mechanisms. We hypothesized that the H+-transport mediated by ANT and uncoupling proteins (UCP) has a similar regulation pattern and can be explained by the fatty acid cycling concept. The reconstitution of purified recombinant ANT1 in the planar lipid bilayers allowed us to measure the membrane current after the direct application of transmembrane potential ΔΨ, which would correspond to the mitochondrial states III and IV. Experimental results reveal that ANT1 does not contribute to a basal proton leak. Instead, it mediates H+ transport only in the presence of long-chain fatty acids (FA), as already known for UCPs. It depends on FA chain length and saturation, implying that FA’s transport is confined to the lipid-protein interface. Purine nucleotides with the preference for ATP and ADP inhibited H+ transport. Specific inhibitors of ATP/ADP transport, carboxyatractyloside or bongkrekic acid, also decreased proton transport. The H+ turnover number was calculated based on ANT1 concentration determined by fluorescence correlation spectroscopy and is equal to 14.6 ± 2.5 s−1. Molecular dynamic simulations revealed a large positively charged area at the protein/lipid interface that might facilitate FA anion’s transport across the membrane. ANT’s dual function—ADP/ATP and H+ transport in the presence of FA—may be important for the regulation of mitochondrial membrane potential and thus for potential-dependent processes in mitochondria. Moreover, the expansion of proton-transport modulating drug targets to ANT1 may improve the therapy of obesity, cancer, steatosis, cardiovascular and neurodegenerative diseases.
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Affiliation(s)
- Jürgen Kreiter
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (A.R.); (K.Ž.); (S.B.)
| | - Anne Rupprecht
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (A.R.); (K.Ž.); (S.B.)
- Institute of Pharmacology and Toxicology, Rostock University Medical Center, 18057 Rostock, Germany
| | - Sanja Škulj
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute,10000 Zagreb, Croatia; (S.Š.); (Z.B.); (M.V.)
| | - Zlatko Brkljača
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute,10000 Zagreb, Croatia; (S.Š.); (Z.B.); (M.V.)
| | - Kristina Žuna
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (A.R.); (K.Ž.); (S.B.)
| | - Denis G. Knyazev
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria;
| | - Sarah Bardakji
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (A.R.); (K.Ž.); (S.B.)
| | - Mario Vazdar
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute,10000 Zagreb, Croatia; (S.Š.); (Z.B.); (M.V.)
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Elena E. Pohl
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (A.R.); (K.Ž.); (S.B.)
- Correspondence:
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104
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Durairaj J, Melillo E, Bouwmeester HJ, Beekwilder J, de Ridder D, van Dijk ADJ. Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases. PLoS Comput Biol 2021; 17:e1008197. [PMID: 33750949 PMCID: PMC8016262 DOI: 10.1371/journal.pcbi.1008197] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 04/01/2021] [Accepted: 02/15/2021] [Indexed: 12/19/2022] Open
Abstract
Sesquiterpene synthases (STSs) catalyze the formation of a large class of plant volatiles called sesquiterpenes. While thousands of putative STS sequences from diverse plant species are available, only a small number of them have been functionally characterized. Sequence identity-based screening for desired enzymes, often used in biotechnological applications, is difficult to apply here as STS sequence similarity is strongly affected by species. This calls for more sophisticated computational methods for functionality prediction. We investigate the specificity of precursor cation formation in these elusive enzymes. By inspecting multi-product STSs, we demonstrate that STSs have a strong selectivity towards one precursor cation. We use a machine learning approach combining sequence and structure information to accurately predict precursor cation specificity for STSs across all plant species. We combine this with a co-evolutionary analysis on the wealth of uncharacterized putative STS sequences, to pinpoint residues and distant functional contacts influencing cation formation and reaction pathway selection. These structural factors can be used to predict and engineer enzymes with specific functions, as we demonstrate by predicting and characterizing two novel STSs from Citrus bergamia.
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Affiliation(s)
- Janani Durairaj
- Bioinformatics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Harro J. Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jules Beekwilder
- Bioscience, Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
- Laboratory of Plant Physiology, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D. J. van Dijk
- Bioinformatics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
- Biometris, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
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105
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Milanesio B, Pepe C, Defelipe LA, Eandi Eberle S, Avalos Gomez V, Chaves A, Albero A, Aguirre F, Fernandez D, Aizpurua L, Paula Dieuzeide M, Turjanski A, Bianchi P, Fermo E, Feliu-Torres A. Six novel variants in the PKLR gene associated with pyruvate kinase deficiency in Argentinian patients. Clin Biochem 2021; 91:26-30. [PMID: 33631127 DOI: 10.1016/j.clinbiochem.2021.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/29/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND Pyruvate kinase deficiency (PKD) is a rare recessive congenital hemolytic anemia caused by mutations in the PKLR gene. The disease shows a marked variability in clinical expression. We studied the molecular features of nine unrelated Argentinian patients with congenital hemolytic anemia associated with erythrocyte pyruvate kinase deficiency. DESIGN AND METHODS Routine hematologic investigations were performed to rule out other causes of chronic hemolytic anemia. Sanger sequencing and in-sílico analysis were carried out to identify and characterize the genetics variants. RESULTS Six different novel missense variants were detected among the 18 studied alleles: c.661 G > C (Asp221His), c.956 G > T (Gly319Val), c.1595 G > C (Arg532Pro), c.347 G > A (Arg116Gln), c.1232 G > T (Gly411Val), c.1021G > A (Gly341Ser). Structural implications of amino-acid substitutions were correlated with the clinical phenotypes seen in the probands. CONCLUSIONS This is the first comprehensive report on molecular characterization of pyruvate kinase deficiency in Argentina and the second from South America that would contribute to our knowledge on the distribution and frequency of PKLR variants in our population but also offer new insights into the interpretation of the effect of PKLR variants and phenotype.
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Affiliation(s)
- Berenice Milanesio
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Carolina Pepe
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Lucas A Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Silvia Eandi Eberle
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Vanesa Avalos Gomez
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Alejandro Chaves
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Agustina Albero
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Fernando Aguirre
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Diego Fernandez
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Luciana Aizpurua
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - María Paula Dieuzeide
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Adrián Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paola Bianchi
- U.O.C. Ematologia, U.O.S. FisiopatologiadelleAnemie, Fondazione IRCCS Ca Granada, OspedaleMaggiore Policlínico, Milan, Italy
| | - Elisa Fermo
- U.O.C. Ematologia, U.O.S. FisiopatologiadelleAnemie, Fondazione IRCCS Ca Granada, OspedaleMaggiore Policlínico, Milan, Italy
| | - Aurora Feliu-Torres
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina.
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106
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de Souza JV, Kondal M, Zaborniak P, Cairns R, Bronowska AK. Controlling the Heterodimerisation of the Phytosulfokine Receptor 1 (PSKR1) via Island Loop Modulation. Int J Mol Sci 2021; 22:1806. [PMID: 33670396 PMCID: PMC7918699 DOI: 10.3390/ijms22041806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 01/17/2023] Open
Abstract
Phytosulfokine (PSK) is a phytohormone responsible for cell-to-cell communication in plants, playing a pivotal role in plant development and growth. The binding of PSK to its cognate receptor, PSKR1, is modulated by the formation of a binding site located between a leucine-rich repeat (LRR) domain of PSKR1 and the loop located in the receptor's island domain (ID). The atomic resolution structure of the extracellular PSKR1 bound to PSK has been reported, however, the intrinsic dynamics of PSK binding and the architecture of the PSKR1 binding site remain to be understood. In this work, we used atomistic molecular dynamics (MD) simulations and free energy calculations to elucidate how the PSKR1 island domain (ID) loop forms and binds PSK. Moreover, we report a novel "druggable" binding site which could be exploited for the targeted modulation of the PSKR1-PSK binding by small molecules. We expect that our results will open new ways to modulate the PSK signalling cascade via small molecules, which can result in new crop control and agricultural applications.
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Affiliation(s)
- João V. de Souza
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (M.K.); (P.Z.)
| | - Matthew Kondal
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (M.K.); (P.Z.)
| | - Piotr Zaborniak
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (M.K.); (P.Z.)
| | - Ryland Cairns
- Fontus Environmental, High Garth, Thirsk YO7 3PX, UK;
| | - Agnieszka K. Bronowska
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (M.K.); (P.Z.)
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107
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Cryo-EM structures of engineered active bc 1-cbb 3 type CIII 2CIV super-complexes and electronic communication between the complexes. Nat Commun 2021; 12:929. [PMID: 33568648 PMCID: PMC7876108 DOI: 10.1038/s41467-021-21051-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
Respiratory electron transport complexes are organized as individual entities or combined as large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc1 (Complex III, CIII2), and may have specific cbb3-type cyt c oxidases (Complex IV, CIV) instead of the canonical aa3-type CIV. Electron transfer between these complexes is mediated by soluble (c2) and membrane-anchored (cy) cyts. Here, we report the structure of an engineered bc1-cbb3 type SC (CIII2CIV, 5.2 Å resolution) and three conformers of native CIII2 (3.3 Å resolution). The SC is active in vivo and in vitro, contains all catalytic subunits and cofactors, and two extra transmembrane helices attributed to cyt cy and the assembly factor CcoH. The cyt cy is integral to SC, its cyt domain is mobile and it conveys electrons to CIV differently than cyt c2. The successful production of a native-like functional SC and determination of its structure illustrate the characteristics of membrane-confined and membrane-external respiratory electron transport pathways in Gram-negative bacteria.
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108
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Sivaccumar J, Sandomenico A, Vitagliano L, Ruvo M. Monoclonal Antibodies: A Prospective and Retrospective View. Curr Med Chem 2021; 28:435-471. [PMID: 32072887 DOI: 10.2174/0929867327666200219142231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Monoclonal Antibodies (mAbs) represent one of the most important classes of biotherapeutic agents. They are used to cure many diseases, including cancer, autoimmune diseases, cardiovascular diseases, angiogenesis-related diseases and, more recently also haemophilia. They can be highly varied in terms of format, source, and specificity to improve efficacy and to obtain more targeted applications. This can be achieved by leaving substantially unchanged the basic structural components for paratope clustering. OBJECTIVES The objective was to trace the most relevant findings that have deserved prestigious awards over the years, to report the most important clinical applications and to emphasize their latest emerging therapeutic trends. RESULTS We report the most relevant milestones and new technologies adopted for antibody development. Recent efforts in generating new engineered antibody-based formats are briefly reviewed. The most important antibody-based molecules that are (or are going to be) used for pharmacological practice have been collected in useful tables. CONCLUSION The topics here discussed prove the undisputed role of mAbs as innovative biopharmaceuticals molecules and as vital components of targeted pharmacological therapies.
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Affiliation(s)
- Jwala Sivaccumar
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
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109
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Ferreira DDSS, de Santana CS, Santana IB, Araújo JSC, Souza BCD, Leite FHA, Kato RB, Benevides RG, Góes-Neto A. Functional annotation and comparative modeling of ligninolytic enzymes from Trametes villosa (SW.) Kreisel for biotechnological applications. J Biomol Struct Dyn 2021; 40:6330-6339. [PMID: 33554764 DOI: 10.1080/07391102.2021.1883479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Functional annotation of Trametes villosa genome was performed to search Class II peroxidase proteins in this white-rot fungus, which can be valuable for several biotechnological processes. After sequence identification and manual curation, five proteins were selected to build 3 D models by comparative modeling. Analysis of sequential and structural sequences from selected targets revealed the presence of two putative Lignin Peroxidase and three putative Manganese Peroxidase on this fungal genome. All 3 D models had a similar folding pattern from selected 3 D structure templates. After minimization and validation steps, the best 3 D models were subjected to docking studies and molecular dynamics to identify structural requirements and the interactions required for molecular recognition. Two reliable 3 D models of Class II peroxidases, with typical catalytic site and architecture, and its protein sequences are indicated to recombinant production in biotechnological applications, such as bioenergy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Isis Bugia Santana
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana (UEFS), Bahia, Brazil
| | | | - Bruno Cruz de Souza
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana (UEFS), Bahia, Brazil
| | | | - Rodrigo Bentes Kato
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | | | - Aristóteles Góes-Neto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
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110
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N H, P SR, Sura M, Daddam JR. Structure prediction, molecular simulations of RmlD from Mycobacterium tuberculosis, and interaction studies of Rhodanine derivatives for anti-tuberculosis activity. J Mol Model 2021; 27:75. [PMID: 33547544 DOI: 10.1007/s00894-021-04696-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 01/26/2021] [Indexed: 12/14/2022]
Abstract
Tuberculosis is the most dangerous disease causing maximum deaths than any other, caused by single infectious agent. Due to multidrug resistant of Mycobacterium tuberculosis strains, there is a need of new drugs and drug targets. In this work, we have selected RmlD (α-dTDP-6-deoxy-lyxo-4-hexulose reductase) in the dTDP Rhamnose pathway as drug target to control tuberculosis using Rhodanine analogues. In order to study interaction of RmlD with Rhodanine analogues, a three-dimensional model based on crystal structures such as 1VLO from Clostridium, 1KBZ from Salmonella typhimurium, and 2GGS from Sulfolobus was generated using Modeller 9v7. The modeled structure reliability has been checked using programs such as Procheck, What if, Prosa, Verify 3D, and Errat. In an attempt to find new inhibitors for RmlD enzyme, docking studies were done with a series of Rhodanine and its analogues. Detailed analysis of enzyme-inhibitor interactions identified specific key residues, SER5, VAL9, ILE51, HIS54, and GLY55 which were important in forming hydrogen bonds in binding affinity. Homology modeling and docking studies on RmlD model provided valuable insight information for designing better inhibitors as novel anti-tuberculosis drugs by rational method.
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Affiliation(s)
- Harathi N
- Department of Biochemistry, G. Pulla Reddy Dental College, Kurnool, India
| | - Sreenivasa Reddy P
- Department of Oral and Maxillofacial Surgery, G. Pulla Reddy Dental College & Hospital, Kurnool, 518002, India
| | - Mounica Sura
- Department of Foodtechnology, Jawaharlalnehru Technological University Anantapur, Anantapur, 515001, India
| | - Jayasimha Rayalu Daddam
- Cardiovascular and Mitochondria Related Diseases Research Center, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan.
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111
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Rinaldi DE, Ontiveros MQ, Saffioti NA, Vigil MA, Mangialavori IC, Rossi RC, Rossi JP, Espelt MV, Ferreira-Gomes MS. Epigallocatechin 3-gallate inhibits the plasma membrane Ca 2+-ATPase: effects on calcium homeostasis. Heliyon 2021; 7:e06337. [PMID: 33681501 PMCID: PMC7930289 DOI: 10.1016/j.heliyon.2021.e06337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/16/2021] [Accepted: 02/17/2021] [Indexed: 12/27/2022] Open
Abstract
Flavonoids are natural compounds responsible for the health benefits of green tea. Some of the flavonoids present in green tea are catechins, among which are: epigallocatechin, epicatechin-3-gallate, epicatechin, catechin and epigallocatechin-3-gallate (EGCG). The latter was found to induce apoptosis, reduce reactive oxygen species, in some conditions though in others it acts as an oxidizing agent, induce cell cycle arrest, and inhibit carcinogenesis. EGCG also was found to be involved in calcium (Ca2+) homeostasis in excitable and in non-excitable cells. In this study, we investigate the effect of catechins on plasma membrane Ca2+-ATPase (PMCA), which is one of the main mechanisms that extrude Ca2+ out of the cell. Our studies comprised experiments on the isolated PMCA and on cells overexpressing the pump. Among catechins that inhibited PMCA activity, the most potent inhibitor was EGCG. EGCG inhibited PMCA activity in a reversible way favoring E1P conformation. EGCG inhibition also occurred in the presence of calmodulin, the main pump activator. Finally, the effect of EGCG on PMCA activity was studied in human embryonic kidney cells (HEK293T) that transiently overexpress hPMCA4. Results show that EGCG inhibited PMCA activity in HEK293T cells, suggesting that the effects observed on isolated PMCA occur in living cells.
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Affiliation(s)
| | | | - Nicolas A. Saffioti
- IQUIFIB – Instituto de Química y Fisicoquímica Biológicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Junín 956, 1113 Buenos Aires, Argentina
| | - Maximiliano A. Vigil
- IQUIFIB – Instituto de Química y Fisicoquímica Biológicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Junín 956, 1113 Buenos Aires, Argentina
| | - Irene C. Mangialavori
- IQUIFIB – Instituto de Química y Fisicoquímica Biológicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Junín 956, 1113 Buenos Aires, Argentina
| | - Rolando C. Rossi
- IQUIFIB – Instituto de Química y Fisicoquímica Biológicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Junín 956, 1113 Buenos Aires, Argentina
| | - Juan P. Rossi
- IQUIFIB – Instituto de Química y Fisicoquímica Biológicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Junín 956, 1113 Buenos Aires, Argentina
| | - María V. Espelt
- IQUIFIB – Instituto de Química y Fisicoquímica Biológicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Junín 956, 1113 Buenos Aires, Argentina
| | - Mariela S. Ferreira-Gomes
- IQUIFIB – Instituto de Química y Fisicoquímica Biológicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Junín 956, 1113 Buenos Aires, Argentina
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112
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Palmitoylation Controls NMDA Receptor Function and Steroid Sensitivity. J Neurosci 2021; 41:2119-2134. [PMID: 33526476 DOI: 10.1523/jneurosci.2654-20.2021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/08/2020] [Accepted: 01/06/2021] [Indexed: 11/21/2022] Open
Abstract
NMDARs are ligand-gated ion channels that cause an influx of Na+ and Ca2+ into postsynaptic neurons. The resulting intracellular Ca2+ transient triggers synaptic plasticity. When prolonged, it may induce excitotoxicity, but it may also activate negative feedback to control the activity of NMDARs. Here, we report that a transient rise in intracellular Ca2+ (Ca2+ challenge) increases the sensitivity of NMDARs but not AMPARs/kainate receptors to the endogenous inhibitory neurosteroid 20-oxo-5β-pregnan-3α-yl 3-sulfate and to its synthetic analogs, such as 20-oxo-5β-pregnan-3α-yl 3-hemipimelate (PAhPim). In cultured hippocampal neurons, 30 μm PAhPim had virtually no effect on NMDAR responses; however, following the Ca2+ challenge, it inhibited the responses by 62%; similarly, the Ca2+ challenge induced a 3.7-fold decrease in the steroid IC50 on recombinant GluN1/GluN2B receptors. The increase in the NMDAR sensitivity to PAhPim was dependent on three cysteines (C849, C854, and C871) located in the carboxy-terminal domain of the GluN2B subunit, previously identified to be palmitoylated (Hayashi et al., 2009). Our experiments suggested that the Ca2+ challenge induced receptor depalmitoylation, and single-channel analysis revealed that this was accompanied by a 55% reduction in the probability of channel opening. Results of in silico modeling indicate that receptor palmitoylation promotes anchoring of the GluN2B subunit carboxy-terminal domain to the plasma membrane and facilitates channel opening. Depalmitoylation-induced changes in the NMDAR pharmacology explain the neuroprotective effect of PAhPim on NMDA-induced excitotoxicity. We propose that palmitoylation-dependent changes in the NMDAR sensitivity to steroids serve as an acute endogenous mechanism that controls NMDAR activity.SIGNIFICANCE STATEMENT There is considerable interest in negative allosteric modulators of NMDARs that could compensate for receptor overactivation by glutamate or de novo gain-of-function mutations in neurodevelopmental disorders. By a combination of electrophysiological, pharmacological, and computational techniques we describe a novel feedback mechanism regulating NMDAR activity. We find that a transient rise in intracellular Ca2+ increases NMDAR sensitivity to inhibitory neurosteroids in a process dependent on GluN2B subunit depalmitoylation. These results improve our understanding of the molecular mechanisms of steroid action at the NMDAR and indeed of the basic properties of this important glutamate-gated ion channel and may aid in the development of therapeutics for treating neurologic and psychiatric diseases related to overactivation of NMDARs without affecting normal physiological functions.
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113
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Škulj S, Brkljača Z, Kreiter J, Pohl EE, Vazdar M. Molecular Dynamics Simulations of Mitochondrial Uncoupling Protein 2. Int J Mol Sci 2021; 22:ijms22031214. [PMID: 33530558 PMCID: PMC7866055 DOI: 10.3390/ijms22031214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
Molecular dynamics (MD) simulations of uncoupling proteins (UCP), a class of transmembrane proteins relevant for proton transport across inner mitochondrial membranes, represent a complicated task due to the lack of available structural data. In this work, we use a combination of homology modelling and subsequent microsecond molecular dynamics simulations of UCP2 in the DOPC phospholipid bilayer, starting from the structure of the mitochondrial ATP/ADP carrier (ANT) as a template. We show that this protocol leads to a structure that is impermeable to water, in contrast to MD simulations of UCP2 structures based on the experimental NMR structure. We also show that ATP binding in the UCP2 cavity is tight in the homology modelled structure of UCP2 in agreement with experimental observations. Finally, we corroborate our results with conductance measurements in model membranes, which further suggest that the UCP2 structure modeled from ANT protein possesses additional key functional elements, such as a fatty acid-binding site at the R60 region of the protein, directly related to the proton transport mechanism across inner mitochondrial membranes.
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Affiliation(s)
- Sanja Škulj
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (S.Š.); (Z.B.)
| | - Zlatko Brkljača
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (S.Š.); (Z.B.)
| | - Jürgen Kreiter
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Elena E. Pohl
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, 1210 Vienna, Austria;
- Correspondence: (E.E.P.); (M.V.)
| | - Mario Vazdar
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (S.Š.); (Z.B.)
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Correspondence: (E.E.P.); (M.V.)
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114
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Roura Padrosa D, Marchini V, Paradisi F. CapiPy: python based GUI-application to assist in protein immobilization. Bioinformatics 2021; 37:2761-2762. [PMID: 33459767 DOI: 10.1093/bioinformatics/btab030] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/14/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Protein immobilization, while widespread to unlock enzyme potential in biocatalysis, remains tied to a trial an error approach. Nonetheless, several databases and computational methods have been developed for protein characterization and their study. CapiPy is a user-friendly application for protein model creation and subsequent analysis with a special focus on the ease of use and interpretation of the results to help the users to make an informed decision on the immobilization approach which should be ideal for a protein of interest. The package has been tested with three separate random sets of 150 protein sequences from Uniprot with more than a 70% overall success rate (see Supplementary information and Supplementary Dataset). AVAILABILITY AND IMPLEMENTATION The package is free to use under the GNU General Public License v3.0. All necessary files can be downloaded from https://github.com/drou0302/CapiPy or https://pypi.org/project/CapiPy/. All external requirements are also freely available, with some restrictions for non-academic users. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David Roura Padrosa
- Department of Chemistry and Biochemistry, Freiestrasse 3, Bern, 3012, Switzerland
| | - Valentina Marchini
- Department of Chemistry and Biochemistry, Freiestrasse 3, Bern, 3012, Switzerland
| | - Francesca Paradisi
- Department of Chemistry and Biochemistry, Freiestrasse 3, Bern, 3012, Switzerland
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115
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Jonniya NA, Sk MF, Kar P. Characterizing an allosteric inhibitor-induced inactive state in with-no-lysine kinase 1 using Gaussian accelerated molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:7343-7358. [DOI: 10.1039/d0cp05733a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The binding of an allosteric inhibitor in WNK1 leads to the inactive state.
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Affiliation(s)
- Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, MP
- India
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, MP
- India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, MP
- India
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116
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Sebastian-Valverde M, Wu H, Al Rahim M, Sanchez R, Kumar K, De Vita RJ, Pasinetti GM. Discovery and characterization of small-molecule inhibitors of NLRP3 and NLRC4 inflammasomes. J Biol Chem 2021; 296:100597. [PMID: 33781745 PMCID: PMC8095128 DOI: 10.1016/j.jbc.2021.100597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/17/2021] [Accepted: 03/25/2021] [Indexed: 12/20/2022] Open
Abstract
Inflammasomes are macromolecular complexes involved in the host response to external and endogenous danger signals. Inflammasome-mediated sterile inflammation plays a central role in several human conditions such as autoimmune diseases, type-2 diabetes, and neurodegenerative disorders, indicating inflammasomes could be appealing therapeutic targets. Previous work has demonstrated that inhibiting the ATPase activity of the nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain-containing protein 3 (NLRP3), disrupts inflammasome assembly and function. However, there is a necessity to find new potent compounds with therapeutic potential. Here we combine computational modeling of the target and virtual screening to discover a group of novel compounds predicted to inhibit NLRP3. We characterized the best compounds and determined their potency, specificity, and ability to inhibit processes downstream from NLRP3 activation. Moreover, we analyzed in mice the competence of a lead candidate to reduce lipopolysaccharide-induced inflammation. We also validated the active pharmacophore shared among all the NLRP3 inhibitors, and through computational docking, we clarify key structural features for compound positioning within the inflammasome ATP-binding site. Our study sets the basis for rational design and optimization of inflammasome-targeting probes and drugs.
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Affiliation(s)
| | - Henry Wu
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Md Al Rahim
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Roberto Sanchez
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kunal Kumar
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert J De Vita
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Giulio Maria Pasinetti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA; James J. Peters Veterans Affairs Medical Center, Bronx, New York, USA.
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117
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Xiao X, Qin M, Zhang F, Su Y, Zhou B, Zhou Z. Understanding the Mechanism of Activation/Deactivation of GLP-1R via Accelerated Molecular Dynamics Simulation. Aust J Chem 2021. [DOI: 10.1071/ch20127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Glucagon-like peptide-1 receptor (GLP-1R), as a member of the class B G protein-coupled receptors (GPCRs), plays a crucial role in regulating blood glucose level signal recognition through its activation. The conformation changes during the activation pathway are of particular importance for its function. To investigate the activation mechanism of GLP-1R, the crystal structures of active and inactive forms are chosen to perform a total of 2 μs of accelerated molecular dynamics (aMD) simulations and 400ns of conventional molecular dynamics (cMD) simulations. With the aid of structural analysis and potential of mean force (PMF) calculations, we reveal the role of different helices in the activation and deactivation process and obtain the intermediate states during activation and deactivation that are difficult to capture in experiments. Protein structure network (PSN) was utilised to clarify the allosteric communication pathways of activation and deactivation and reveal the mechanisms of its activation and deactivation. The results could advance our understanding of the activation mechanism of GLP-1R and the related drug design.
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118
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119
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Sengupta D, Bhattacharya G, Ganguli S, Sengupta M. Structural insights and evaluation of the potential impact of missense variants on the interactions of SLIT2 with ROBO1/4 in cancer progression. Sci Rep 2020; 10:21909. [PMID: 33318575 PMCID: PMC7736846 DOI: 10.1038/s41598-020-78882-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
The cognate interaction of ROBO1/4 with its ligand SLIT2 is known to be involved in lung cancer progression. However, the precise role of genetic variants, disrupting the molecular interactions is less understood. All cancer-associated missense variants of ROBO1/4 and SLIT2 from COSMIC were screened for their pathogenicity. Homology modelling was done in Modeller 9.17, followed by molecular simulation in GROMACS. Rigid docking was performed for the cognate partners in PatchDock with refinement in HADDOCK server. Post-docking alterations in conformational, stoichiometric, as well as structural parameters, were assessed. The disruptive variants were ranked using a weighted scoring scheme. In silico prioritisation of 825 variants revealed 379 to be potentially pathogenic out of which, about 12% of the variants, i.e. ROBO1 (14), ROBO4 (8), and SLIT2 (23) altered the cognate docking. Six variants of ROBO1 and 5 variants of ROBO4 were identified as "high disruptors" of interactions with SLIT2 wild type. Likewise, 17 and 13 variants of SLIT2 were found to be "high disruptors" of its interaction with ROBO1 and ROBO4, respectively. Our study is the first report on the impact of cancer-associated missense variants on ROBO1/4 and SLIT2 interactions that might be the drivers of lung cancer progression.
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Affiliation(s)
- Debmalya Sengupta
- Department of Genetics, University of Calcutta, University College of Science (UCSTA), 35, Ballygunge Circular Road, Kolkata, 700 019, India
| | - Gairika Bhattacharya
- Department of Genetics, University of Calcutta, University College of Science (UCSTA), 35, Ballygunge Circular Road, Kolkata, 700 019, India
- Cactus Communications, Mumbai, India
| | - Sayak Ganguli
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700 016, India.
| | - Mainak Sengupta
- Department of Genetics, University of Calcutta, University College of Science (UCSTA), 35, Ballygunge Circular Road, Kolkata, 700 019, India.
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120
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Amatore Z, Gunn S, Harris LK. An Educational Bioinformatics Project to Improve Genome Annotation. Front Microbiol 2020; 11:577497. [PMID: 33365016 PMCID: PMC7750189 DOI: 10.3389/fmicb.2020.577497] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/27/2020] [Indexed: 01/28/2023] Open
Abstract
Scientific advancement is hindered without proper genome annotation because biologists lack a complete understanding of cellular protein functions. In bacterial cells, hypothetical proteins (HPs) are open reading frames with unknown functions. HPs result from either an outdated database or insufficient experimental evidence (i.e., indeterminate annotation). While automated annotation reviews help keep genome annotation up to date, often manual reviews are needed to verify proper annotation. Students can provide the manual review necessary to improve genome annotation. This paper outlines an innovative classroom project that determines if HPs have outdated or indeterminate annotation. The Hypothetical Protein Characterization Project uses multiple well-documented, freely available, web-based, bioinformatics resources that analyze an amino acid sequence to (1) detect sequence similarities to other proteins, (2) identify domains, (3) predict tertiary structure including active site characterization and potential binding ligands, and (4) determine cellular location. Enough evidence can be generated from these analyses to support re-annotation of HPs or prioritize HPs for experimental examinations such as structural determination via X-ray crystallography. Additionally, this paper details several approaches for selecting HPs to characterize using the Hypothetical Protein Characterization Project. These approaches include student- and instructor-directed random selection, selection using differential gene expression from mRNA expression data, and selection based on phylogenetic relations. This paper also provides additional resources to support instructional use of the Hypothetical Protein Characterization Project, such as example assignment instructions with grading rubrics, links to training videos in YouTube, and several step-by-step example projects to demonstrate and interpret the range of achievable results that students might encounter. Educational use of the Hypothetical Protein Characterization Project provides students with an opportunity to learn and apply knowledge of bioinformatic programs to address scientific questions. The project is highly customizable in that HP selection and analysis can be specifically formulated based on the scope and purpose of each student's investigations. Programs used for HP analysis can be easily adapted to course learning objectives. The project can be used in both online and in-seat instruction for a wide variety of undergraduate and graduate classes as well as undergraduate capstone, honor's, and experiential learning projects.
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Affiliation(s)
- Zoie Amatore
- Science Department, Harris Interdisciplinary Research, Davenport University, Lansing, MI, United States
| | - Susan Gunn
- College of Urban Education, Davenport University, Grand Rapids, MI, United States
| | - Laura K. Harris
- Science Department, Harris Interdisciplinary Research, Davenport University, Lansing, MI, United States
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121
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Salekeen R, Mou SN, Islam ME, Ahmed A, Billah MM, Rahman SMM, Islam KMD. Predicting multi-enzyme inhibition in the arachidonic acid metabolic network by Heritiera fomes extracts. J Biomol Struct Dyn 2020; 40:4259-4272. [PMID: 33283657 DOI: 10.1080/07391102.2020.1855248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Heritiera fomes is a mangrove plant with a rich history of ethnomedicinal usage against chronic inflammation. Biochemical analyses of H. fomes have exposed a plethora of bioactive phytochemicals that contribute to this therapeutic effect by perturbing enzymes of a complex inflammatory network mediated by arachidonic acid (AA) metabolism. This study is the first instance of utilizing cheminformatic approaches to elucidate a molecular linkage between these phytochemical interventions and the multi-enzyme AA metabolic network regulation. Analysis of the simulations reflects H. fomes as a functional reservoir of multiple safe and potent natural anti-inflammatory compounds. The investigation suggests two phytocompounds extracted from the plant: a sesquiterpene lactone and a flavone glycoside, as candidate inhibitors of multiple catalytic checkpoints of the inflammatory network. The outcomes of this research act as a primary guideline for future laboratory and clinical testing of anti-inflammatory potentials of H. fomes as an exploitable source of safe and potent drug-like molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahagir Salekeen
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Sadia Noor Mou
- Department of Biochemistry and Molecular Biology, Faculty of Biological Science, University of Dhaka, Dhaka, Bangladesh
| | - Md Emdadul Islam
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Asif Ahmed
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Morsaline Billah
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - S M Mahbubur Rahman
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Kazi Mohammed Didarul Islam
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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122
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Meitlis I, Allenspach EJ, Bauman BM, Phan IQ, Dabbah G, Schmitt EG, Camp ND, Torgerson TR, Nickerson DA, Bamshad MJ, Hagin D, Luthers CR, Stinson JR, Gray J, Lundgren I, Church JA, Butte MJ, Jordan MB, Aceves SS, Schwartz DM, Milner JD, Schuval S, Skoda-Smith S, Cooper MA, Starita LM, Rawlings DJ, Snow AL, James RG. Multiplexed Functional Assessment of Genetic Variants in CARD11. Am J Hum Genet 2020; 107:1029-1043. [PMID: 33202260 PMCID: PMC7820631 DOI: 10.1016/j.ajhg.2020.10.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 10/27/2020] [Indexed: 12/28/2022] Open
Abstract
Genetic testing has increased the number of variants identified in disease genes, but the diagnostic utility is limited by lack of understanding variant function. CARD11 encodes an adaptor protein that expresses dominant-negative and gain-of-function variants associated with distinct immunodeficiencies. Here, we used a "cloning-free" saturation genome editing approach in a diploid cell line to simultaneously score 2,542 variants for decreased or increased function in the region of CARD11 associated with immunodeficiency. We also described an exon-skipping mechanism for CARD11 dominant-negative activity. The classification of reported clinical variants was sensitive (94.6%) and specific (88.9%), which rendered the data immediately useful for interpretation of seven coding and splicing variants implicated in immunodeficiency found in our clinic. This approach is generalizable for variant interpretation in many other clinically actionable genes, in any relevant cell type.
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Affiliation(s)
- Iana Meitlis
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Eric J Allenspach
- Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Bradly M Bauman
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Isabelle Q Phan
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Gina Dabbah
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Erica G Schmitt
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, MO 63130, USA
| | - Nathan D Camp
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | | | - Deborah A Nickerson
- Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - David Hagin
- Allergy and Clinical Immunology Unit, Department of Medicine, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, University of Tel Aviv, Tel Aviv 62919, Israel
| | - Christopher R Luthers
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Jeffrey R Stinson
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Jessica Gray
- Divisions of Immunobiology, and Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Joseph A Church
- Department of Pediatrics, Keck School of Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Manish J Butte
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California Los Angeles, Los Angeles, CA 90404, USA
| | - Mike B Jordan
- Divisions of Immunobiology, and Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Seema S Aceves
- Division of Allergy Immunology, Departments of Pediatrics and Medicine, University of California, San Diego, and Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Joshua D Milner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Susan Schuval
- Department of Pediatrics, Stonybrook University, Stony Brook, NY 11794, USA
| | - Suzanne Skoda-Smith
- Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, MO 63130, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - David J Rawlings
- Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Andrew L Snow
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Richard G James
- Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA.
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Secretory production in Escherichia coli of a GH46 chitosanase from Chromobacterium violaceum, suitable to generate antifungal chitooligosaccharides. Int J Biol Macromol 2020; 165:1482-1495. [PMID: 33017605 DOI: 10.1016/j.ijbiomac.2020.09.221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 01/23/2023]
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Sučec I, Wang Y, Dakhlaoui O, Weinhäupl K, Jores T, Costa D, Hessel A, Brennich M, Rapaport D, Lindorff-Larsen K, Bersch B, Schanda P. Structural basis of client specificity in mitochondrial membrane-protein chaperones. SCIENCE ADVANCES 2020; 6:eabd0263. [PMID: 33355130 PMCID: PMC11206218 DOI: 10.1126/sciadv.abd0263] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Chaperones are essential for assisting protein folding and for transferring poorly soluble proteins to their functional locations within cells. Hydrophobic interactions drive promiscuous chaperone-client binding, but our understanding of how additional interactions enable client specificity is sparse. Here, we decipher what determines binding of two chaperones (TIM8·13 and TIM9·10) to different integral membrane proteins, the all-transmembrane mitochondrial carrier Ggc1 and Tim23, which has an additional disordered hydrophilic domain. Combining NMR, SAXS, and molecular dynamics simulations, we determine the structures of Tim23/TIM8·13 and Tim23/TIM9·10 complexes. TIM8·13 uses transient salt bridges to interact with the hydrophilic part of its client, but its interactions to the transmembrane part are weaker than in TIM9·10. Consequently, TIM9·10 outcompetes TIM8·13 in binding hydrophobic clients, while TIM8·13 is tuned to few clients with both hydrophilic and hydrophobic parts. Our study exemplifies how chaperones fine-tune the balance of promiscuity versus specificity.
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Affiliation(s)
- Iva Sučec
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044 Grenoble, France
| | - Yong Wang
- Structural Biology and NMR Laboratory, the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Ons Dakhlaoui
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044 Grenoble, France
| | - Katharina Weinhäupl
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044 Grenoble, France.
| | - Tobias Jores
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Doriane Costa
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044 Grenoble, France
| | - Audrey Hessel
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044 Grenoble, France
| | - Martha Brennich
- European Molecular Biology Laboratory, 38042 Grenoble, France
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Beate Bersch
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044 Grenoble, France.
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044 Grenoble, France.
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125
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Gomez-Perosanz M, Sanchez-Trincado JL, Fernandez-Arquero M, Sidney J, Sette A, Lafuente EM, Reche PA. Human rhinovirus-specific CD8 T cell responses target conserved and unusual epitopes. FASEB J 2020; 35:e21208. [PMID: 33230881 PMCID: PMC7753581 DOI: 10.1096/fj.202002165r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022]
Abstract
Human Rhinovirus (HRV) is a major cause of common cold, bronchiolitis, and exacerbations of chronic pulmonary diseases such as asthma. CD8 T cell responses likely play an important role in the control of HRV infection but, surprisingly, HRV‐specific CD8 T cell epitopes remain yet to be identified. Here, we approached the discovery and characterization of conserved HRV‐specific CD8 T cell epitopes from species A (HRV A) and C (HRV C), the most frequent subtypes in the clinics of various pulmonary diseases. We found IFNγ‐ELISPOT positive responses to 23 conserved HRV‐specific peptides on peripheral blood mononuclear cells (PBMCs) from 14 HLA I typed subjects. Peptide‐specific IFNγ production by CD8 T cells and binding to the relevant HLA I were confirmed for six HRV A‐specific and three HRV C‐specific CD8 T cell epitopes. In addition, we validated A*02:01‐restricted epitopes by DimerX staining and found out that these peptides mediated cytotoxicity. All these A*02:01‐restricted epitopes were 9‐mers but, interestingly, we also identified and validated an unusually long 16‐mer epitope peptide restricted by A*02:01, HRVC1791‐1806 (GLEPLDLNTSAGFPYV). HRV‐specific CD8 T cell epitopes describe here are expected to elicit CD8 T cell responses in up to 87% of the population and could be key for developing an HRV vaccine.
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Affiliation(s)
- Marta Gomez-Perosanz
- Department of Immunology, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Jose L Sanchez-Trincado
- Department of Immunology, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | | | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Esther M Lafuente
- Department of Immunology, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Pedro A Reche
- Department of Immunology, School of Medicine, Complutense University of Madrid, Madrid, Spain
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Grund ME, Choi SJ, McNitt DH, Barbier M, Hu G, LaSala PR, Cote CK, Berisio R, Lukomski S. Burkholderia collagen-like protein 8, Bucl8, is a unique outer membrane component of a putative tetrapartite efflux pump in Burkholderia pseudomallei and Burkholderia mallei. PLoS One 2020; 15:e0242593. [PMID: 33227031 PMCID: PMC7682875 DOI: 10.1371/journal.pone.0242593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/06/2020] [Indexed: 12/19/2022] Open
Abstract
Bacterial efflux pumps are an important pathogenicity trait because they extrude a variety of xenobiotics. Our laboratory previously identified in silico Burkholderia collagen-like protein 8 (Bucl8) in the hazardous pathogens Burkholderia pseudomallei and Burkholderia mallei. We hypothesize that Bucl8, which contains two predicted tandem outer membrane efflux pump domains, is a component of a putative efflux pump. Unique to Bucl8, as compared to other outer membrane proteins, is the presence of an extended extracellular region containing a collagen-like (CL) domain and a non-collagenous C-terminus (Ct). Molecular modeling and circular dichroism spectroscopy with a recombinant protein, corresponding to this extracellular CL-Ct portion of Bucl8, demonstrated that it adopts a collagen triple helix, whereas functional assays screening for Bucl8 ligands identified binding to fibrinogen. Bioinformatic analysis of the bucl8 gene locus revealed it resembles a classical efflux-pump operon. The bucl8 gene is co-localized with downstream fusCDE genes encoding fusaric acid (FA) resistance, and with an upstream gene, designated as fusR, encoding a LysR-type transcriptional regulator. Using reverse transcriptase (RT)-qPCR, we defined the boundaries and transcriptional organization of the fusR-bucl8-fusCDE operon. We found exogenous FA induced bucl8 transcription over 80-fold in B. pseudomallei, while deletion of the entire bucl8 locus decreased the minimum inhibitory concentration of FA 4-fold in its isogenic mutant. We furthermore showed that the putative Bucl8-associated pump expressed in the heterologous Escherichia coli host confers FA resistance. On the contrary, the Bucl8-associated pump did not confer resistance to a panel of clinically-relevant antimicrobials in Burkholderia and E. coli. We finally demonstrated that deletion of the bucl8-locus drastically affects the growth of the mutant in L-broth. We determined that Bucl8 is a component of a novel tetrapartite efflux pump, which confers FA resistance, fibrinogen binding, and optimal growth.
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Affiliation(s)
- Megan E. Grund
- Department of Microbiology, Immunology and Cell Biology, School of
Medicine, West Virginia University, Morgantown, WV, United States of
America
| | - Soo J. Choi
- Department of Microbiology, Immunology and Cell Biology, School of
Medicine, West Virginia University, Morgantown, WV, United States of
America
| | - Dudley H. McNitt
- Department of Microbiology, Immunology and Cell Biology, School of
Medicine, West Virginia University, Morgantown, WV, United States of
America
| | - Mariette Barbier
- Department of Microbiology, Immunology and Cell Biology, School of
Medicine, West Virginia University, Morgantown, WV, United States of
America
| | - Gangqing Hu
- Department of Microbiology, Immunology and Cell Biology, School of
Medicine, West Virginia University, Morgantown, WV, United States of
America
- Cancer Center, West Virginia University, Morgantown, WV, United States of
America
- Bioinformatics Core, West Virginia University, Morgantown, WV, United
States of America
| | - P. Rocco LaSala
- Department of Pathology, West Virginia University, Morgantown, WV, United
States of America
| | - Christopher K. Cote
- Bacteriology Division, The United States Army Medical Research Institute
of Infectious Diseases (USAMRIID), Frederick, MD, United States of
America
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, National Research Council,
Naples, Italy
| | - Slawomir Lukomski
- Department of Microbiology, Immunology and Cell Biology, School of
Medicine, West Virginia University, Morgantown, WV, United States of
America
- Cancer Center, West Virginia University, Morgantown, WV, United States of
America
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Serçinoğlu O, Senturk D, Altinisik Kaya FE, Avci FG, Frlan R, Tomašič T, Ozbek P, Orelle C, Jault JM, Sariyar Akbulut B. Identification of novel inhibitors of the ABC transporter BmrA. Bioorg Chem 2020; 105:104452. [PMID: 33212311 DOI: 10.1016/j.bioorg.2020.104452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/23/2020] [Accepted: 11/01/2020] [Indexed: 01/02/2023]
Abstract
The resistance of microbes to commonly used antibiotics has become a worldwide health problem. A major underlying mechanism of microbial antibiotic resistance is the export of drugs from bacterial cells. Drug efflux is mediated through the action of multidrug resistance efflux pumps located in the bacterial cell membranes. The critical role of bacterial efflux pumps in antibiotic resistance has directed research efforts to the identification of novel efflux pump inhibitors that can be used alongside antibiotics in clinical settings. Here, we aimed to find potential inhibitors of the archetypical ATP-binding cassette (ABC) efflux pump BmrA of Bacillus subtilis via virtual screening of the Mu.Ta.Lig. Chemotheca small molecule library. Molecular docking calculations targeting the nucleotide-binding domain of BmrA were performed using AutoDock Vina. Following a further drug-likeness filtering step based on Lipinski's Rule of Five, top 25 scorers were identified. These ligands were then clustered into separate groups based on their contact patterns with the BmrA nucleotide-binding domain. Six ligands with distinct contact patterns were used for further in vitro inhibition assays based on intracellular ethidium bromide accumulation. Using this methodology, we identified two novel inhibitors of BmrA from the Chemotheca small molecule library.
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Affiliation(s)
- Onur Serçinoğlu
- Department of Bioengineering, Recep Tayyip Erdogan University, Fener 53100, Rize, Turkey
| | - Duygu Senturk
- Department of Bioengineering, Marmara University, Kadikoy 34722, Istanbul, Turkey
| | | | - Fatma Gizem Avci
- Department of Bioengineering, Uskudar University, Uskudar 34662, Istanbul, Turkey
| | - Rok Frlan
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Pemra Ozbek
- Department of Bioengineering, Marmara University, Kadikoy 34722, Istanbul, Turkey
| | - Cédric Orelle
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", 7 passage du Vercors, 69367 Lyon Cedex 7, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", 7 passage du Vercors, 69367 Lyon Cedex 7, France
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128
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Interaction between GABA A receptor α 1 and β 2 subunits at the N-terminal peripheral regions is crucial for receptor binding and gating. Biochem Pharmacol 2020; 183:114338. [PMID: 33189674 DOI: 10.1016/j.bcp.2020.114338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023]
Abstract
Pentameric ligand gated ion channels (pLGICs) are crucial in electrochemical signaling but exact molecular mechanisms of their activation remain elusive. So far, major effort focused on the top-down molecular pathway between the ligand binding site and the channel gate. However, recent studies revealed that pLGIC activation is associated with coordinated subunit twisting in the membrane plane. This suggests a key role of intersubunit interactions but the underlying mechanisms remain largely unknown. Herein, we investigated a "peripheral" subunit interface region of GABAA receptor where structural modeling indicated interaction between N-terminal α1F14 and β2F31 residues. Our experiments underscored a crucial role of this interaction in ligand binding and gating, especially preactivation and opening, showing that the intersubunit cross-talk taking place outside (above) the top-down pathway can be strongly involved in receptor activation. Thus, described here intersubunit interaction appears to operate across a particularly long distance, affecting vast portions of the macromolecule.
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129
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Reddy CN, Manzar N, Ateeq B, Sankararamakrishnan R. Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-X L: Role of Non-Hot Spot Residues. Biochemistry 2020; 59:4379-4394. [PMID: 33146015 DOI: 10.1021/acs.biochem.0c00661] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Interactions between pro- and anti-apoptotic Bcl-2 proteins decide the fate of the cell. The BH3 domain of pro-apoptotic Bcl-2 proteins interacts with the exposed hydrophobic groove of their anti-apoptotic counterparts. Through their design and development, BH3 mimetics that target the hydrophobic groove of specific anti-apoptotic Bcl-2 proteins have the potential to become anticancer drugs. We have developed a novel computational method for designing sequences with BH3 domain features that can bind specifically to anti-apoptotic Mcl-1 or Bcl-XL. In this method, we retained the four highly conserved hydrophobic and aspartic residues of wild-type BH3 sequences and randomly substituted all other positions to generate a large number of BH3-like sequences. We modeled 20000 complex structures with Mcl-1 or Bcl-XL using the BH3-like sequences derived from five wild-type pro-apoptotic BH3 peptides. Peptide-protein interaction energies calculated from these models for each set of BH3-like sequences resulted in negatively skewed extreme value distributions. The selected BH3-like sequences from the extreme negative tail regions have highly favorable interaction energies with Mcl-1 or Bcl-XL. They are enriched in acidic and basic residues when they bind to Mcl-1 and Bcl-XL, respectively. With the charged residues often away from the binding interface, the overall electric field generated by the charged residues results in strong long-range electrostatic interaction energies between the peptide and the protein giving rise to high specificity. Cell viability studies of representative BH3-like peptides further validated the predicted specificity. This study has revealed the importance of non-hot spot residues in BH3-mimetic peptides in providing specificity to a particular anti-apoptotic protein.
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130
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Arya G, Pal M, Sharma M, Singh B, Singh S, Agrawal V, Chaba R. Molecular insights into effector binding by DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism in Escherichia coli. Mol Microbiol 2020; 115:591-609. [PMID: 33068046 DOI: 10.1111/mmi.14625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 01/23/2023]
Abstract
Several GntR/FadR transcriptional regulators govern sugar acid metabolism in bacteria. Although effectors have been identified for a few sugar acid regulators, the mode of effector binding is unknown. Even in the overall FadR subfamily, there are limited details on effector-regulator interactions. Here, we identified the effector-binding cavity in Escherichia coli DgoR, a FadR subfamily transcriptional repressor of D-galactonate metabolism that employs D-galactonate as its effector. Using a genetic screen, we isolated several dgoR superrepressor alleles. Blind docking suggested eight amino acids corresponding to these alleles to form a part of the effector-binding cavity. In vivo and in vitro assays showed that these mutations compromise the inducibility of DgoR without affecting its oligomeric status or affinity for target DNA. Taking Bacillus subtilis GntR as a representative, we demonstrated that the effector-binding cavity is similar among FadR subfamily sugar acid regulators. Finally, a comparison of sugar acid regulators with other FadR members suggested conserved features of effector-regulator recognition within the FadR subfamily. Sugar acid metabolism is widely implicated in bacterial colonization and virulence. The present study sets the basis to investigate the influence of natural genetic variations in FadR subfamily regulators on their sensitivity to sugar acids and ultimately on host-bacterial interactions.
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Affiliation(s)
- Garima Arya
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Mohinder Pal
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, India
| | - Bhupinder Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Swati Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Vishal Agrawal
- Department of Biochemistry, Panjab University, Chandigarh, India
| | - Rachna Chaba
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
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131
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Costa LSM, Pires ÁS, Damaceno NB, Rigueiras PO, Maximiano MR, Franco OL, Porto WF. In silico characterization of class II plant defensins from Arabidopsis thaliana. PHYTOCHEMISTRY 2020; 179:112511. [PMID: 32931963 DOI: 10.1016/j.phytochem.2020.112511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Defensins comprise a polyphyletic group of multifunctional defense peptides. Cis-defensins, also known as cysteine stabilized αβ (CSαβ) defensins, are one of the most ancient defense peptide families. In plants, these peptides have been divided into two classes, according to their precursor organization. Class I defensins are composed of the signal peptide and the mature sequence, while class II defensins have an additional C-terminal prodomain, which is proteolytically cleaved. Class II defensins have been described in Solanaceae and Poaceae species, indicating this class could be spread among all flowering plants. Here, a search by regular expression (RegEx) was applied to the Arabidopsis thaliana proteome, a model plant with more than 300 predicted defensin genes. Two sequences were identified, A7REG2 and A7REG4, which have a typical plant defensin structure and an additional C-terminal prodomain. TraVA database indicated they are expressed in flower, ovules and seeds, and being duplicated genes, this indicates they could be a result of a subfunctionalization process. The presence of class II defensin sequences in Brassicaceae and Solanaceae and evolutionary distance between them suggest class II defensins may be present in other eudicots. Discovery of class II defensins in other plants could shed some light on flower, ovules and seed physiology, as this class is expressed in these locations.
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Affiliation(s)
- Laura S M Costa
- Centro de Análises Proteômicas e Bioquímicas. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Departamento de Biologia, Programa de Pós-Graduação em Genética e Biotecnologia, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, MG, Brazil
| | - Állan S Pires
- Centro de Análises Proteômicas e Bioquímicas. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Neila B Damaceno
- Centro de Análises Proteômicas e Bioquímicas. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Pietra O Rigueiras
- Centro de Análises Proteômicas e Bioquímicas. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Mariana R Maximiano
- Centro de Análises Proteômicas e Bioquímicas. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Octavio L Franco
- Centro de Análises Proteômicas e Bioquímicas. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Departamento de Biologia, Programa de Pós-Graduação em Genética e Biotecnologia, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, MG, Brazil; S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - William F Porto
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil; Porto Reports, Brasília, DF, Brazil.
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132
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Chen C, Meng Y, Shopan J, Whelan J, Hu Z, Yang J, Zhang M. Identification and characterization of Arabidopsis thaliana mitochondrial F 1F 0-ATPase inhibitor factor 1. JOURNAL OF PLANT PHYSIOLOGY 2020; 254:153264. [PMID: 33032063 DOI: 10.1016/j.jplph.2020.153264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Mitochondrial F1F0-ATP synthase (F1F0-ATPase) inhibitor factor 1 (IF1) has been extensively characterized as an endogenous inhibitor that prevents the hydrolysis of adenosine-5'-triphosphate (ATP) by mitochondrial ATPases in mammals and yeasts; however, IF1's functions in plants remain unclear. Here, a comprehensive bioinformatic analysis was performed to identify plant mitochondrial F1F0-ATPase IF1 orthologs. Plant IF1s contain a conserved F1F0-ATPase inhibitory domain, but lack the antiparallel α-helical coiled-coil structure compared with mammalian IF1s. A subcellular localization analysis in Arabidopsis thaliana revealed that AtIF1-green fluorescent protein was present only in mitochondria. Additionally, AtIF1 was widely expressed in diverse organs and intense β-glucuronidase staining was observed in reproductive tissues and germinating seeds. Compared with the wild-type and p35S:AtIF1-if1 etiolated seedlings, the ATP/ADP ratio was significantly lower in the AtIF1 T-DNA knockout seedlings (if1 mutant) growing under dark conditions, suggesting that AtIF1 can influence the energy state of cells. A significant reduction in seed yield and strong growth retardation under dark conditions were observed in the if1 mutant line. Furthermore, if1 plants exhibited a substantially decreased sensitivity to abscisic acid. Thus, the A. thaliana mitochondrial IF1, which is a conserved F1F0-ATPase inhibitor, is crucial for plant growth and responses to abscisic acid.
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Affiliation(s)
- Cuiting Chen
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Yiqing Meng
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Jannat Shopan
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - James Whelan
- Department of Animal, Plant and Soil Science, School of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
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133
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Karlberg M, de Souza JV, Fan L, Kizhedath A, Bronowska AK, Glassey J. QSAR Implementation for HIC Retention Time Prediction of mAbs Using Fab Structure: A Comparison between Structural Representations. Int J Mol Sci 2020; 21:ijms21218037. [PMID: 33126648 PMCID: PMC7663183 DOI: 10.3390/ijms21218037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 12/19/2022] Open
Abstract
Monoclonal antibodies (mAbs) constitute a rapidly growing biopharmaceutical sector. However, their growth is impeded by high failure rates originating from failed clinical trials and developability issues in process development. There is, therefore, a growing need for better in silico tools to aid in risk assessment of mAb candidates to promote early-stage screening of potentially problematic mAb candidates. In this study, a quantitative structure–activity relationship (QSAR) modelling workflow was designed for the prediction of hydrophobic interaction chromatography (HIC) retention times of mAbs. Three novel descriptor sets derived from primary sequence, homology modelling, and atomistic molecular dynamics (MD) simulations were developed and assessed to determine the necessary level of structural resolution needed to accurately capture the relationship between mAb structures and HIC retention times. The results showed that descriptors derived from 3D structures obtained after MD simulations were the most suitable for HIC retention time prediction with a R2 = 0.63 in an external test set. It was found that when using homology modelling, the resulting 3D structures became biased towards the used structural template. Performing an MD simulation therefore proved to be a necessary post-processing step for the mAb structures in order to relax the structures and allow them to attain a more natural conformation. Based on the results, the proposed workflow in this paper could therefore potentially contribute to aid in risk assessment of mAb candidates in early development.
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Affiliation(s)
- Micael Karlberg
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (M.K.); (L.F.); (A.K.)
| | - João Victor de Souza
- Chemistry—School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (J.V.d.S.); (A.K.B.)
| | - Lanyu Fan
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (M.K.); (L.F.); (A.K.)
- Chemistry—School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (J.V.d.S.); (A.K.B.)
| | - Arathi Kizhedath
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (M.K.); (L.F.); (A.K.)
| | - Agnieszka K. Bronowska
- Chemistry—School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (J.V.d.S.); (A.K.B.)
| | - Jarka Glassey
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (M.K.); (L.F.); (A.K.)
- Correspondence:
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Mayanagi K, Oki K, Miyazaki N, Ishino S, Yamagami T, Morikawa K, Iwasaki K, Kohda D, Shirai T, Ishino Y. Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy. BMC Biol 2020; 18:152. [PMID: 33115459 PMCID: PMC7594292 DOI: 10.1186/s12915-020-00889-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/05/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA polymerase D (PolD) is the representative member of the D family of DNA polymerases. It is an archaea-specific DNA polymerase required for replication and unrelated to other known DNA polymerases. PolD consists of a heterodimer of two subunits, DP1 and DP2, which contain catalytic sites for 3'-5' editing exonuclease and DNA polymerase activities, respectively, with both proteins being mutually required for the full activities of each enzyme. However, the processivity of the replicase holoenzyme has additionally been shown to be enhanced by the clamp molecule proliferating cell nuclear antigen (PCNA), making it crucial to elucidate the interaction between PolD and PCNA on a structural level for a full understanding of its functional relevance. We present here the 3D structure of a PolD-PCNA-DNA complex from Thermococcus kodakarensis using single-particle cryo-electron microscopy (EM). RESULTS Two distinct forms of the PolD-PCNA-DNA complex were identified by 3D classification analysis. Fitting the reported crystal structures of truncated forms of DP1 and DP2 from Pyrococcus abyssi onto our EM map showed the 3D atomic structural model of PolD-PCNA-DNA. In addition to the canonical interaction between PCNA and PolD via PIP (PCNA-interacting protein)-box motif, we found a new contact point consisting of a glutamate residue at position 171 in a β-hairpin of PCNA, which mediates interactions with DP1 and DP2. The DNA synthesis activity of a mutant PolD with disruption of the E171-mediated PCNA interaction was not stimulated by PCNA in vitro. CONCLUSIONS Based on our analyses, we propose that glutamate residues at position 171 in each subunit of the PCNA homotrimer ring can function as hooks to lock PolD conformation on PCNA for conversion of its activity. This hook function of the clamp molecule may be conserved in the three domains of life.
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Affiliation(s)
- Kouta Mayanagi
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka, 812-8582, Japan.
| | - Keisuke Oki
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan
| | - Naoyuki Miyazaki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Present address: Life Science Center for Survival Dynamics Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan
| | - Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan
| | - Kosuke Morikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-konoemachi, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kenji Iwasaki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Present address: Life Science Center for Survival Dynamics Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Daisuke Kohda
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka, 812-8582, Japan
| | - Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga, 526-0829, Japan.
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan.
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135
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A bacteriophage mimic of the bacterial nucleoid-associated protein Fis. Biochem J 2020; 477:1345-1362. [PMID: 32207815 PMCID: PMC7166090 DOI: 10.1042/bcj20200146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/19/2020] [Accepted: 03/24/2020] [Indexed: 11/17/2022]
Abstract
We report the identification and characterization of a bacteriophage λ-encoded protein, NinH. Sequence homology suggests similarity between NinH and Fis, a bacterial nucleoid-associated protein (NAP) involved in numerous DNA topology manipulations, including chromosome condensation, transcriptional regulation and phage site-specific recombination. We find that NinH functions as a homodimer and is able to bind and bend double-stranded DNA in vitro. Furthermore, NinH shows a preference for a 15 bp signature sequence related to the degenerate consensus favored by Fis. Structural studies reinforced the proposed similarity to Fis and supported the identification of residues involved in DNA binding which were demonstrated experimentally. Overexpression of NinH proved toxic and this correlated with its capacity to associate with DNA. NinH is the first example of a phage-encoded Fis-like NAP that likely influences phage excision-integration reactions or bacterial gene expression.
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136
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Yan W, Cheng L, Wang W, Wu C, Yang X, Du X, Ma L, Qi S, Wei Y, Lu Z, Yang S, Shao Z. Structure of the human gonadotropin-releasing hormone receptor GnRH1R reveals an unusual ligand binding mode. Nat Commun 2020; 11:5287. [PMID: 33082324 PMCID: PMC7576152 DOI: 10.1038/s41467-020-19109-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/29/2020] [Indexed: 02/05/2023] Open
Abstract
Gonadotrophin-releasing hormone (GnRH), also known as luteinizing hormone-releasing hormone, is the main regulator of the reproductive system, acting on gonadotropic cells by binding to the GnRH1 receptor (GnRH1R). The GnRH-GnRH1R system is a promising therapeutic target for maintaining reproductive function; to date, a number of ligands targeting GnRH1R for disease treatment are available on the market. Here, we report the crystal structure of GnRH1R bound to the small-molecule drug elagolix at 2.8 Å resolution. The structure reveals an interesting N-terminus that could co-occupy the enlarged orthosteric binding site together with elagolix. The unusual ligand binding mode was further investigated by structural analyses, functional assays and molecular docking studies. On the other hand, because of the unique characteristic of lacking a cytoplasmic C-terminal helix, GnRH1R exhibits different microswitch structural features from other class A GPCRs. In summary, this study provides insight into the ligand binding mode of GnRH1R and offers an atomic framework for rational drug design.
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Affiliation(s)
- Wei Yan
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lin Cheng
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Wei Wang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Chao Wu
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xin Yang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaozhe Du
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Liang Ma
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Shiqian Qi
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Yuquan Wei
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Zhiliang Lu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Shengyong Yang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Zhenhua Shao
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Sada M, Saraya T, Ishii H, Okayama K, Hayashi Y, Tsugawa T, Nishina A, Murakami K, Kuroda M, Ryo A, Kimura H. Detailed Molecular Interactions of Favipiravir with SARS-CoV-2, SARS-CoV, MERS-CoV, and Influenza Virus Polymerases In Silico. Microorganisms 2020; 8:E1610. [PMID: 33092045 PMCID: PMC7589801 DOI: 10.3390/microorganisms8101610] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/15/2020] [Accepted: 10/18/2020] [Indexed: 12/20/2022] Open
Abstract
Favipiravir was initially developed as an antiviral drug against influenza and is currently used in clinical trials against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection (COVID-19). This agent is presumably involved in RNA chain termination during influenza virus replication, although the molecular interactions underlying its potential impact on the coronaviruses including SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) remain unclear. We performed in silico studies to elucidate detailed molecular interactions between favipiravir and the SARS-CoV-2, SARS-CoV, MERS-CoV, and influenza virus RNA-dependent RNA polymerases (RdRp). As a result, no interactions between favipiravir ribofuranosyl-5'-triphosphate (F-RTP), the active form of favipiravir, and the active sites of RdRps (PB1 proteins) from influenza A (H1N1)pdm09 virus were found, yet the agent bound to the tunnel of the replication genome of PB1 protein leading to the inhibition of replicated RNA passage. In contrast, F-RTP bound to the active sites of coronavirus RdRp in the presence of the agent and RdRp. Further, the agent bound to the replicated RNA terminus in the presence of agent, magnesium ions, nucleotide triphosphate, and RdRp proteins. These results suggest that favipiravir exhibits distinct mechanisms of action against influenza virus and various coronaviruses.
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Affiliation(s)
- Mitsuru Sada
- Advanced Medical Science Research Center, Gunma Paz University, Shibukawa, Gunma 377-0008, Japan;
- Department of Respiratory medicine, Kyorin University Hospital of medicine, Mitaka, Tokyo 181-8611, Japan; (T.S.); (H.I.)
| | - Takeshi Saraya
- Department of Respiratory medicine, Kyorin University Hospital of medicine, Mitaka, Tokyo 181-8611, Japan; (T.S.); (H.I.)
| | - Haruyuki Ishii
- Department of Respiratory medicine, Kyorin University Hospital of medicine, Mitaka, Tokyo 181-8611, Japan; (T.S.); (H.I.)
| | - Kaori Okayama
- School of Medical Technology, Faculty of Health Science, Gumma Paz University, Takasaki, Gunma 370-0006, Japan; (K.O.); (Y.H.)
| | - Yuriko Hayashi
- School of Medical Technology, Faculty of Health Science, Gumma Paz University, Takasaki, Gunma 370-0006, Japan; (K.O.); (Y.H.)
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8543, Japan;
| | - Atsuyoshi Nishina
- College of Science and Technology, Nihon University, Tokyo 101-0062, Japan;
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan;
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, Japan;
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan;
| | - Hirokazu Kimura
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan;
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, Takasaki, Gunma 370-0006, Japan
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138
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Chen J, Wang W, Sun H, Pang L, Yin B. Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics. J Comput Aided Mol Des 2020; 34:1289-1305. [DOI: 10.1007/s10822-020-00355-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022]
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139
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Cartilage oligomeric matrix protein fine-tunes disturbed flow-induced endothelial activation and atherogenesis. Matrix Biol 2020; 95:32-51. [PMID: 33068727 DOI: 10.1016/j.matbio.2020.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/15/2020] [Accepted: 10/11/2020] [Indexed: 12/27/2022]
Abstract
Disturbed flow leads to increased inflammatory responses of endothelial cells (ECs) prone to atherogenic state. Currently, little is known about the physiological mechanisms protecting vasculature against disturbed flow-activated ECs leading to atherosclerosis. Understanding the protective mediators involved in EC activation could provide novel therapeutic strategies for atherosclerosis. The extracellular matrix microenvironment profoundly regulates cellular homeostasis. A non-EC resident ECM protein, cartilage oligomeric matrix protein (COMP), has diverse protective roles in the cardiovascular system. To determine whether COMP could protect against disturbed flow-activated EC and atherosclerosis, we compared oscillatory shear stress (OSS) induced EC activation coated with various ECM proteins. Purified COMP inhibited EC activation caused by OSS. EC activation was upregulated in the aortic arch where the flow is disturbed in COMP-/- mice as compared with wild-type mice under physiological conditions or pathologically in partially ligated mouse carotid arteries. Mechanistically, co-immunoprecipitation, mammalian two-hybrid and FRET assay results suggest that COMP bound directly to integrin α5 via its C-terminus. We next synthesized a COMP-derived peptidomimetics (CCPep24) mimicking a specific COMP-integrin α5 interaction and found that CCPep24 protected against EC activation and atherogenesis in vivo. This study extends our current understanding of how ECM and flow coordinately fine-tune EC homeostasis and reveals the potential therapeutic effect of COMP or COMP-derived peptidomimetics on blocking aberrant integrin α5 activation, inflammatory EC activation and atherosclerosis pathogenesis.
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Papathoti NK, Saengchan C, Daddam JR, Thongprom N, Tonpho K, Thanh TL, Buensanteai N. Plant systemic acquired resistance compound salicylic acid as a potent inhibitor against SCF (SKP1-CUL1-F-box protein) mediated complex in Fusarium oxysporum by homology modeling and molecular dynamics simulations. J Biomol Struct Dyn 2020; 40:1472-1479. [PMID: 33047664 DOI: 10.1080/07391102.2020.1828168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Fusarium oxysporum causes significant economic losses in many crop plants by causing root rot, necrosis, and wilting symptoms. Homology and molecular dynamics studies are promising tools for the detection in F. oxysporum of the systemic resistance compound, salicylic acid, for control of the SKP1-CUL1-F-box protein complex. The structure of SKP1-CUL1-F-box subunit Skp1 from F. oxysporum is produced by Modeler 9v7 for the conduct of docking studies. The Skp1 structure is based on the yeast Cdc4/Skp1 (PDB ID: 3MKS A) crystal structure collected by the Protein data bank. Applying molecular dynamic model simulation methods to the final predicted structure and further evaluated by 3D and PROCHECK test programmers, the final model is verified to be accurate. Applying GOLD 3.0.1, SCF Complex Skp1 is used to prevent stress-tolerant operation. The SKP1-CUL1-F-box model is predicted to be stabilized and tested as a stable docking structure. The predicted model of the SCF structure has been stabilized and confirmed to be a reliable structure for docking studies. The results indicated that GLN8, LYS9, VAL10, TRP11, GLU48, ASN49 in SCF complex are important determinant residues in binding as they have strong hydrogen bonding with salicylic acid, which showed best docking results with SKP1-CUL1-F-box complex subunit Skp1 with docking score 25.25KJ/mol. Insilco studies have been used to determine the mode of action of salicylic acid for Fusarium control. Salicylic acid hinders the SKP1-CUL1-F-box complex, which is important in protein-like interactions through hydrogen bodings. Results from docking studies have shown that the best energy for SKP1-CUL1-F-box was salicylic acid.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Narendra Kumar Papathoti
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Chanon Saengchan
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Jayasimha Rayulu Daddam
- Department of Cardiovascular and Mitochondrial Related Disease Research Center, Hualien Tzu Chi Hospital, Hualien, Taiwan
| | - Nattaya Thongprom
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Kodchaphon Tonpho
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Toan Le Thanh
- Crop Protection Department, College of Agriculture, Can Tho University, Can Tho city, Vietnam
| | - Natthiya Buensanteai
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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Sarfaraz S, Muneer I, Liu H. Combining fragment docking with graph theory to improve ligand docking for homology model structures. J Comput Aided Mol Des 2020; 34:1237-1259. [PMID: 33034007 PMCID: PMC7544562 DOI: 10.1007/s10822-020-00345-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/24/2020] [Indexed: 11/30/2022]
Abstract
Computational protein–ligand docking is well-known to be prone to inaccuracies in input receptor structures, and it is challenging to obtain good docking results with computationally predicted receptor structures (e.g. through homology modeling). Here we introduce a fragment-based docking method and test if it reduces requirements on the accuracy of an input receptor structures relative to non-fragment docking approaches. In this method, small rigid fragments are docked first using AutoDock Vina to generate a large number of favorably docked poses spanning the receptor binding pocket. Then a graph theory maximum clique algorithm is applied to find combined sets of docked poses of different fragment types onto which the complete ligand can be properly aligned. On the basis of these alignments, possible binding poses of complete ligand are determined. This docking method is first tested for bound docking on a series of Cytochrome P450 (CYP450) enzyme–substrate complexes, in which experimentally determined receptor structures are used. For all complexes tested, ligand poses of less than 1 Å root mean square deviations (RMSD) from the actual binding positions can be recovered. Then the method is tested for unbound docking with modeled receptor structures for a number of protein–ligand complexes from different families including the very recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protease. For all complexes, poses with RMSD less than 3 Å from actual binding positions can be recovered. Our results suggest that for docking with approximately modeled receptor structures, fragment-based methods can be more effective than common complete ligand docking approaches.
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Affiliation(s)
- Sara Sarfaraz
- School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Iqra Muneer
- School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Haiyan Liu
- School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China.
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142
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Nawaz MS, Asghar R, Pervaiz N, Ali S, Hussain I, Xing P, Bao Y, Abbasi AA. Molecular evolutionary and structural analysis of human UCHL1 gene demonstrates the relevant role of intragenic epistasis in Parkinson's disease and other neurological disorders. BMC Evol Biol 2020; 20:130. [PMID: 33028204 PMCID: PMC7542113 DOI: 10.1186/s12862-020-01684-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 09/07/2020] [Indexed: 12/04/2022] Open
Abstract
Background Parkinson’s disease (PD) is the second most common neurodegenerative disorder. PD associated human UCHL1 (Ubiquitin C-terminal hydrolase L1) gene belongs to the family of deubiquitinases and is known to be highly expressed in neurons (1–2% in soluble form). Several functions of UCHL1 have been proposed including ubiquitin hydrolyze activity, ubiquitin ligase activity and stabilization of the mono-ubiquitin. Mutations in human UCHL1 gene have been associated with PD and other neurodegenerative disorders. The present study aims to decipher the sequence evolutionary pattern and structural dynamics of UCHL1. Furthermore, structural and interactional analysis of UCHL1 was performed to help elucidate the pathogenesis of PD. Results The phylogenetic tree topology suggests that the UCHL1 gene had originated in early gnathostome evolutionary history. Evolutionary rate analysis of orthologous sequences reveals strong purifying selection on UCHL1. Comparative structural analysis of UCHL1 pinpoints an important protein segment spanning amino acid residues 32 to 39 within secretion site with crucial implications in evolution and PD pathogenesis through a well known phenomenon called intragenic epistasis. Identified critical protein segment appears to play an indispensable role in protein stability, proper protein conformation as well as harboring critical interaction sites. Conclusions Conclusively, the critical protein segment of UCHL1 identified in the present study not only demonstrates the relevant role of intraprotein conformational epistasis in the pathophysiology of PD but also offers a novel therapeutic target for the disease.
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Affiliation(s)
- Muhammad Saqib Nawaz
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Razia Asghar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nashaiman Pervaiz
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Peiqi Xing
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiming Bao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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143
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N U, S K. Molecular dynamics simulation study on Thermotoga maritima EngA: GTP/GDP bound state of the second G-domain influences the domain-domain interface interactions. J Biomol Struct Dyn 2020; 40:1387-1399. [PMID: 33016853 DOI: 10.1080/07391102.2020.1826359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
EngA, a GTPase involved in the late steps of ribosome maturation, consists of two GTP binding domains (G-domains) [GD1, GD2] and a C-terminal domain. The combination of GTP/GDP in G-domains dictates its binding to the ribosomal subunits by altering its conformation. Studies and comparisons on the available structures of EngA enable us to understand the correlation between nucleotide bound states and its conformation. Using all-atom molecular dynamics (MD) simulations, we have explored the conformational behavior of EngA from Thermotoga maritima (TmDer) upon binding the various combinations of GTP and GDP. Analyses of Root Mean Square Deviation (RMSD), Radius of Gyration (Rg) and Root Mean Square Fluctuation (RMSF) emphasize the importance of the second G-domain nucleotide bound state. RMSD and Rg exhibit slightly lower values when GTP is embedded in GD2 compared to GDP. These lower values are due to Sw-II of GD2, which has been observed from RMSF plot. Further investigation on the effects of GD2 nucleotide bound state using Principal Component Analysis (PCA) and Free Energy Landscape (FEL) analysis manifests an allosteric connection between GD2 nucleotide bound state and the GD1-KH interface. This is further validated by extracting electrostatic interactions and H-bonds at the GD1-KH interface. In silico mutations at the GD1 interface of KH domain affect the Sw-II mobility of GD2 by showing inverted behavior. This suggests using the second G-domain as an antibacterial target and further simulation studies on different species of EngA are to be explored.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Upendra N
- Department of Studies in Physics, Manasagangotri, University of Mysore, Mysuru, India
| | - Krishnaveni S
- Department of Studies in Physics, Manasagangotri, University of Mysore, Mysuru, India
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144
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Franke B, Veses-Garcia M, Diederichs K, Allison H, Rigden DJ, Mayans O. Structural annotation of the conserved carbohydrate esterase vb_24B_21 from Shiga toxin-encoding bacteriophage Φ24B. J Struct Biol 2020; 212:107596. [DOI: 10.1016/j.jsb.2020.107596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 12/24/2022]
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145
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Ben Yekhlef R, Felicori L, Santos LH, F. B. Oliveira C, Fadhloun R, Torabi E, Shahbazzadeh D, Pooshang Bagheri K, Salgado Ferreira R, Borchani L. Antigenic and Substrate Preference Differences between Scorpion and Spider Dermonecrotic Toxins, a Comparative Investigation. Toxins (Basel) 2020; 12:E631. [PMID: 33019554 PMCID: PMC7601583 DOI: 10.3390/toxins12100631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 11/16/2022] Open
Abstract
The Hemiscorpius lepturus scorpion and brown spider Loxosceles intermedia represent a public health problem in Asia and America, respectively. Although distinct, these organisms contain similar toxins responsible for the principal clinical signs of envenomation. To better understand the properties of these toxins, we designed a study to compare recombinant Heminecrolysin (rHNC) and rLiD1, the major phospholipase D toxins of scorpion and spider venom, respectively. Using a competitive ELISA and a hemolytic inhibition test, we come to spot a cross reaction between scorpion and spider venoms along with an epitopic similarity between rHNC and rLiD1 associated with neutralizing antibodies. Results show that the ability of the rHNC to hydrolyze lysophosphatidylcholine (LPC) is equivalent to that of rLiD1 to hydrolyze sphingomyelin and vice-versa. rHNC exclusively catalyze transphosphatidylation of LPC producing cyclic phosphatidic acid (cPA). The in-silico analysis of hydrogen bonds between LPC and toxins provides a possible explanation for the higher transphosphatidylase activity of rHNC. Interestingly, for the first time, we reveal that lysophosphatidic acid (LPA) can be a substrate for both enzymes using cellular and enzymatic assays. The finding of the usage of LPA as a substrate as well as the formation of cPA as an end product could shed more light on the molecular basis of Hemiscorpius lepturus envenomation as well as on loxoscelism.
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Affiliation(s)
- Ramla Ben Yekhlef
- Laboratoire des Venins et Biomolécules Thérapeutiques LR16IPT08, Université de Tunis El Manar, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (R.B.Y.); (R.F.)
| | - Liza Felicori
- Departamento de Bioquímica e Imunologia, Universida de Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (L.F.); (L.H.S.); (C.F.B.O.); (R.S.F.)
| | - Lucianna Helene Santos
- Departamento de Bioquímica e Imunologia, Universida de Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (L.F.); (L.H.S.); (C.F.B.O.); (R.S.F.)
| | - Camila F. B. Oliveira
- Departamento de Bioquímica e Imunologia, Universida de Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (L.F.); (L.H.S.); (C.F.B.O.); (R.S.F.)
| | - Raoudha Fadhloun
- Laboratoire des Venins et Biomolécules Thérapeutiques LR16IPT08, Université de Tunis El Manar, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (R.B.Y.); (R.F.)
| | - Elham Torabi
- Venom and Biotherapeutic Molecules Lab., Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 13169-43551, Iran; (E.T.); (D.S.); (K.P.B.)
| | - Delavar Shahbazzadeh
- Venom and Biotherapeutic Molecules Lab., Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 13169-43551, Iran; (E.T.); (D.S.); (K.P.B.)
| | - Kamran Pooshang Bagheri
- Venom and Biotherapeutic Molecules Lab., Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 13169-43551, Iran; (E.T.); (D.S.); (K.P.B.)
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Universida de Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (L.F.); (L.H.S.); (C.F.B.O.); (R.S.F.)
| | - Lamia Borchani
- Laboratoire des Venins et Biomolécules Thérapeutiques LR16IPT08, Université de Tunis El Manar, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (R.B.Y.); (R.F.)
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146
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Alagar S, Bahadur RP. DSS1 allosterically regulates the conformation of the tower domain of BRCA2 that has dsDNA binding specificity for homologous recombination. Int J Biol Macromol 2020; 165:918-929. [PMID: 33011260 DOI: 10.1016/j.ijbiomac.2020.09.230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 09/02/2020] [Accepted: 09/25/2020] [Indexed: 11/17/2022]
Abstract
DSS1 is an evolutionary conserved, small intrinsically disordered protein that regulates various cellular functions. Although several studies have elucidated the role of DSS1 in stabilizing BRCA2 and its importance in homologous recombination repair (HRR), yet the structural mechanism behind the stability and HRR remains elusive. In this study, using molecular dynamics simulation we show that DSS1 stabilizes linearly arranged DNA/DSS1 binding domains of BRCA2 with many native contacts. These contacts are absent in the complexes with two missense DSS1 mutants associated with germline breast cancer and somatic mouth carcinoma. Most importantly, our protein energy-based network models show DSS1 allosterically regulates the conformation of the distant tower domain of BRCA2 that has dsDNA binding specificity for HRR. We further postulate that the unique conformation of the tower domain with kinked-helices might be responsible for DNA strand invasion and initiation of HRR. Induced conformation of the tower domain by the kinked-helices is absent in the unbound BRCA2, as well as in the two mutant DSS1-BRCA2 complexes. This suggests that DSS1 allosterically regulates the tower domain conformations of BRCA2 that affects dsDNA binding, essential for HRR. Our results add a new dimension to the function of DSS1 and its role in regulating HRR.
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Affiliation(s)
- Suresh Alagar
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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147
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Navarro G, Gonzalez A, Campanacci S, Rivas-Santisteban R, Reyes-Resina I, Casajuana-Martin N, Cordomí A, Pardo L, Franco R. Experimental and computational analysis of biased agonism on full-length and a C-terminally truncated adenosine A 2A receptor. Comput Struct Biotechnol J 2020; 18:2723-2732. [PMID: 33101610 PMCID: PMC7550916 DOI: 10.1016/j.csbj.2020.09.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/24/2022] Open
Abstract
Biased agonism, the ability of agonists to differentially activate downstream signaling pathways by stabilizing specific receptor conformations, is a key issue for G protein-coupled receptor (GPCR) signaling. The C-terminal domain might influence this functional selectivity of GPCRs as it engages G proteins, GPCR kinases, β-arrestins, and several other proteins. Thus, the aim of this paper is to compare the agonist-dependent selectivity for intracellular pathways in a heterologous system expressing the full-length (A2AR) and a C-tail truncated (A2AΔ40R lacking the last 40 amino acids) adenosine A2A receptor, a GPCR that is already targeted in Parkinson’s disease using a first-in-class drug. Experimental data such as ligand binding, cAMP production, β-arrestin recruitment, ERK1/2 phosphorylation and dynamic mass redistribution assays, which correspond to different aspects of signal transduction, were measured upon the action of structurally diverse compounds (the agonists adenosine, NECA, CGS-21680, PSB-0777 and LUF-5834 and the SCH-58261 antagonist) in cells expressing A2AR and A2AΔ40R. The results show that taking cAMP levels and the endogenous adenosine agonist as references, the main difference in bias was obtained with PSB-0777 and LUF-5834. The C-terminus is dispensable for both G-protein and β-arrestin recruitment and also for MAPK activation. Unrestrained molecular dynamics simulations, at the μs timescale, were used to understand the structural arrangements of the binding cavity, triggered by these chemically different agonists, facilitating G protein binding with different efficacy.
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Affiliation(s)
- Gemma Navarro
- Dept. Biochemistry and Physiology, Faculty of Pharmacy and Food Science. Universitat de Barcelona. Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas. Instituto de Salud Carlos III, Madrid, Spain
| | - Angel Gonzalez
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain d Faculty of Chemistry, Universitat de Barcelona, Barcelona, Spain
| | - Stefano Campanacci
- Dept. Biochemistry and Molecular Biomedicine. School of Biology. Universitat de Barcelona. Barcelona. Spain
| | - Rafael Rivas-Santisteban
- Dept. Biochemistry and Physiology, Faculty of Pharmacy and Food Science. Universitat de Barcelona. Barcelona, Spain
- Dept. Biochemistry and Molecular Biomedicine. School of Biology. Universitat de Barcelona. Barcelona. Spain
| | - Irene Reyes-Resina
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas. Instituto de Salud Carlos III, Madrid, Spain
- Dept. Biochemistry and Molecular Biomedicine. School of Biology. Universitat de Barcelona. Barcelona. Spain
| | - Nil Casajuana-Martin
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain d Faculty of Chemistry, Universitat de Barcelona, Barcelona, Spain
| | - Arnau Cordomí
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain d Faculty of Chemistry, Universitat de Barcelona, Barcelona, Spain
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain d Faculty of Chemistry, Universitat de Barcelona, Barcelona, Spain
| | - Rafael Franco
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas. Instituto de Salud Carlos III, Madrid, Spain
- School of Chemistry. Universitat de Barcelona. Barcelona. Spain
- Corresponding author at: School of Chemistry, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain.
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148
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Garg R, Borbora SM, Bansia H, Rao S, Singh P, Verma R, Balaji KN, Nagaraja V. Mycobacterium tuberculosis Calcium Pump CtpF Modulates the Autophagosome in an mTOR-Dependent Manner. Front Cell Infect Microbiol 2020; 10:461. [PMID: 33042857 PMCID: PMC7525011 DOI: 10.3389/fcimb.2020.00461] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/28/2020] [Indexed: 12/17/2022] Open
Abstract
Calcium is a very important second messenger, whose concentration in various cellular compartments is under tight regulation. A disturbance in the levels of calcium in these compartments can play havoc in the cell, as it regulates various cellular processes by direct or indirect mechanisms. Here, we have investigated the functional importance of a calcium transporting P2A ATPase, CtpF of Mycobacterium tuberculosis (Mtb) in the pathogen's interaction with the host. Among its uncanny ways of dealing with the host with umpteen strategies for survival and persistence in humans, CtpF is identified as a new player. The levels of ctpF are upregulated in macrophage stresses like hypoxia, high nitric oxide levels and acidic pH. Using confocal microscopy and fluorimetry, we show that CtpF effluxes calcium in macrophages in early stages of Mtb infection. Downregulation of ctpF expression by conditional knockdown resulted in perturbation of host calcium levels and consequent decreased activation of mTOR. We present a mechanism how calcium efflux by the pathogen inhibits mTOR-dependent autophagy and enhances bacterial survival. Our work highlights how Mtb engages its metal efflux pumps to exploit host autophagic process for its proliferation.
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Affiliation(s)
- Rajni Garg
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Salik Miskat Borbora
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Harsh Bansia
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sandhya Rao
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Prakruti Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Rinkee Verma
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | | | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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149
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IMPROvER: the Integral Membrane Protein Stability Selector. Sci Rep 2020; 10:15165. [PMID: 32938971 PMCID: PMC7495477 DOI: 10.1038/s41598-020-71744-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 08/04/2020] [Indexed: 01/20/2023] Open
Abstract
Identifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein Stability Selector (IMPROvER) provides a rational approach to variant selection by employing three independent approaches: deep-sequence, model-based and data-driven. In silico tests using known stability data, and in vitro tests using three membrane protein targets with 7, 11 and 16 transmembrane helices provided measures of success. In vitro, individual approaches alone all identified stabilising variants at a rate better than expected by random selection. Low numbers of overlapping predictions between approaches meant a greater success rate was achieved (fourfold better than random) when approaches were combined and selections restricted to the highest ranked sites. The mix of information IMPROvER uses can be extracted for any helical membrane protein. We have developed the first general-purpose tool for selecting stabilising variants of \documentclass[12pt]{minimal}
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\begin{document}$$\upalpha$$\end{document}α-helical membrane proteins, increasing efficiency and reducing workload. IMPROvER can be accessed at http://improver.ddns.net/IMPROvER/.
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150
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Gholampour-Faroji N, Shakeri MS, Hemmat J, Rastegar-Moghadam M, Haddad-Mashadrizeh A. Modeling, Mutagenesis and In-silico Structural Stability Assay of the Model of Superoxide Dismutase of Lactococcus Lactis Subsp. Cremoris MG1363. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2256. [PMID: 32884954 PMCID: PMC7461707 DOI: 10.30498/ijb.2020.129046.2256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background: Characterizing the structure and function of superoxide dismutase (SOD), as an antioxidant enzyme providing opportunities for its application in food supplements. Objectives: In this study, the features of the Manganese-SOD of Lactococcus Lactis (SDLL), subsp. Cremoris MG1363, as probiotic bacteria, were determined on the basis of the computational methods. Materials and Methods: The protein’s physicochemical properties and the prediction of its secondary structure were determined via the ProtParam server and the GOR program respectively. Moreover, the 3D structures of the proteins were constructed via the MODELLER on the basis of the homology method and the threading algorithm MUSTER. On the other hand, the structural stability of the models was assayed under the quasi-physiological conditions by the GROMACS program via the GROMOS96 43a1 force field in Linux system. Finally, using the Molecular Docking Studies, the functionality features of the models were predicted through their affinity with the corresponding substrates. Results: The results revealed the physicochemical properties of the SDLL and a 3D model of a chain of the enzyme being similar
to the SOD from the Bacillus Subtilis (SDBS). The model of the SDLL was checked for quality control purposes including the Ramachandran plot,
the ERRAT and the Verifiy3D. The model was suggestive of the structural stability in quasi-physiological conditions; yet, less than that of the SDBS. Assessing the cause of the instability in the SDLL model was indicative of two unstable regions in the area far from the enzyme’s active position, they were considered suitable for mutagenesis. Accordingly, the loop substitution for the corresponding region of SDBS and the deletion of the loop positioned at the C terminal of SDLL resulted in a mutant of SDLL with more stability and appropriate affinity with the corresponding substrate. Conclusion: In general, the study provides a new model of SDLL with certain thermostable features, and a new mutant with suitable stability and functionality on the basis of the direct mutagenesis being used in different applications.
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Affiliation(s)
- Nazanin Gholampour-Faroji
- Biotechnology Department, Iranian Research Organization for Science and Technology (IROST). Tehran, Iran
| | - Monir-Sadat Shakeri
- Biotechnology Department, Research Institute of Food Science and Technology. Mashhad, Iran
| | - Jafar Hemmat
- Biotechnology Department, Iranian Research Organization for Science and Technology (IROST). Tehran, Iran
| | | | - Aliakbar Haddad-Mashadrizeh
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
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