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Vijayanathan M, Vadakkepat AK, Mahendran KR, Sharaf A, Frandsen KEH, Bandyopadhyay D, Pillai MR, Soniya EV. Structural and mechanistic insights into Quinolone Synthase to address its functional promiscuity. Commun Biol 2024; 7:566. [PMID: 38745065 PMCID: PMC11093982 DOI: 10.1038/s42003-024-06152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/07/2024] [Indexed: 05/16/2024] Open
Abstract
Quinolone synthase from Aegle marmelos (AmQNS) is a type III polyketide synthase that yields therapeutically effective quinolone and acridone compounds. Addressing the structural and molecular underpinnings of AmQNS and its substrate interaction in terms of its high selectivity and specificity can aid in the development of numerous novel compounds. This paper presents a high-resolution AmQNS crystal structure and explains its mechanistic role in synthetic selectivity. Additionally, we provide a model framework to comprehend structural constraints on ketide insertion and postulate that AmQNS's steric and electrostatic selectivity plays a role in its ability to bind to various core substrates, resulting in its synthetic diversity. AmQNS prefers quinolone synthesis and can accommodate large substrates because of its wide active site entrance. However, our research suggests that acridone is exclusively synthesized in the presence of high malonyl-CoA concentrations. Potential implications of functionally relevant residue mutations were also investigated, which will assist in harnessing the benefits of mutations for targeted polyketide production. The pharmaceutical industry stands to gain from these findings as they expand the pool of potential drug candidates, and these methodologies can also be applied to additional promising enzymes.
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Affiliation(s)
- Mallika Vijayanathan
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
- Department of Plant and Environment Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Abhinav Koyamangalath Vadakkepat
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE17HB, UK
| | - Kozhinjampara R Mahendran
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Abdoallah Sharaf
- SequAna Core Facility, Department of Biology, University of Konstanz, Konstanz, Germany
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt
| | - Kristian E H Frandsen
- Department of Plant and Environment Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Debashree Bandyopadhyay
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - M Radhakrishna Pillai
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Eppurath Vasudevan Soniya
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India.
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2
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Montanucci L, Brünger T, Bhattarai N, Boßelmann CM, Kim S, Allen JP, Zhang J, Klöckner C, Fariselli P, May P, Lemke JR, Myers SJ, Yuan H, Traynelis SF, Lal D. Distances from ligands as main predictive features for pathogenicity and functional effect of variants in NMDA receptors. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.06.24306939. [PMID: 38766179 PMCID: PMC11100844 DOI: 10.1101/2024.05.06.24306939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genetic variants in genes GRIN1 , GRIN2A , GRIN2B , and GRIN2D , which encode subunits of the N-methyl-D-aspartate receptor (NMDAR), have been associated with severe and heterogeneous neurologic diseases. Missense variants in these genes can result in gain or loss of the NMDAR function, requiring opposite therapeutic treatments. Computational methods that predict pathogenicity and molecular functional effects are therefore crucial for accurate diagnosis and therapeutic applications. We assembled missense variants: 201 from patients, 631 from general population, and 159 characterized by electrophysiological readouts showing whether they can enhance or reduce the receptor function. This includes new functional data from 47 variants reported here, for the first time. We found that pathogenic/benign variants and variants that increase/decrease the channel function were distributed unevenly on the protein structure, with spatial proximity to ligands bound to the agonist and antagonist binding sites being key predictive features. Leveraging distances from ligands, we developed two independent machine learning-based predictors for NMDAR missense variants: a pathogenicity predictor which outperforms currently available predictors (AUC=0.945, MCC=0.726), and the first binary predictor of molecular function (increase or decrease) (AUC=0.809, MCC=0.523). Using these, we reclassified variants of uncertain significance in the ClinVar database and refined a previous genome-informed epidemiological model to estimate the birth incidence of molecular mechanism-defined GRIN disorders. Our findings demonstrate that distance from ligands is an important feature in NMDARs that can enhance variant pathogenicity prediction and enable functional prediction. Further studies with larger numbers of phenotypically and functionally characterized variants will enhance the potential clinical utility of this method.
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Cruz FM, Macías Á, Moreno-Manuel AI, Gutiérrez LK, Vera-Pedrosa ML, Martínez-Carrascoso I, Pérez PS, Robles JMR, Bermúdez-Jiménez FJ, Díaz-Agustín A, de Benito FM, Arias-Santiago S, Braza-Boils A, Martín-Martínez M, Gutierrez-Rodríguez M, Bernal JA, Zorio E, Jiménez-Jaimez J, Jalife J. Extracellular Kir2.1 C122Y Mutant Upsets Kir2.1-PIP 2 Bonds and Is Arrhythmogenic in Andersen-Tawil Syndrome. Circ Res 2024; 134:e52-e71. [PMID: 38497220 PMCID: PMC11009053 DOI: 10.1161/circresaha.123.323895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/29/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Andersen-Tawil syndrome type 1 is a rare heritable disease caused by mutations in the gene coding the strong inwardly rectifying K+ channel Kir2.1. The extracellular Cys (cysteine)122-to-Cys154 disulfide bond in the channel structure is crucial for proper folding but has not been associated with correct channel function at the membrane. We evaluated whether a human mutation at the Cys122-to-Cys154 disulfide bridge leads to Kir2.1 channel dysfunction and arrhythmias by reorganizing the overall Kir2.1 channel structure and destabilizing its open state. METHODS We identified a Kir2.1 loss-of-function mutation (c.366 A>T; p.Cys122Tyr) in an ATS1 family. To investigate its pathophysiological implications, we generated an AAV9-mediated cardiac-specific mouse model expressing the Kir2.1C122Y variant. We employed a multidisciplinary approach, integrating patch clamping and intracardiac stimulation, molecular biology techniques, molecular dynamics, and bioluminescence resonance energy transfer experiments. RESULTS Kir2.1C122Y mice recapitulated the ECG features of ATS1 independently of sex, including corrected QT prolongation, conduction defects, and increased arrhythmia susceptibility. Isolated Kir2.1C122Y cardiomyocytes showed significantly reduced inwardly rectifier K+ (IK1) and inward Na+ (INa) current densities independently of normal trafficking. Molecular dynamics predicted that the C122Y mutation provoked a conformational change over the 2000-ns simulation, characterized by a greater loss of hydrogen bonds between Kir2.1 and phosphatidylinositol 4,5-bisphosphate than wild type (WT). Therefore, the phosphatidylinositol 4,5-bisphosphate-binding pocket was destabilized, resulting in a lower conductance state compared with WT. Accordingly, on inside-out patch clamping, the C122Y mutation significantly blunted Kir2.1 sensitivity to increasing phosphatidylinositol 4,5-bisphosphate concentrations. In addition, the Kir2.1C122Y mutation resulted in channelosome degradation, demonstrating temporal instability of both Kir2.1 and NaV1.5 proteins. CONCLUSIONS The extracellular Cys122-to-Cys154 disulfide bond in the tridimensional Kir2.1 channel structure is essential for the channel function. We demonstrate that breaking disulfide bonds in the extracellular domain disrupts phosphatidylinositol 4,5-bisphosphate-dependent regulation, leading to channel dysfunction and defects in Kir2.1 energetic stability. The mutation also alters functional expression of the NaV1.5 channel and ultimately leads to conduction disturbances and life-threatening arrhythmia characteristic of Andersen-Tawil syndrome type 1.
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Affiliation(s)
- Francisco M. Cruz
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Álvaro Macías
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | | | - Lilian K. Gutiérrez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | | | | | | | | | - Francisco J Bermúdez-Jiménez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- Servicio de Cardiología, Hospital Universitario Virgen de las Nieves, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada IBS, Granada, Spain
| | - Aitor Díaz-Agustín
- Instituto de Química Médica (IQM), Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Fernando Martínez de Benito
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Salvador Arias-Santiago
- Servicio de Dermatología Hospital Universitario Virgen de las Nieves
- Instituto de Investigación Biosanitaria de Granada IBS, Granada, Spain
| | - Aitana Braza-Boils
- Unit of Inherited Cardiomyopathies and Sudden Death (CAFAMUSME), Health Research Institute La Fe, La Fe Hospital, Valencia, Spain
- Cardiology Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Mercedes Martín-Martínez
- Instituto de Química Médica (IQM), Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Marta Gutierrez-Rodríguez
- Instituto de Química Médica (IQM), Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Juan A. Bernal
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Esther Zorio
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Unit of Inherited Cardiomyopathies and Sudden Death (CAFAMUSME), Health Research Institute La Fe, La Fe Hospital, Valencia, Spain
- Cardiology Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Juan Jiménez-Jaimez
- Servicio de Cardiología, Hospital Universitario Virgen de las Nieves, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada IBS, Granada, Spain
| | - José Jalife
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Departments of Medicine and Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
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4
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Chomicz D, Kończak J, Wróbel S, Satława T, Dudzic P, Janusz B, Tarkowski M, Deszyński P, Gawłowski T, Kostyn A, Orłowski M, Klaus T, Schulte L, Martin K, Comeau SR, Krawczyk K. Benchmarking antibody clustering methods using sequence, structural, and machine learning similarity measures for antibody discovery applications. Front Mol Biosci 2024; 11:1352508. [PMID: 38606289 PMCID: PMC11008471 DOI: 10.3389/fmolb.2024.1352508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/09/2024] [Indexed: 04/13/2024] Open
Abstract
Antibodies are proteins produced by our immune system that have been harnessed as biotherapeutics. The discovery of antibody-based therapeutics relies on analyzing large volumes of diverse sequences coming from phage display or animal immunizations. Identification of suitable therapeutic candidates is achieved by grouping the sequences by their similarity and subsequent selection of a diverse set of antibodies for further tests. Such groupings are typically created using sequence-similarity measures alone. Maximizing diversity in selected candidates is crucial to reducing the number of tests of molecules with near-identical properties. With the advances in structural modeling and machine learning, antibodies can now be grouped across other diversity dimensions, such as predicted paratopes or three-dimensional structures. Here we benchmarked antibody grouping methods using clonotype, sequence, paratope prediction, structure prediction, and embedding information. The results were benchmarked on two tasks: binder detection and epitope mapping. We demonstrate that on binder detection no method appears to outperform the others, while on epitope mapping, clonotype, paratope, and embedding clusterings are top performers. Most importantly, all the methods propose orthogonal groupings, offering more diverse pools of candidates when using multiple methods than any single method alone. To facilitate exploring the diversity of antibodies using different methods, we have created an online tool-CLAP-available at (clap.naturalantibody.com) that allows users to group, contrast, and visualize antibodies using the different grouping methods.
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Affiliation(s)
| | | | - Sonia Wróbel
- NaturalAntibody, Szczecin, West Pomeranian, Poland
| | | | - Paweł Dudzic
- NaturalAntibody, Szczecin, West Pomeranian, Poland
| | | | | | | | | | | | - Marek Orłowski
- Pure Biologics, Wrocław, Poland
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | | | - Lukas Schulte
- Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Kyle Martin
- Biotherapeutics Discovery, Boehringer Ingelheim, Biberach, Germany
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5
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Vargas-Gasca F, Franco B, Vargas-Maya NI, Vicente-Gómez M, Olmedo-Monfil V. Pseudomonas environmental strain produces a DegQ-derived and PDZ domain containing peptide with protease activity. Antonie Van Leeuwenhoek 2024; 117:41. [PMID: 38400879 DOI: 10.1007/s10482-024-01939-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 01/28/2024] [Indexed: 02/26/2024]
Abstract
In the search of new enzymatic activities with a possible industrial application, we focused on those microorganisms and their molecular mechanisms that allow them to succeed in the environment, particularly in the proteolytic activity and its central role in the microorganisms' successful permanence. The use of highly active serine proteases for industrial applications is a modern need, especially for the formulation of detergents, protein processing, and hair removal from animal skins. This report provides the isolation and identification of a highly proteolytic fragment derived from DegQ produced by a Pseudomonas fluorescens environmental strain isolated from a frog carcass. Zymograms demonstrate that a 10 kDa protein mainly generates the total proteolytic activity of this strain, which is enhanced by the detergent SDS. Mass spectroscopy analysis revealed that the protein derived a couple of peptides, the ones showing the highest coverage belonging to DegQ. Interestingly, this small protein fragment contains a PDZ domain but no obvious residues indicating that it is a protease. Protein model analysis shows that this fragment corresponds to the main PDZ domain from DegQ, and its unique sequence and structure render a proteolytic peptide. The results presented here indicate that a novel DegQ fragment is sufficient for obtaining high protease activity highlighting that the analysis of environmental microorganisms can render new strains or enzymes with helpful biotechnological characteristics.
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Affiliation(s)
- Francisco Vargas-Gasca
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta S/N, 36050, Guanajuato, GTO, México
| | - Bernardo Franco
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta S/N, 36050, Guanajuato, GTO, México
| | - Naurú Idalia Vargas-Maya
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta S/N, 36050, Guanajuato, GTO, México
| | - Marcos Vicente-Gómez
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta S/N, 36050, Guanajuato, GTO, México
| | - Vianey Olmedo-Monfil
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta S/N, 36050, Guanajuato, GTO, México.
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6
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Giri-Rachman EA, Effendy VV, Azmi MHS, Yamahoki N, Stephanie R, Agustiyanti DF, Wisnuwardhani PH, Angelina M, Rubiyana Y, Aditama R, Ningrum RA, Wardiana A, Fibriani A. The SARS-CoV-2 M pro Dimer-Based Screening System: A Synthetic Biology Tool for Identifying Compounds with Dimerization Inhibitory Potential. ACS Synth Biol 2024; 13:509-520. [PMID: 38316139 PMCID: PMC10877612 DOI: 10.1021/acssynbio.3c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024]
Abstract
The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability of high biosafety level laboratory facilities for drug screening is limited in number. To address this issue, a screening system that could be utilized at lower biosafety levels remains essential. This study aimed to develop a novel SARS-CoV-2 main protease (Mpro) dimer-based screening system (DBSS) utilizing synthetic biology in Escherichia coli BL21(DE3). We linked the SARS-CoV-2 Mpro with the DNA-binding domain of AraC regulatory protein, which regulates the reporter gene expression. Protein modeling and molecular docking showed that saquinavir could bind to AraC-Mpro both in its monomer and dimer forms. The constructed DBSS assay indicated the screening system could detect saquinavir inhibitory activity at a concentration range of 4-10 μg/mL compared to the untreated control (P ≤ 0.05). The Vero E6 cell assay validated the DBSS result that saquinavir at 4-10 μg/mL exhibited antiviral activity against SARS-CoV-2. Our DBSS could be used for preliminary screening of numerous drug candidates that possess a dimerization inhibitor activity of SARS-CoV-2 Mpro and also minimize the use of a high biosafety level laboratory.
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Affiliation(s)
| | - Vergio V. Effendy
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Muhammad H. S. Azmi
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Nicholas Yamahoki
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Rebecca Stephanie
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Dian F. Agustiyanti
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Popi H. Wisnuwardhani
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Marissa Angelina
- Research
Center for Pharmaceutical Ingredients and Traditional Medicine, Indonesian National Research and Innovation Agency
(BRIN), Serpong 15314, Indonesia
| | - Yana Rubiyana
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Reza Aditama
- Biochemistry
Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Ratih A. Ningrum
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Andri Wardiana
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Azzania Fibriani
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
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7
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Kutlutürk I, Tokuç EÖ, Karabaş L, Rückert R, Kaya M, Karagöz A, Munk MR. How the immune response to the structural proteins of SARS-CoV-2 affects the retinal vascular endothelial cells: an immune thrombotic and/or endotheliopathy process with in silico modeling. Immunol Res 2024; 72:50-71. [PMID: 37642808 DOI: 10.1007/s12026-023-09412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/28/2023] [Indexed: 08/31/2023]
Abstract
Thrombotic events associated with SARS-CoV-2 at the vascular endothelium still remains unclear. The aim of the current study is to determine the relationship between cellular proteins on the (ocular) vascular endothelial surface and the immune thrombotic and/or endotheliopathy process elicited by SARS-CoV-2 using an in-silico modeling. The structural S (spike glycoprotein), N (nucleocapsid protein), M (membrane protein), and E (envelope protein) proteins, an accessory protein (ORF1ab) of SARS-CoV-2 and 158 cellular proteins associated with retinal vascular endothelial cell surface or structure were included in this study for comparison of three-dimensional (3D) structure and sequence. Sixty-nine of the retinal proteins were obtained from the Uniprot database. Remaining proteins not included in the database were included in the study after they were converted into 3D structures using the RaptorX web tool. Sequence and three-dimensional structure of SARS-COV-2 S, N, M, E, ORF1ab proteins and retinal vascular endothelial proteins were compared with mTM-align server. Proteins with significant similarity (score above 0.5) were validated with the TM-align web server. Immune and thrombosis-related protein-receptor interactions of similar proteins was checked with CABS-dock. We detected a high level of structural similarity between E protein and ACE, ACE2, LAT1, and TM9SF4 endothelial proteins. In addition, PECAM-1 was found to be structurally similar to ORF1ab and S protein. When we evaluated the likelihood/potential to stimulate an immune responses/a cytokine release, TLR-2 and TLR-3, which are highly susceptible to SARS-CoV2, showed a potential receptor-protein interaction with retinal vascular endothelial proteins. Our study demonstrates that SARS-CoV-2 proteins may have structural similarities with vascular endothelial proteins, and therefore, as immunological target sites, the counterpart proteins on the endothelial surface of many organs may also be secondarily affected by any immune response against SARS-CoV-2 structural proteins.
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Affiliation(s)
- Işıl Kutlutürk
- Division of Ophthalmology, Ümraniye Trn. And Rch. Hospital, Istanbul, Turkey.
| | - Ecem Önder Tokuç
- Ophthalmology Department, University of Health Science, Derince Training and Research Hospital, Izmit-Kocaeli, Turkey
| | - Levent Karabaş
- Ophthalmology Department, Kocaeli University School of Medicine, Izmit-Kocaeli, Turkey
| | | | | | - Ali Karagöz
- Koşuyolu High Specialization Education and Research Hospital, Istanbul, Turkey
| | - Marion R Munk
- Inselspital, University Hospital Bern, Bern, Switzerland
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Augenarzt-Praxisgemeinschaft Gutblick AG, Bern, Switzerland
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8
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Karlin DG. WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection. J Gen Virol 2024; 105. [PMID: 38193819 DOI: 10.1099/jgv.0.001948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
The most powerful approach to detect distant homologues of a protein is based on structure prediction and comparison. Yet this approach is still inapplicable to many viral proteins. Therefore, we applied a powerful sequence-based procedure to identify distant homologues of viral proteins. It relies on three principles: (1) traces of sequence similarity can persist beyond the significance cutoff of homology detection programmes; (2) candidate homologues can be identified among proteins with weak sequence similarity to the query by using 'contextual' information, e.g. taxonomy or type of host infected; (3) these candidate homologues can be validated using highly sensitive profile-profile comparison. As a test case, this approach was applied to a protein without known homologues, encoded by ORF4 of Lake Sinai viruses (which infect bees). We discovered that the ORF4 protein contains a domain that has homologues in proteins from >20 taxa of viruses infecting arthropods. We called this domain 'widespread, intriguing, versatile' (WIV), because it is found in proteins with a wide variety of functions and within varied domain contexts. For example, WIV is found in the NSs protein of tospoviruses, a global threat to food security, which infect plants as well as their arthropod vectors; in the RNA2 ORF1-encoded protein of chronic bee paralysis virus, a widespread virus of bees; and in various proteins of cypoviruses, which infect the silkworm Bombyx mori. Structural modelling with AlphaFold indicated that the WIV domain has a previously unknown fold, and bibliographical evidence suggests that it facilitates infection of arthropods.
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Affiliation(s)
- David G Karlin
- Division Phytomedicine, Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55/57, D-14195 Berlin, Germany
- Independent Researcher, Marseille, France
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9
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Liu S, Hu R, Peng N, Zhou Z, Chen R, He Z, Wang C. Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments. THE ISME JOURNAL 2023; 17:2313-2325. [PMID: 37880540 PMCID: PMC10689504 DOI: 10.1038/s41396-023-01544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
Mangrove sediment is a crucial component in the global mercury (Hg) cycling and acts as a hotspot for methylmercury (MeHg) production. Early evidence has documented the ubiquity of well-studied Hg methylators in mangrove superficial sediments; however, their diversity and metabolic adaptation in the more anoxic and highly reduced subsurface sediments are lacking. Through MeHg biogeochemical assay and metagenomic sequencing, we found that mangrove subsurface sediments (20-100 cm) showed a less hgcA gene abundance but higher diversity of Hg methylators than superficial sediments (0-20 cm). Regional-scale investigation of mangrove subsurface sediments spanning over 1500 km demonstrated a prevalence and family-level novelty of Hg-methylating microbial lineages (i.e., those affiliated to Anaerolineae, Phycisphaerae, and Desulfobacterales). We proposed the candidate phylum Zixibacteria lineage with sulfate-reducing capacity as a currently understudied Hg methylator across anoxic environments. Unlike other Hg methylators, the Zixibacteria lineage does not use the Wood-Ljungdahl pathway but has unique capabilities of performing methionine synthesis to donate methyl groups. The absence of cobalamin biosynthesis pathway suggests that this Hg-methylating lineage may depend on its syntrophic partners (i.e., Syntrophobacterales members) for energy in subsurface sediments. Our results expand the diversity of subsurface Hg methylators and uncover their unique ecophysiological adaptations in mangrove sediments.
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Affiliation(s)
- Songfeng Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Nenglong Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruihan Chen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
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10
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An L, Hicks DR, Zorine D, Dauparas J, Wicky BIM, Milles LF, Courbet A, Bera AK, Nguyen H, Kang A, Carter L, Baker D. Hallucination of closed repeat proteins containing central pockets. Nat Struct Mol Biol 2023; 30:1755-1760. [PMID: 37770718 PMCID: PMC10643118 DOI: 10.1038/s41594-023-01112-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/28/2023] [Indexed: 09/30/2023]
Abstract
In pseudocyclic proteins, such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern, giving rise to a central cavity that can serve as a pocket for ligand binding or enzymatic activity. Inspired by these proteins, we devised a deep-learning-based approach to broadly exploring the space of closed repeat proteins starting from only a specification of the repeat number and length. Biophysical data for 38 structurally diverse pseudocyclic designs produced in Escherichia coli are consistent with the design models, and the three crystal structures we were able to obtain are very close to the designed structures. Docking studies suggest the diversity of folds and central pockets provide effective starting points for designing small-molecule binders and enzymes.
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Affiliation(s)
- Linna An
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
| | - Derrick R Hicks
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Dmitri Zorine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Basile I M Wicky
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lukas F Milles
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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11
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Padilla-Vaca F, de la Mora J, García-Contreras R, Ramírez-Prado JH, Vicente-Gómez M, Vargas-Gasca F, Anaya-Velázquez F, Páramo-Pérez I, Rangel-Serrano Á, Cuéllar-Mata P, Vargas-Maya NI, Franco B. Theoretical study of ArcB and its dimerization, interaction with anaerobic metabolites, and activation of ArcA. PeerJ 2023; 11:e16309. [PMID: 37849831 PMCID: PMC10578306 DOI: 10.7717/peerj.16309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
The complex metabolism of Escherichia coli has been extensively studied, including its response to oxygen availability. The ArcA/B two-component system (TCS) is the key regulator for the transition between these two environmental conditions and has been thoroughly characterized using genetic and biochemical approaches. Still, to date, limited structural data is available. The breakthrough provided by AlphaFold2 in 2021 has brought a reliable tool to the scientific community for assessing the structural features of complex proteins. In this report, we analyzed the structural aspects of the ArcA/B TCS using AlphaFold2 models. The models are consistent with the experimentally determined structures of ArcB kinase. The predicted structure of the dimeric form of ArcB is consistent with the extensive genetic and biochemical data available regarding mechanistic signal perception and regulation. The predicted interaction of the dimeric form of ArcB with its cognate response regulator (ArcA) is also consistent with both the forward and reverse phosphotransfer mechanisms. The ArcB model was used to detect putative binding cavities to anaerobic metabolites, encouraging testing of these predictions experimentally. Finally, the highly accurate models of other ArcB homologs suggest that different experimental approaches are needed to determine signal perception in kinases lacking the PAS domain. Overall, ArcB is a kinase with features that need further testing, especially in determining its crystal structure under different conditions.
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Affiliation(s)
| | - Javier de la Mora
- Genética Molecular, Instituto de Fisiología Celular, Mexico City, Mexico City, México
| | | | | | | | | | | | | | | | | | | | - Bernardo Franco
- Biology, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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12
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Paredes A, Justo-Méndez R, Jiménez-Blasco D, Núñez V, Calero I, Villalba-Orero M, Alegre-Martí A, Fischer T, Gradillas A, Sant'Anna VAR, Were F, Huang Z, Hernansanz-Agustín P, Contreras C, Martínez F, Camafeita E, Vázquez J, Ruiz-Cabello J, Area-Gómez E, Sánchez-Cabo F, Treuter E, Bolaños JP, Estébanez-Perpiñá E, Rupérez FJ, Barbas C, Enríquez JA, Ricote M. γ-Linolenic acid in maternal milk drives cardiac metabolic maturation. Nature 2023; 618:365-373. [PMID: 37225978 DOI: 10.1038/s41586-023-06068-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/11/2023] [Indexed: 05/26/2023]
Abstract
Birth presents a metabolic challenge to cardiomyocytes as they reshape fuel preference from glucose to fatty acids for postnatal energy production1,2. This adaptation is triggered in part by post-partum environmental changes3, but the molecules orchestrating cardiomyocyte maturation remain unknown. Here we show that this transition is coordinated by maternally supplied γ-linolenic acid (GLA), an 18:3 omega-6 fatty acid enriched in the maternal milk. GLA binds and activates retinoid X receptors4 (RXRs), ligand-regulated transcription factors that are expressed in cardiomyocytes from embryonic stages. Multifaceted genome-wide analysis revealed that the lack of RXR in embryonic cardiomyocytes caused an aberrant chromatin landscape that prevented the induction of an RXR-dependent gene expression signature controlling mitochondrial fatty acid homeostasis. The ensuing defective metabolic transition featured blunted mitochondrial lipid-derived energy production and enhanced glucose consumption, leading to perinatal cardiac dysfunction and death. Finally, GLA supplementation induced RXR-dependent expression of the mitochondrial fatty acid homeostasis signature in cardiomyocytes, both in vitro and in vivo. Thus, our study identifies the GLA-RXR axis as a key transcriptional regulatory mechanism underlying the maternal control of perinatal cardiac metabolism.
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Affiliation(s)
- Ana Paredes
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Raquel Justo-Méndez
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Daniel Jiménez-Blasco
- Institute of Functional Biology and Genomics (IBFG), University of Salamanca, CSIC, Salamanca, Spain
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Madrid, Spain
| | - Vanessa Núñez
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Irene Calero
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - María Villalba-Orero
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Departamento de Medicina y Cirugía Animal, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Andrea Alegre-Martí
- Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine (IBUB) of the University of Barcelona (UB), Barcelona, Spain
| | - Thierry Fischer
- Department of Immunology and Oncology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB/CSIC), Campus Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Ana Gradillas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | | | - Felipe Were
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Zhiqiang Huang
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Pablo Hernansanz-Agustín
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Carmen Contreras
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Fernando Martínez
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Emilio Camafeita
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Jesús Vázquez
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Jesús Ruiz-Cabello
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento de Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense Madrid (UCM), Madrid, Spain
| | - Estela Area-Gómez
- Departament of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
- Department of Neurology, Columbia University Medical Campus, New York, NY, USA
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Eckardt Treuter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Juan Pedro Bolaños
- Institute of Functional Biology and Genomics (IBFG), University of Salamanca, CSIC, Salamanca, Spain
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Madrid, Spain
| | - Eva Estébanez-Perpiñá
- Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine (IBUB) of the University of Barcelona (UB), Barcelona, Spain
| | - Francisco Javier Rupérez
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - José Antonio Enríquez
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Madrid, Spain
| | - Mercedes Ricote
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
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13
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Khazaei-Poul Y, Mirmotalebisohi SA, Zali H, Molavi Z, Mohammadi-Yeganeh S. Identification of miR-3182 and miR-3143 target genes involved in the cell cycle as a novel approach in TNBC treatment: A systems biology approach. Chem Biol Drug Des 2023; 101:662-677. [PMID: 36310371 DOI: 10.1111/cbdd.14167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 10/15/2022] [Accepted: 10/24/2022] [Indexed: 02/04/2023]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a poor prognosis, lacking therapeutic targets. miRNAs play crucial roles in TNBC through regulating various mechanisms, including cellular growth and proliferation. This study aims to identify critical target genes of two novel miRNAs (miR-3143 and miR-3182) involved in the cell cycle of TNBC as possible therapeutic targets and investigates their regulatory and therapeutic roles through a systems biology approach and in vitro experiment. Datasets related to the TNBC cell line (MDA-MB-231) were screened and retrieved, and Gene regulatory networks were constructed. Significant regulatory motifs were detected and analyzed using the FANMOD and Cytoscape analyzer, and the clusters and seeds were identified using the MCODE. Functional enrichment analysis was also performed using DAVID and STRING. The most critical genes were determined using the analysis of GRN motifs and PPI clusters. The essential genes involved in the cell cycle were selected and verified using the bc-GenExMiner v4.7. We overexpressed miR-3143 and miR-3182 in the MDA-MB-231 cell line using human umbilical cord mesenchymal stem cell (HUCMSC)-miRNA loaded exosomes, and the expression of the critical target genes was investigated using RT-qPCR. We identified eight critical genes as potential therapeutic targets. Their expression decreased by overexpression of miR-3143 and miR-3182 in RT-qPCR. The identified critical genes have probably significant roles in the pathogenesis of TNBC through the cell cycle. We suggest that the overexpression of miR-3143 and miR-3182 could be a new therapeutic candidate in TNBC and is worth more investigation.
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Affiliation(s)
- Yalda Khazaei-Poul
- Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Amir Mirmotalebisohi
- Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hakimeh Zali
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Molavi
- Proteomics Research Center, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Samira Mohammadi-Yeganeh
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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14
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Sharma A, Mahur P, Muthukumaran J, Singh AK, Jain M. Shedding light on structure, function and regulation of human sirtuins: a comprehensive review. 3 Biotech 2023; 13:29. [PMID: 36597461 PMCID: PMC9805487 DOI: 10.1007/s13205-022-03455-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/25/2022] [Indexed: 01/01/2023] Open
Abstract
Sirtuins play an important role in signalling pathways associated with various metabolic regulations. They possess mono-ADP-ribosyltransferase or deacylase activity like demalonylase, deacetylase, depalmitoylase, demyristoylase and desuccinylase activity. Sirtuins are histone deacetylases which depends upon nicotinamide adenine dinucleotide (NAD) that deacetylate lysine residues. There are a total of seven human sirtuins that have been identified namely, SIRT1, SIRT2, SIRT3, SIRT4, SIRT5, SIRT6 and SIRT7. The subcellular location of mammalian sirtuins, SIRT1, SIRT6, and SIRT7 are in the nucleus; SIRT3, SIRT4, and SIRT5 are in mitochondria, and SIRT2 is in cytoplasm. Structurally sirtuins contains a N-terminal, a C-terminal and a Zn+ binding domain. The sirtuin family has been found to be crucial for maintaining lipid and glucose homeostasis, and also for regulating insulin secretion and sensitivity, DNA repair pathways, neurogenesis, inflammation, and ageing. Based on the literature, sirtuins are overexpressed and play an important role in tumorigenicity in various types of cancer such as non-small cell lung cancer, colorectal cancer, etc. In this review, we have discussed about the different types of human sirtuins along with their structural and functional features. We have also discussed about the various natural and synthetic regulators of sirtuin activities like resveratrol. Our overall study shows that the correct regulation of sirtuins can be a good target for preventing and treating various diseases for improving the human lifespan. To investigate the true therapeutic potential of sirtuin proteins and their efficacy in a variety of pathological diseases, a better knowledge of the link between the structure and function of sirtuin proteins would be necessary.
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Affiliation(s)
- Abhishek Sharma
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh India
| | - Pragati Mahur
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh India
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh India
| | - Monika Jain
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh India
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15
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Structural and Genomic Evolution of RRNPPA Systems and Their Pheromone Signaling. mBio 2022; 13:e0251422. [PMID: 36259720 PMCID: PMC9765709 DOI: 10.1128/mbio.02514-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Abstract
In Firmicutes, important processes such as competence development, sporulation, virulence, and biofilm formation are regulated by cytoplasmic quorum sensing (QS) receptors of the RRNPPA family using peptide-based communication. Although these systems regulate important processes in a variety of bacteria, their origin and diversification are poorly understood. Here, we integrate structural, genomic, and phylogenetic evidence to shed light on RRNPPA protein origin and diversification. The family is constituted by seven different subfamilies with different domain architectures and functions. Among these, three were found in Lactobacillales (Rgg, ComR, and PrgX) and four in Bacillales (AimR, NprR, PlcR, and Rap). The patterns of presence and the phylogeny of these proteins show that subfamilies diversified a long time ago, resulting in key structural and functional differences. The concordance between the distribution of subfamilies and the bacterial phylogeny was somewhat unexpected, since many of the subfamilies are very abundant in mobile genetic elements, such as phages, plasmids, and phage-plasmids. The existence of diverse propeptide architectures raises intriguing questions about their export and maturation. It also suggests the existence of diverse roles for the RRNPPA systems. Some systems encode multiple pheromones on the same propeptide or multiple similar propeptides, suggesting that they act as "chatterers." Many others lack pheromone genes and may be "eavesdroppers." Interestingly, AimR systems without associated propeptide genes were particularly abundant in chromosomal regions not classed as prophages, suggesting that either the bacterium or other mobile elements are eavesdropping on phage activity. IMPORTANCE Quorum sensing (QS) is a mechanism of bacterial communication, coordinating important decisions depending on bacterial population. QS regulates important processes not only in bacterial behavior but also in genetic mobile elements and host-guest interactions. In Firmicutes, the most important family of QS receptors is the RRNPPA family. Despite the importance of such systems in microbiology, we know little about RRNPPA origin and diversification. In this work, the combination of sequence analysis and structural biology allowed us to identify a very large number of novel systems but also to class of them in functional families and thereby study of their origin and functional diversification. Moreover, peptide pheromone analysis revealed new and intriguing mechanisms of communication, such as "eavesdropper" systems which only listen for the pheromone and "chatterers" that take control of the communication in their microenvironment.
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16
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Vargas-Maya NI, Olmedo-Monfil V, Ramírez-Prado JH, Reyes-Cortés R, Padilla-Vaca F, Franco B. Catalases in the pathogenesis of Sporothrix schenckii research. PeerJ 2022; 10:e14478. [PMID: 36523453 PMCID: PMC9745942 DOI: 10.7717/peerj.14478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Pathogenic fungal infection success depends on the ability to escape the immune response. Most strategies for fungal infection control are focused on the inhibition of virulence factors and increasing the effectiveness of antifungal drugs. Nevertheless, little attention has been focused on their physiological resistance to the host immune system. Hints may be found in pathogenic fungi that also inhabit the soil. In nature, the saprophyte lifestyle of fungi is also associated with predators that can induce oxidative stress upon cell damage. The natural sources of nutrients for fungi are linked to cellulose degradation, which in turn generates reactive oxygen species (ROS). Overall, the antioxidant arsenal needed to thrive both in free-living and pathogenic lifestyles in fungi is fundamental for success. In this review, we present recent findings regarding catalases and oxidative stress in fungi and how these can be in close relationship with pathogenesis. Additionally, special focus is placed on catalases of Sporothrix schenckii as a pathogenic model with a dual lifestyle. It is assumed that catalase expression is activated upon exposure to H2O2, but there are reports where this is not always the case. Additionally, it may be relevant to consider the role of catalases in S. schenckii survival in the saprophytic lifestyle and why their study can assess their involvement in the survival and therefore, in the virulence phenotype of different species of Sporothrix and when each of the three catalases are required. Also, studying antioxidant mechanisms in other isolates of pathogenic and free-living fungi may be linked to the virulence phenotype and be potential therapeutic and diagnostic targets. Thus, the rationale for this review to place focus on fungal catalases and their role in pathogenesis in addition to counteracting the effect of immune system reactive oxygen species. Fungi that thrive in soil and have mammal hosts could shed light on the importance of these enzymes in the two types of lifestyles. We look forward to encouraging more research in a myriad of areas on catalase biology with a focus on basic and applied objectives and placing these enzymes as virulence determinants.
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Affiliation(s)
| | | | | | - Ruth Reyes-Cortés
- Biology Department, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Felipe Padilla-Vaca
- Biology Department, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Bernardo Franco
- Biology Department, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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17
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Mocchetti E, Morette L, Mulliert G, Mathiot S, Guillot B, Dehez F, Chauvat F, Cassier-Chauvat C, Brochier-Armanet C, Didierjean C, Hecker A. Biochemical and Structural Characterization of Chi-Class Glutathione Transferases: A Snapshot on the Glutathione Transferase Encoded by sll0067 Gene in the Cyanobacterium Synechocystis sp. Strain PCC 6803. Biomolecules 2022; 12:biom12101466. [PMID: 36291676 PMCID: PMC9599700 DOI: 10.3390/biom12101466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/24/2022] Open
Abstract
Glutathione transferases (GSTs) constitute a widespread superfamily of enzymes notably involved in detoxification processes and/or in specialized metabolism. In the cyanobacterium Synechocsytis sp. PCC 6803, SynGSTC1, a chi-class GST (GSTC), is thought to participate in the detoxification process of methylglyoxal, a toxic by-product of cellular metabolism. A comparative genomic analysis showed that GSTCs were present in all orders of cyanobacteria with the exception of the basal order Gloeobacterales. These enzymes were also detected in some marine and freshwater noncyanobacterial bacteria, probably as a result of horizontal gene transfer events. GSTCs were shorter of about 30 residues compared to most cytosolic GSTs and had a well-conserved SRAS motif in the active site (10SRAS13 in SynGSTC1). The crystal structure of SynGSTC1 in complex with glutathione adopted the canonical GST fold with a very open active site because the α4 and α5 helices were exceptionally short. A transferred multipolar electron-density analysis allowed a fine description of the solved structure. Unexpectedly, Ser10 did not have an electrostatic influence on glutathione as usually observed in serinyl-GSTs. The S10A variant was only slightly less efficient than the wild-type and molecular dynamics simulations suggested that S10 was a stabilizer of the protein backbone rather than an anchor site for glutathione.
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Affiliation(s)
- Eva Mocchetti
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France
| | - Laura Morette
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | | | | | - Benoît Guillot
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France
| | - François Dehez
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Franck Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91190 Gif-sur-Yvette, France
| | - Corinne Cassier-Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91190 Gif-sur-Yvette, France
| | | | - Claude Didierjean
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France
- Correspondence: (C.D.); (A.H.)
| | - Arnaud Hecker
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
- Correspondence: (C.D.); (A.H.)
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18
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Sylvestre-Gonon E, Morette L, Viloria M, Mathiot S, Boutilliat A, Favier F, Rouhier N, Didierjean C, Hecker A. Biochemical and Structural Insights on the Poplar Tau Glutathione Transferase GSTU19 and 20 Paralogs Binding Flavonoids. Front Mol Biosci 2022; 9:958586. [PMID: 36032685 PMCID: PMC9412104 DOI: 10.3389/fmolb.2022.958586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022] Open
Abstract
Glutathione transferases (GSTs) constitute a widespread superfamily of enzymes notably involved in xenobiotic detoxification and/or in specialized metabolism. Populus trichocarpa genome (V4.1 assembly, Phytozome 13) consists of 74 genes coding for full-length GSTs and ten likely pseudogenes. These GSTs are divided into 11 classes, in which the tau class (GSTU) is the most abundant with 54 isoforms. PtGSTU19 and 20, two paralogs sharing more than 91% sequence identity (95% of sequence similarity), would have diverged from a common ancestor of P. trichocarpa and P. yatungensis species. These enzymes display the distinctive glutathione (GSH)-conjugation and peroxidase activities against model substrates. The resolution of the crystal structures of these proteins revealed significant structural differences despite their high sequence identity. PtGSTU20 has a well-defined deep pocket in the active site whereas the bottom of this pocket is disordered in PtGSTU19. In a screen of potential ligands, we were able to identify an interaction with flavonoids. Some of them, previously identified in poplar (chrysin, galangin, and pinocembrin), inhibited GSH-conjugation activity of both enzymes with a more pronounced effect on PtGSTU20. The crystal structures of PtGSTU20 complexed with these molecules provide evidence for their potential involvement in flavonoid transport in P. trichocarpa.
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Affiliation(s)
| | - Laura Morette
- Université de Lorraine, INRAE, IAM, Nancy, France
- Université de Lorraine, CNRS, CRM2, Nancy, France
| | | | | | | | | | | | - Claude Didierjean
- Université de Lorraine, CNRS, CRM2, Nancy, France
- *Correspondence: Claude Didierjean, ; Arnaud Hecker,
| | - Arnaud Hecker
- Université de Lorraine, INRAE, IAM, Nancy, France
- *Correspondence: Claude Didierjean, ; Arnaud Hecker,
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19
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Yip MC, Sedor SF, Shao S. Mechanism of client selection by the protein quality-control factor UBE2O. Nat Struct Mol Biol 2022; 29:774-780. [PMID: 35915257 PMCID: PMC9526450 DOI: 10.1038/s41594-022-00807-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 02/03/2023]
Abstract
The E2/E3 enzyme UBE2O ubiquitylates diverse clients to mediate important processes, including targeting unassembled 'orphan' proteins for quality control and clearing ribosomes during erythropoiesis. How quality-control factors, such as UBE2O, select clients on the basis of heterogeneous features is largely unknown. Here, we show that UBE2O client selection is regulated by ubiquitin binding and a cofactor, NAP1L1. Attaching a single ubiquitin onto a client enhances UBE2O binding and multi-mono-ubiquitylation. UBE2O also repurposes the histone chaperone NAP1L1 as an adapter to recruit a subset of clients. Cryo-EM structures of human UBE2O in complex with NAP1L1 reveal a malleable client recruitment interface that is autoinhibited by the intrinsically reactive UBC domain. Adding a ubiquitylated client identifies a distinct ubiquitin-binding SH3-like domain required for client selection. Our findings reveal how multivalency and a feed-forward mechanism drive the selection of protein quality-control clients.
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Affiliation(s)
- Matthew C.J. Yip
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115
| | - Samantha F. Sedor
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115,Correspondence:
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20
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Duarte-Velázquez I, de la Mora J, Ramírez-Prado JH, Aguillón-Bárcenas A, Tornero-Gutiérrez F, Cordero-Loreto E, Anaya-Velázquez F, Páramo-Pérez I, Rangel-Serrano Á, Muñoz-Carranza SR, Romero-González OE, Cardoso-Reyes LR, Rodríguez-Ojeda RA, Mora-Montes HM, Vargas-Maya NI, Padilla-Vaca F, Franco B. Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships. PeerJ 2022; 10:e13772. [PMID: 35880217 PMCID: PMC9308461 DOI: 10.7717/peerj.13772] [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: 03/29/2022] [Accepted: 07/01/2022] [Indexed: 01/17/2023] Open
Abstract
Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. Escherichia coli has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied. To date, 58 TFs remain poorly characterized, although their binding sites have been experimentally determined. This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors. Most of these transcription factors are in areas of the genome where abundant repetitive and mobile elements are present. Sequence divergence points to groups with distinctive sequence signatures but maintaining the same type of DNA binding domain. Finally, the analysis of the promoter sequences of the 58 TFs showed A+T rich regions that agree with the features of horizontally transferred genes. The findings reported here pave the way for future research of these TFs that may uncover their role as spare factors in case of lose-of-function mutations in core TFs and trace back their evolutionary history.
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Affiliation(s)
- Isabel Duarte-Velázquez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Javier de la Mora
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autonoma de Mexico, Mexico City, México
| | | | - Alondra Aguillón-Bárcenas
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Fátima Tornero-Gutiérrez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Eugenia Cordero-Loreto
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Fernando Anaya-Velázquez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Itzel Páramo-Pérez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Ángeles Rangel-Serrano
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | | | | | - Luis Rafael Cardoso-Reyes
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | | | - Héctor Manuel Mora-Montes
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Naurú Idalia Vargas-Maya
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Felipe Padilla-Vaca
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Bernardo Franco
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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21
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Molecular mechanism of interaction between fatty acid delta 6 desaturase and acyl-CoA by computational prediction. AMB Express 2022; 12:69. [PMID: 35680699 PMCID: PMC9184693 DOI: 10.1186/s13568-022-01410-0] [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: 12/10/2021] [Accepted: 05/27/2022] [Indexed: 11/17/2022] Open
Abstract
Enzyme catalyzed desaturation of intracellular fatty acids plays an important role in various physiological and pathological processes related to lipids. Limited to the multiple transmembrane domains, it is difficult to obtain their three-dimensional structure of fatty acid desaturases. So how they interact with their substrates is unclear. Here, we predicted the complex of Micromonas pusilla delta 6 desaturase (MpFADS6) with the substrate linoleinyl-CoA (ALA-CoA) by trRosetta software and docking poses by Dock 6 software. The potential enzyme–substrate binding sites were anchored by analysis of the complex. Then, site-directed mutagenesis and activity verification clarified that W290, W224, and F352 were critical residues of the substrate tunnel and directly bonded to ALA-CoA. H94 and H69 were indispensable for transporting electrons with heme. H452, N445, and H358 significantly influenced the recognition and attraction of MpFADS6 to the substrate. These findings provide new insights and methods to determine the structure, mechanisms and directed transformation of membrane-bound desaturases. The structure of the Δ6 fatty acid desaturase and substrate complex is modeled. The substrate tunnel and key residues of MpFADS6 catalytic activity are determined. The new insights to determine the mechanism of the membrane-bound desaturases.
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22
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Zhang Y, Bhosle A, Bae S, McIver LJ, Pishchany G, Accorsi EK, Thompson KN, Arze C, Wang Y, Subramanian A, Kearney SM, Pawluk A, Plichta DR, Rahnavard A, Shafquat A, Xavier RJ, Vlamakis H, Garrett WS, Krueger A, Huttenhower C, Franzosa EA. Discovery of bioactive microbial gene products in inflammatory bowel disease. Nature 2022; 606:754-760. [PMID: 35614211 PMCID: PMC9913614 DOI: 10.1038/s41586-022-04648-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/15/2022] [Indexed: 01/26/2023]
Abstract
Microbial communities and their associated bioactive compounds1-3 are often disrupted in conditions such as the inflammatory bowel diseases (IBD)4. However, even in well-characterized environments (for example, the human gastrointestinal tract), more than one-third of microbial proteins are uncharacterized and often expected to be bioactive5-7. Here we systematically identified more than 340,000 protein families as potentially bioactive with respect to gut inflammation during IBD, about half of which have not to our knowledge been functionally characterized previously on the basis of homology or experiment. To validate prioritized microbial proteins, we used a combination of metagenomics, metatranscriptomics and metaproteomics to provide evidence of bioactivity for a subset of proteins that are involved in host and microbial cell-cell communication in the microbiome; for example, proteins associated with adherence or invasion processes, and extracellular von Willebrand-like factors. Predictions from high-throughput data were validated using targeted experiments that revealed the differential immunogenicity of prioritized Enterobacteriaceae pilins and the contribution of homologues of von Willebrand factors to the formation of Bacteroides biofilms in a manner dependent on mucin levels. This methodology, which we term MetaWIBELE (workflow to identify novel bioactive elements in the microbiome), is generalizable to other environmental communities and human phenotypes. The prioritized results provide thousands of candidate microbial proteins that are likely to interact with the host immune system in IBD, thus expanding our understanding of potentially bioactive gene products in chronic disease states and offering a rational compendium of possible therapeutic compounds and targets.
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Affiliation(s)
- Yancong Zhang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Amrisha Bhosle
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sena Bae
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Lauren J. McIver
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Gleb Pishchany
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Emma K. Accorsi
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Kelsey N. Thompson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Cesar Arze
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ya Wang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ayshwarya Subramanian
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sean M. Kearney
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - April Pawluk
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Damian R. Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ali Rahnavard
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Afrah Shafquat
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ramnik J. Xavier
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wendy S. Garrett
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andy Krueger
- Takeda Pharmaceutical Company Limited, Cambridge, MA, USA
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Eric A. Franzosa
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,These authors jointly supervised this work: Curtis Huttenhower & Eric A. Franzosa
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23
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Evseev P, Shneider M, Miroshnikov K. Evolution of Phage Tail Sheath Protein. Viruses 2022; 14:v14061148. [PMID: 35746620 PMCID: PMC9230969 DOI: 10.3390/v14061148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 02/06/2023] Open
Abstract
Sheath proteins comprise a part of the contractile molecular machinery present in bacteriophages with myoviral morphology, contractile injection systems, and the type VI secretion system (T6SS) found in many Gram-negative bacteria. Previous research on sheath proteins has demonstrated that they share common structural features, even though they vary in their size and primary sequence. In this study, 112 contractile phage tail sheath proteins (TShP) representing different groups of bacteriophages and archaeal viruses with myoviral morphology have been modelled with the novel machine learning software, AlphaFold 2. The obtained structures have been analysed and conserved and variable protein parts and domains have been identified. The common core domain of all studied sheath proteins, including viral and T6SS proteins, comprised both N-terminal and C-terminal parts, whereas the other parts consisted of one or several moderately conserved domains, presumably added during phage evolution. The conserved core appears to be responsible for interaction with the tail tube protein and assembly of the phage tail. Additional domains may have evolved to maintain the stability of the virion or for adsorption to the host cell. Evolutionary relations between TShPs representing distinct viral groups have been proposed using a phylogenetic analysis based on overall structural similarity and other analyses.
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24
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Chagot ME, Boutilliat A, Kriznik A, Quinternet M. Structural Analysis of the Plasmodial Proteins ZNHIT3 and NUFIP1 Provides Insights into the Selectivity of a Conserved Interaction. Biochemistry 2022; 61:479-493. [PMID: 35315277 DOI: 10.1021/acs.biochem.1c00792] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Malaria is a widespread and lethal disease caused by the Plasmodium parasites that can infect human beings through Anopheles mosquitoes. For that reason, the biology of Plasmodium needs to be studied to develop antimalarial treatments. By determining the three-dimensional structures of macromolecules, structural biology helps to understand the function of proteins and can reveal how interactions occur between biological partners. Here, we studied the ZNHIT3 and NUFIP1 proteins from Plasmodium falciparum, two proteins tightly linked to the ribosome biology. Due to their important functions in post-translational modifications of ribosomal RNAs and in ribophagy, these proteins participate in the survival of cells. In this study, we solved the three-dimensional structure of a thermally stable and species-dependent complex between fragments of these proteins. Our results were compared to the AlphaFold predictions, which motivated the study of the free ZNHIT3 fragment that binds NUFIP1. We showed that the latter fragment multimerized in vitro but also had the inner ability to change its conformation to escape the solvent exposition of key hydrophobic residues involved in the interaction with NUFIP1. Our data could open the gate to selective drug discovery processes involving these two proteins.
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Affiliation(s)
| | | | - Alexandre Kriznik
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France.,Université de Lorraine, CNRS, INSERM, IBSLor, F-54000 Nancy, France
| | - Marc Quinternet
- Université de Lorraine, CNRS, INSERM, IBSLor, F-54000 Nancy, France
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25
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Structural Analysis of the Effect of Asn107Ser Mutation on Alg13 Activity and Alg13-Alg14 Complex Formation and Expanding the Phenotypic Variability of ALG13-CDG. Biomolecules 2022; 12:biom12030398. [PMID: 35327592 PMCID: PMC8945535 DOI: 10.3390/biom12030398] [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: 10/16/2021] [Accepted: 03/02/2022] [Indexed: 11/16/2022] Open
Abstract
Congenital Disorders of Glycosylation (CDG) are multisystemic metabolic disorders showing highly heterogeneous clinical presentation, molecular etiology, and laboratory results. Here, we present different transferrin isoform patterns (obtained by isoelectric focusing) from three female patients harboring the ALG13 c.320A>G mutation. Contrary to other known variants of type I CDGs, where transferrin isoelectric focusing revealed notably increased asialo- and disialotransferrin fractions, a normal glycosylation pattern was observed in the probands. To verify this data and give novel insight into this variant, we modeled the human Alg13 protein and analyzed the dynamics of the apo structure and the complex with the UDP-GlcNAc substrate. We also modeled the Alg13-Alg14 heterodimer and ran multiple simulations of the complex in the presence of the substrate. Finally, we proposed a plausible complex formation mechanism.
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26
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Muchaamba F, Eshwar AK, Stevens MJA, Stephan R, Tasara T. Different Shades of Listeria monocytogenes: Strain, Serotype, and Lineage-Based Variability in Virulence and Stress Tolerance Profiles. Front Microbiol 2022; 12:792162. [PMID: 35058906 PMCID: PMC8764371 DOI: 10.3389/fmicb.2021.792162] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/11/2021] [Indexed: 12/30/2022] Open
Abstract
Listeria monocytogenes is a public health and food safety challenge due to its virulence and natural stress resistance phenotypes. The variable distribution of L. monocytogenes molecular subtypes with respect to food products and processing environments and among human and animal clinical listeriosis cases is observed. Sixty-two clinical and food-associated L. monocytogenes isolates were examined through phenome and genome analysis. Virulence assessed using a zebrafish infection model revealed serotype and genotype-specific differences in pathogenicity. Strains of genetic lineage I serotype 4b and multilocus sequence type clonal complexes CC1, CC2, CC4, and CC6 grew and survived better and were more virulent than serotype 1/2a and 1/2c lineage II, CC8, and CC9 strains. Hemolysis, phospholipase activity, and lysozyme tolerance profiles were associated with the differences observed in virulence. Osmotic stress resistance evaluation revealed serotype 4b lineage I CC2 and CC4 strains as more osmotolerant, whereas serotype 1/2c lineage II CC9 strains were more osmo-sensitive than others. Variable tolerance to the widely used quaternary ammonium compound benzalkonium chloride (BC) was observed. Some outbreak and sporadic clinical case associated strains demonstrated BC tolerance, which might have contributed to their survival and transition in the food-processing environment facilitating food product contamination and ultimately outbreaks or sporadic listeriosis cases. Genome comparison uncovered various moderate differences in virulence and stress associated genes between the strains indicating that these differences in addition to gene expression regulation variations might largely be responsible for the observed virulence and stress sensitivity phenotypic differences. Overall, our study uncovered strain and genotype-dependent variation in virulence and stress resilience among clinical and food-associated L. monocytogenes isolates with potential public health risk implications. The extensive genome and phenotypic data generated provide a basis for developing improved Listeria control strategies and policies.
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Affiliation(s)
- Francis Muchaamba
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Athmanya K Eshwar
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Marc J A Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
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27
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López-López A, Keech O, Rouhier N. Maturation and Assembly of Iron-Sulfur Cluster-Containing Subunits in the Mitochondrial Complex I From Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:916948. [PMID: 35677241 PMCID: PMC9168917 DOI: 10.3389/fpls.2022.916948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/04/2022] [Indexed: 05/13/2023]
Abstract
In plants, the mitochondrial complex I is the protein complex encompassing the largest number of iron-sulfur (Fe-S) clusters. The whole, membrane-embedded, holo-complex is assembled stepwise from assembly intermediates. The Q and N modules are combined to form a peripheral arm in the matrix, whereas the so-called membrane arm is formed after merging a carbonic anhydrase (CA) module with so-called Pp (proximal) and the Pd (distal) domains. A ferredoxin bridge connects both arms. The eight Fe-S clusters present in the peripheral arm for electron transfer reactions are synthesized via a dedicated protein machinery referred to as the iron-sulfur cluster (ISC) machinery. The de novo assembly occurs on ISCU scaffold proteins from iron, sulfur and electron delivery proteins. In a second step, the preformed Fe-S clusters are transferred, eventually converted and inserted in recipient apo-proteins. Diverse molecular actors, including a chaperone-cochaperone system, assembly factors among which proteins with LYR motifs, and Fe-S cluster carrier/transfer proteins, have been identified as contributors to the second step. This mini-review highlights the recent progresses in our understanding of how specificity is achieved during the delivery of preformed Fe-S clusters to complex I subunits.
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Affiliation(s)
- Alicia López-López
- INRAE, IAM, Université de Lorraine, Nancy, France
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Nicolas Rouhier
- INRAE, IAM, Université de Lorraine, Nancy, France
- *Correspondence: Nicolas Rouhier,
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28
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Rosier K, McDevitt MT, Smet J, Floyd BJ, Verschoore M, Marcaida MJ, Bingman CA, Lemmens I, Dal Peraro M, Tavernier J, Cravatt BF, Gounko NV, Vints K, Monnens Y, Bhalla K, Aerts L, Rashan EH, Vanlander AV, Van Coster R, Régal L, Pagliarini DJ, Creemers JW. Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function. iScience 2021; 24:103460. [PMID: 34888501 PMCID: PMC8634043 DOI: 10.1016/j.isci.2021.103460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/27/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Deficiency of the serine hydrolase prolyl endopeptidase-like (PREPL) causes a recessive metabolic disorder characterized by neonatal hypotonia, feeding difficulties, and growth hormone deficiency. The pathophysiology of PREPL deficiency and the physiological substrates of PREPL remain largely unknown. In this study, we connect PREPL with mitochondrial gene expression and oxidative phosphorylation by analyzing its protein interactors. We demonstrate that the long PREPLL isoform localizes to mitochondria, whereas PREPLS remains cytosolic. Prepl KO mice showed reduced mitochondrial complex activities and disrupted mitochondrial gene expression. Furthermore, mitochondrial ultrastructure was abnormal in a PREPL-deficient patient and Prepl KO mice. In addition, we reveal that PREPL has (thio)esterase activity and inhibition of PREPL by Palmostatin M suggests a depalmitoylating function. We subsequently determined the crystal structure of PREPL, thereby providing insight into the mechanism of action. Taken together, PREPL is a (thio)esterase rather than a peptidase and PREPLL is involved in mitochondrial homeostasis.
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Affiliation(s)
- Karen Rosier
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Molly T. McDevitt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joél Smet
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Brendan J. Floyd
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Maxime Verschoore
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Maria J. Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Irma Lemmens
- Center for Medical Biotechnology, VIB, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jan Tavernier
- Center for Medical Biotechnology, VIB, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Benjamin F. Cravatt
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Natalia V. Gounko
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Yenthe Monnens
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Kritika Bhalla
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Laetitia Aerts
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Edrees H. Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Arnaud V. Vanlander
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Rudy Van Coster
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Luc Régal
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Neurology and Metabolism, UZ Brussel, Brussels, Belgium
| | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Departments of Cell Biology and Physiology, Biochemistry and Molecular Biophysics, and Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - John W.M. Creemers
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
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Lewis AJO, Hegde RS. A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC. BMC Biol 2021; 19:266. [PMID: 34911545 PMCID: PMC8675477 DOI: 10.1186/s12915-021-01171-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/21/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Protein transporters translocate hydrophilic segments of polypeptide across hydrophobic cell membranes. Two protein transporters are ubiquitous and date back to the last universal common ancestor: SecY and YidC. SecY consists of two pseudosymmetric halves, which together form a membrane-spanning protein-conducting channel. YidC is an asymmetric molecule with a protein-conducting hydrophilic groove that partially spans the membrane. Although both transporters mediate insertion of membrane proteins with short translocated domains, only SecY transports secretory proteins and membrane proteins with long translocated domains. The evolutionary origins of these ancient and essential transporters are not known. RESULTS The features conserved by the two halves of SecY indicate that their common ancestor was an antiparallel homodimeric channel. Structural searches with SecY's halves detect exceptional similarity with YidC homologs. The SecY halves and YidC share a fold comprising a three-helix bundle interrupted by a helical hairpin. In YidC, this hairpin is cytoplasmic and facilitates substrate delivery, whereas in SecY, it is transmembrane and forms the substrate-binding lateral gate helices. In both transporters, the three-helix bundle forms a protein-conducting hydrophilic groove delimited by a conserved hydrophobic residue. Based on these similarities, we propose that SecY originated as a YidC homolog which formed a channel by juxtaposing two hydrophilic grooves in an antiparallel homodimer. We find that archaeal YidC and its eukaryotic descendants use this same dimerisation interface to heterodimerise with a conserved partner. YidC's sufficiency for the function of simple cells is suggested by the results of reductive evolution in mitochondria and plastids, which tend to retain SecY only if they require translocation of large hydrophilic domains. CONCLUSIONS SecY and YidC share previously unrecognised similarities in sequence, structure, mechanism, and function. Our delineation of a detailed correspondence between these two essential and ancient transporters enables a deeper mechanistic understanding of how each functions. Furthermore, key differences between them help explain how SecY performs its distinctive function in the recognition and translocation of secretory proteins. The unified theory presented here explains the evolution of these features, and thus reconstructs a key step in the origin of cells.
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Affiliation(s)
- Aaron J O Lewis
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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30
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Pan X, Kortemme T. De novo protein fold families expand the designable ligand binding site space. PLoS Comput Biol 2021; 17:e1009620. [PMID: 34807909 PMCID: PMC8648124 DOI: 10.1371/journal.pcbi.1009620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 12/06/2021] [Accepted: 11/08/2021] [Indexed: 11/19/2022] Open
Abstract
A major challenge in designing proteins de novo to bind user-defined ligands with high affinity is finding backbones structures into which a new binding site geometry can be engineered with high precision. Recent advances in methods to generate protein fold families de novo have expanded the space of accessible protein structures, but it is not clear to what extend de novo proteins with diverse geometries also expand the space of designable ligand binding functions. We constructed a library of 25,806 high-quality ligand binding sites and developed a fast protocol to place (“match”) these binding sites into both naturally occurring and de novo protein families with two fold topologies: Rossman and NTF2. Each matching step involves engineering new binding site residues into each protein “scaffold”, which is distinct from the problem of comparing already existing binding pockets. 5,896 and 7,475 binding sites could be matched to the Rossmann and NTF2 fold families, respectively. De novo designed Rossman and NTF2 protein families can support 1,791 and 678 binding sites that cannot be matched to naturally existing structures with the same topologies, respectively. While the number of protein residues in ligand binding sites is the major determinant of matching success, ligand size and primary sequence separation of binding site residues also play important roles. The number of matched binding sites are power law functions of the number of members in a fold family. Our results suggest that de novo sampling of geometric variations on diverse fold topologies can significantly expand the space of designable ligand binding sites for a wealth of possible new protein functions. De novo design of proteins that can bind to novel and highly diverse user-defined small molecule ligands could have broad biomedical and synthetic biology applications. Because ligand binding site geometries need to be accommodated by protein backbone scaffolds at high accuracy, the diversity of scaffolds is a major limitation for designing new ligand binding functions. Advances in computational protein structure design methods have significantly increased the number of accessible stable scaffold structures. Understanding how many new ligand binding sites can be designed into the de novo scaffolds is important for engineering novel ligand binding proteins. To answer this question, we constructed a large library of ligand binding sites from the Protein Data Bank (PDB). We tested the number of ligand binding sites that can be designed into de novo scaffolds and naturally existing scaffolds with the same fold topologies. The results showed that de novo scaffolds significantly expanded the potential ligand binding space of their respective fold topologies. We also identified factors that affect difficulties of binding site accommodation, as well as the relationship between the number of scaffolds and the accessible ligand binding site space. We believe our findings will benefit future method development and applications of ligand binding protein design.
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Affiliation(s)
- Xingjie Pan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (XP); (TK)
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail: (XP); (TK)
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31
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Rice CJ, Kelly SA, O’Brien SC, Melaugh EM, Ganacias JCB, Chai ZH, Gilmore BF, Skvortsov T. Novel Phage-Derived Depolymerase with Activity against Proteus mirabilis Biofilms. Microorganisms 2021; 9:2172. [PMID: 34683494 PMCID: PMC8539402 DOI: 10.3390/microorganisms9102172] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/18/2022] Open
Abstract
The adherence of Proteus mirabilis to the surface of urinary catheters leads to colonization and eventual blockage of the catheter lumen by unique crystalline biofilms produced by these opportunistic pathogens, making P. mirabilis one of the leading causes of catheter-associated urinary tract infections. The Proteus biofilms reduce efficiency of antibiotic-based treatment, which in turn increases the risk of antibiotic resistance development. Bacteriophages and their enzymes have recently become investigated as alternative treatment options. In this study, a novel Proteus bacteriophage (vB_PmiS_PM-CJR) was isolated from an environmental sample and fully characterized. The phage displayed depolymerase activity and the subsequent genome analysis revealed the presence of a pectate lyase domain in its tail spike protein. The protein was heterologously expressed and purified; the ability of the purified tail spike to degrade Proteus biofilms was tested. We showed that the application of the tail spike protein was able to reduce the adherence of bacterial biofilm to plastic pegs in a MBEC (minimum biofilm eradication concentration) assay and improve the survival of Galleria mellonella larvae infected with Proteus mirabilis. Our study is the first to successfully isolate and characterize a biofilm depolymerase from a Proteus phage, demonstrating the potential of this group of enzymes in treatment of Proteus infections.
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Affiliation(s)
| | | | | | | | | | | | | | - Timofey Skvortsov
- School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, UK; (C.J.R.); (S.A.K.); (S.C.O.); (E.M.M.); (J.C.B.G.); (Z.H.C.); (B.F.G.)
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32
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Zhou LL, Xu H, Huang Y, Yang CG. Targeting the RNA demethylase FTO for cancer therapy. RSC Chem Biol 2021; 2:1352-1369. [PMID: 34704042 PMCID: PMC8496078 DOI: 10.1039/d1cb00075f] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/26/2021] [Indexed: 01/02/2023] Open
Abstract
N 6-Methyladenosine (m6A) is the most prevalent internal modification on mRNA and represents a new layer of gene expression in eukaryotes. The field of m6A-encoded epitranscriptomics was rejuvenated with the discovery of fat mass and obesity-associated protein (FTO) as the first m6A demethylase responsible for RNA modification in cells. Increasing evidence has revealed that FTO is significantly involved in physiological processes, and its dysregulation is implicated in various human diseases. Considering this functional significance, developing small-molecule modulators of the FTO protein represents a novel direction for biology research. However, such modulators remain in the early stages of development. Here, our review mainly focuses on the progress of FTO inhibitor development to date. We summarize screening methods used to identify FTO modulators, techniques used to assess the biological effects of these modulators, strategies used to achieve selective inhibition of FTO rather than its homologues, and the results of investigations of FTO modulator modes of action and anticancer efficacy. Thus, this review aims to facilitate novel chemical entity discovery, probe FTO biology, and promote the validation of FTO as a clinical drug target for cancer treatment.
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Affiliation(s)
- Lin-Lin Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of the Chinese Academy of Sciences Beijing 100049 China
| | - Hongjiao Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of the Chinese Academy of Sciences Beijing 100049 China
| | - Yue Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of the Chinese Academy of Sciences Beijing 100049 China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
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Abstract
Protein alignment finds its application in refining results of sequence alignment and understanding protein function. A previous study aligned single molecules, making use of the minimization of sums of the squares of eigenvalues, obtained for the antisymmetric Cartesian coordinate distance matrices Dx and Dy. This is used in our program to search for similarities between amino acids by comparing the sums of the squares of eigenvalues associated with the Dx, Dy, and Dz distance matrices. These matrices are obtained by removing atoms that could lead to low similarity. Candidates are aligned, and trilateration is used to attach all previously striped atoms. A TM-score is the scoring function that chooses the best alignment from supplied candidates. Twenty essential amino acids that take many forms in nature are selected for comparison. The correct alignment is taken into account most of the time by the alignment algorithm. It was numerically detected by the TM-score 70% of the time, on average, and 15% more cases with close scores can be easily distinguished by human observation.
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34
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Ng AMJ, Yang R, Zhang H, Xue B, Yew WS, Nguyen GKT. A Novel Lipase from Lasiodiplodia theobromae Efficiently Hydrolyses C8-C10 Methyl Esters for the Preparation of Medium-Chain Triglycerides' Precursors. Int J Mol Sci 2021; 22:10339. [PMID: 34638680 PMCID: PMC8508680 DOI: 10.3390/ijms221910339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/18/2022] Open
Abstract
Medium-chain triglycerides (MCTs) are an emerging choice to treat neurodegenerative disorders such as Alzheimer's disease. They are triesters of glycerol and three medium-chain fatty acids, such as capric (C8) and caprylic (C10) acids. The availability of C8-C10 methyl esters (C8-C10 ME) from vegetable oil processes has presented an opportunity to use methyl esters as raw materials for the synthesis of MCTs. However, there are few reports on enzymes that can efficiently hydrolyse C8-C10 ME to industrial specifications. Here, we report the discovery and identification of a novel lipase from Lasiodiplodia theobromae fungus (LTL1), which hydrolyses C8-C10 ME efficiently. LTL1 can perform hydrolysis over pH ranges from 3.0 to 9.0 and maintain thermotolerance up to 70 °C. It has high selectivity for monoesters over triesters and displays higher activity over commercially available lipases for C8-C10 ME to achieve 96.17% hydrolysis within 31 h. Structural analysis by protein X-ray crystallography revealed LTL1's well-conserved lipase core domain, together with a partially resolved N-terminal subdomain and an inserted loop, which may suggest its hydrolytic preference for monoesters. In conclusion, our results suggest that LTL1 provides a tractable route towards to production of C8-C10 fatty acids from methyl esters for the synthesis of MCTs.
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Affiliation(s)
- Andre Mong Jie Ng
- WIL@NUS Corporate Laboratory, Wilmar International Limited, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore; (A.M.J.N.); (R.Y.); (H.Z.)
- Wilmar Innovation Centre, Wilmar International Limited, 28 Biopolis Road, Singapore 138568, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117596, Singapore;
- NUS Synthetic Biology for Clinical and Technological Innovation, Centre for Life Sciences, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
- NUS Synthetic Biology Translational Research Programme, Centre for Translational Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Renliang Yang
- WIL@NUS Corporate Laboratory, Wilmar International Limited, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore; (A.M.J.N.); (R.Y.); (H.Z.)
- Wilmar Innovation Centre, Wilmar International Limited, 28 Biopolis Road, Singapore 138568, Singapore
| | - Hongfang Zhang
- WIL@NUS Corporate Laboratory, Wilmar International Limited, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore; (A.M.J.N.); (R.Y.); (H.Z.)
- Wilmar Innovation Centre, Wilmar International Limited, 28 Biopolis Road, Singapore 138568, Singapore
| | - Bo Xue
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117596, Singapore;
- NUS Synthetic Biology for Clinical and Technological Innovation, Centre for Life Sciences, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
- NUS Synthetic Biology Translational Research Programme, Centre for Translational Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117596, Singapore;
- NUS Synthetic Biology for Clinical and Technological Innovation, Centre for Life Sciences, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
- NUS Synthetic Biology Translational Research Programme, Centre for Translational Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Giang Kien Truc Nguyen
- WIL@NUS Corporate Laboratory, Wilmar International Limited, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore; (A.M.J.N.); (R.Y.); (H.Z.)
- Wilmar Innovation Centre, Wilmar International Limited, 28 Biopolis Road, Singapore 138568, Singapore
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35
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Beaudoin CA, Jamasb AR, Alsulami AF, Copoiu L, van Tonder AJ, Hala S, Bannerman BP, Thomas SE, Vedithi SC, Torres PH, Blundell TL. Predicted structural mimicry of spike receptor-binding motifs from highly pathogenic human coronaviruses. Comput Struct Biotechnol J 2021; 19:3938-3953. [PMID: 34234921 PMCID: PMC8249111 DOI: 10.1016/j.csbj.2021.06.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/26/2021] [Accepted: 06/27/2021] [Indexed: 12/19/2022] Open
Abstract
Potential coronavirus spike protein mimicry revealed by structural comparison. Human and non-human protein potential interactions with virus identified. Predicted structural mimicry corroborated by protein–protein docking. Epitope-based alignments may help guide vaccine efforts.
Viruses often encode proteins that mimic host proteins in order to facilitate infection. Little work has been done to understand the potential mimicry of the SARS-CoV-2, SARS-CoV, and MERS-CoV spike proteins, particularly the receptor-binding motifs, which could be important in determining tropism and druggability of the virus. Peptide and epitope motifs have been detected on coronavirus spike proteins using sequence homology approaches; however, comparing the three-dimensional shape of the protein has been shown as more informative in predicting mimicry than sequence-based comparisons. Here, we use structural bioinformatics software to characterize potential mimicry of the three coronavirus spike protein receptor-binding motifs. We utilize sequence-independent alignment tools to compare structurally known protein models with the receptor-binding motifs and verify potential mimicked interactions with protein docking simulations. Both human and non-human proteins were returned for all three receptor-binding motifs. For example, all three were similar to several proteins containing EGF-like domains: some of which are endogenous to humans, such as thrombomodulin, and others exogenous, such as Plasmodium falciparum MSP-1. Similarity to human proteins may reveal which pathways the spike protein is co-opting, while analogous non-human proteins may indicate shared host interaction partners and overlapping antibody cross-reactivity. These findings can help guide experimental efforts to further understand potential interactions between human and coronavirus proteins.
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Affiliation(s)
- Christopher A. Beaudoin
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, United Kingdom
- Corresponding authors.
| | - Arian R. Jamasb
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, United Kingdom
- Department of Computer Science & Technology, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0FD, United Kingdom
| | - Ali F. Alsulami
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, United Kingdom
| | - Liviu Copoiu
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, United Kingdom
| | - Andries J. van Tonder
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge CB3 0ES, United Kingdom
| | - Sharif Hala
- King Abdullah International Medical Research Centre – Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Bridget P. Bannerman
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, United Kingdom
| | - Sherine E. Thomas
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, United Kingdom
| | - Sundeep Chaitanya Vedithi
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, United Kingdom
| | - Pedro H.M. Torres
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Tom L. Blundell
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, United Kingdom
- Corresponding authors.
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36
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Adzhubei AA, Kulkarni A, Tolstova AP, Anashkina AA, Sviridov D, Makarov AA, Bukrinsky MI. Direct interaction between ABCA1 and HIV-1 Nef: Molecular modeling and virtual screening for inhibitors. Comput Struct Biotechnol J 2021; 19:3876-3884. [PMID: 34584633 PMCID: PMC8440812 DOI: 10.1016/j.csbj.2021.06.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/23/2021] [Accepted: 06/30/2021] [Indexed: 12/18/2022] Open
Abstract
HIV-1 infection impairs cellular cholesterol efflux by downmodulating the cholesterol transporter ABCA1, leading to metabolic co-morbidities like cardio-vascular disease. The main mechanism of this effect is impairment by the HIV-1 protein Nef of the ABCA1 interaction with the endoplasmic reticulum chaperone calnexin, which leads to a block in ABCA1 maturation followed by its degradation. However, ABCA1 is also downmodulated by Nef delivered with the extracellular vesicles, suggesting involvement of a direct Nef:ABCA1 interaction at the plasma membrane. Here, we present an optimized model of the Nef:ABCA1 interaction, which identifies interaction sites and provides an opportunity to perform a virtual screening for potential inhibitors. Interestingly, the predicted sites on Nef involved in the ABCA1 interaction overlap with those involved in the interaction with calnexin. The compounds previously shown to block Nef:calnexin interaction were among the top ranking ligands in docking simulations with ABCA1-interacting sites on Nef, suggesting the possibility that both interactions can be inhibited by the same chemical compounds. This study identifies a series of compounds for potential development as inhibitors of Nef-mediated co-morbidities of HIV infection.
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Affiliation(s)
- Alexei A. Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Amol Kulkarni
- Howard University College of Pharmacy, Washington, District of Columbia, USA
| | - Anna P. Tolstova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Dmitri Sviridov
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Michael I. Bukrinsky
- The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
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37
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Cappele J, Mohamad Ali A, Leblond-Bourget N, Mathiot S, Dhalleine T, Payot S, Savko M, Didierjean C, Favier F, Douzi B. Structural and Biochemical Analysis of OrfG: The VirB8-like Component of the Conjugative Type IV Secretion System of ICE St3 From Streptococcus thermophilus. Front Mol Biosci 2021; 8:642606. [PMID: 33816557 PMCID: PMC8012802 DOI: 10.3389/fmolb.2021.642606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/01/2021] [Indexed: 12/02/2022] Open
Abstract
Conjugative transfer is a major threat to global health since it contributes to the spread of antibiotic resistance genes and virulence factors among commensal and pathogenic bacteria. To allow their transfer, mobile genetic elements including Integrative and Conjugative Elements (ICEs) use a specialized conjugative apparatus related to Type IV secretion systems (Conj-T4SS). Therefore, Conj-T4SSs are excellent targets for strategies that aim to limit the spread of antibiotic resistance. In this study, we combined structural, biochemical and biophysical approaches to study OrfG, a protein that belongs to Conj-T4SS of ICESt3 from Streptococcus thermophilus. Structural analysis of OrfG by X-ray crystallography revealed that OrfG central domain is similar to VirB8-like proteins but displays a different quaternary structure in the crystal. To understand, at a structural level, the common and the diverse features between VirB8-like proteins from both Gram-negative and -positive bacteria, we used an in silico structural alignment method that allowed us to identify different structural classes of VirB8-like proteins. Biochemical and biophysical characterizations of purified OrfG soluble domain and its central and C-terminal subdomains indicated that they are mainly monomeric in solution but able to form an unprecedented 6-mer oligomers. Our study provides new insights into the structural analysis of VirB8-like proteins and discusses the interplay between tertiary and quaternary structures of these proteins as an essential component of the conjugative transfer.
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Affiliation(s)
| | | | | | | | | | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, Nancy, France
| | - Martin Savko
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP 48, Gif-sur-Yvette, France
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38
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Lange A, Patel PH, Heames B, Damry AM, Saenger T, Jackson CJ, Findlay GD, Bornberg-Bauer E. Structural and functional characterization of a putative de novo gene in Drosophila. Nat Commun 2021; 12:1667. [PMID: 33712569 PMCID: PMC7954818 DOI: 10.1038/s41467-021-21667-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/03/2021] [Indexed: 11/26/2022] Open
Abstract
Comparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from noncoding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus. Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and circular dichroism (CD) data, we show that Goddard protein contains a large central α-helix, but is otherwise partially disordered. We find similar results for Goddard's orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddard's structure appears to have been maintained with only minor changes over millions of years.
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Affiliation(s)
- Andreas Lange
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Prajal H Patel
- Department of Biology, College of the Holy Cross, Worcester, MA, USA
| | - Brennen Heames
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Adam M Damry
- Research School of Chemistry, ANU College of Science, Canberra, Australia
| | - Thorsten Saenger
- Department of Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany
| | - Colin J Jackson
- Research School of Chemistry, ANU College of Science, Canberra, Australia
| | | | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
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39
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Structural and molecular mechanisms for membrane protein biogenesis by the Oxa1 superfamily. Nat Struct Mol Biol 2021; 28:234-239. [PMID: 33664512 DOI: 10.1038/s41594-021-00567-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Members of the Oxa1 superfamily perform membrane protein insertion in bacteria, the eukaryotic endoplasmic reticulum (ER), and endosymbiotic organelles. Here, we review recent structures of the three ER-resident insertases and discuss the extent to which structure and function are conserved with their bacterial counterpart YidC.
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Perez-Garcia P, Kobus S, Gertzen CGW, Hoeppner A, Holzscheck N, Strunk CH, Huber H, Jaeger KE, Gohlke H, Kovacic F, Smits SHJ, Streit WR, Chow J. A promiscuous ancestral enzyme´s structure unveils protein variable regions of the highly diverse metallo-β-lactamase family. Commun Biol 2021; 4:132. [PMID: 33514861 PMCID: PMC7846560 DOI: 10.1038/s42003-021-01671-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
The metallo-β-lactamase fold is an ancient protein structure present in numerous enzyme families responsible for diverse biological processes. The crystal structure of the hyperthermostable crenarchaeal enzyme Igni18 from Ignicoccus hospitalis was solved at 2.3 Å and could resemble a possible first archetype of a multifunctional metallo-β-lactamase. Ancestral enzymes at the evolutionary origin are believed to be promiscuous all-rounders. Consistently, Igni18´s activity can be cofactor-dependently directed from β-lactamase to lactonase, lipase, phosphodiesterase, phosphotriesterase or phospholipase. Its core-domain is highly conserved within metallo-β-lactamases from Bacteria, Archaea and Eukarya and gives insights into evolution and function of enzymes from this superfamily. Structural alignments with diverse metallo-β-lactamase-fold-containing enzymes allowed the identification of Protein Variable Regions accounting for modulation of activity, specificity and oligomerization patterns. Docking of different substrates within the active sites revealed the basis for the crucial cofactor dependency of this enzyme superfamily.
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Affiliation(s)
- Pablo Perez-Garcia
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | - Stefanie Kobus
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Christoph G W Gertzen
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Astrid Hoeppner
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Nicholas Holzscheck
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | - Christoph Heinrich Strunk
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426, Jülich, Germany
| | - Harald Huber
- Institute for Microbiology and Archaeal Center, Regensburg University, 93035, Regensburg, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426, Jülich, Germany
| | - Sander H J Smits
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany.
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Delfosse V, Bourguet W, Drin G. Structural and Functional Specialization of OSBP-Related Proteins. ACTA ACUST UNITED AC 2020. [DOI: 10.1177/2515256420946627] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Lipids are precisely distributed in the eukaryotic cell where they help to define organelle identity and function, in addition to their structural role. Once synthesized, many lipids must be delivered to other compartments by non-vesicular routes, a process that is undertaken by proteins called Lipid Transfer Proteins (LTPs). OSBP and the closely-related ORP and Osh proteins constitute a major, evolutionarily conserved family of LTPs in eukaryotes. Most of these target one or more subcellular regions, and membrane contact sites in particular, where two organelle membranes are in close proximity. It was initially thought that such proteins were strictly dedicated to sterol sensing or transport. However, over the last decade, numerous studies have revealed that these proteins have many more functions, and we have expanded our understanding of their mechanisms. In particular, many of them are lipid exchangers that exploit PI(4)P or possibly other phosphoinositide gradients to directionally transfer sterol or PS between two compartments. Importantly, these transfer activities are tightly coupled to processes such as lipid metabolism, cellular signalling and vesicular trafficking. This review describes the molecular architecture of OSBP/ORP/Osh proteins, showing how their specific structural features and internal configurations impart unique cellular functions.
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Affiliation(s)
- Vanessa Delfosse
- Centre de Biochimie Structurale, Inserm, CNRS, Univ Montpellier, Montpellier, France
| | - William Bourguet
- Centre de Biochimie Structurale, Inserm, CNRS, Univ Montpellier, Montpellier, France
| | - Guillaume Drin
- CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur, Valbonne, France
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Biochemical Characterization of Human Retroviral-Like Aspartic Protease 1 (ASPRV1). Biomolecules 2020; 10:biom10071004. [PMID: 32640672 PMCID: PMC7408472 DOI: 10.3390/biom10071004] [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: 05/15/2020] [Revised: 06/26/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022] Open
Abstract
The human retroviral-like aspartic protease 1 (ASPRV1) is a mammalian retroviral-like enzyme that catalyzes a critical proteolytic step during epidermal differentiation; therefore, it is also referred to as skin-specific aspartic protease (SASPase). Neutrophil granulocytes were also found recently to express ASPRV1 that is involved in the progression of acute chronic inflammation of the central nervous system, especially in autoimmune encephalomyelitis. Thus, investigation of ASPRV1 is important due to its therapeutic or diagnostic potential. We investigated the structural characteristics of ASPRV1 by homology modeling; analysis of the proposed structure was used for interpretation of in vitro specificity studies. For in-vitro characterization, activities of SASP28 and SASP14 enzyme forms were measured using synthetic oligopeptide substrates. We demonstrated that self-processing of SASP28 precursor causes autoactivation of the protease. The highest activity was measured for GST-SASP14 at neutral pH and at high ionic strength, and we proved that pepstatin A and acetyl-pepstatin can also inhibit the protease. In agreement with the structural characteristics, the relatively lower urea dissociation constant implied lower dimer stability of SASP14 compared to that of HIV-1 protease. The obtained structural and biochemical characteristics support better understanding of ASPRV1 function in the skin and central nervous system.
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Torng W, Altman RB. High precision protein functional site detection using 3D convolutional neural networks. Bioinformatics 2020; 35:1503-1512. [PMID: 31051039 PMCID: PMC6499237 DOI: 10.1093/bioinformatics/bty813] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 08/14/2018] [Accepted: 09/19/2018] [Indexed: 12/02/2022] Open
Abstract
Motivation Accurate annotation of protein functions is fundamental for understanding molecular and cellular physiology. Data-driven methods hold promise for systematically deriving rules underlying the relationship between protein structure and function. However, the choice of protein structural representation is critical. Pre-defined biochemical features emphasize certain aspects of protein properties while ignoring others, and therefore may fail to capture critical information in complex protein sites. Results In this paper, we present a general framework that applies 3D convolutional neural networks (3DCNNs) to structure-based protein functional site detection. The framework can extract task-dependent features automatically from the raw atom distributions. We benchmarked our method against other methods and demonstrate better or comparable performance for site detection. Our deep 3DCNNs achieved an average recall of 0.955 at a precision threshold of 0.99 on PROSITE families, detected 98.89 and 92.88% of nitric oxide synthase and TRYPSIN-like enzyme sites in Catalytic Site Atlas, and showed good performance on challenging cases where sequence motifs are absent but a function is known to exist. Finally, we inspected the individual contributions of each atom to the classification decisions and show that our models successfully recapitulate known 3D features within protein functional sites. Availability and implementation The 3DCNN models described in this paper are available at https://simtk.org/projects/fscnn. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wen Torng
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Russ B Altman
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
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Pang WC, Ramli ANM, Hamid AAA. Comparative modelling studies of fruit bromelain using molecular dynamics simulation. J Mol Model 2020; 26:142. [PMID: 32417971 DOI: 10.1007/s00894-020-04398-1] [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] [Received: 10/15/2019] [Accepted: 04/28/2020] [Indexed: 12/25/2022]
Abstract
Fruit bromelain is a cysteine protease accumulated in pineapple fruits. This proteolytic enzyme has received high demand for industrial and therapeutic applications. In this study, fruit bromelain sequences QIM61759, QIM61760 and QIM61761 were retrieved from the National Center for Biotechnology Information (NCBI) Genbank Database. The tertiary structure of fruit bromelain QIM61759, QIM61760 and QIM61761 was generated by using MODELLER. The result revealed that the local stereochemical quality of the generated models was improved by using multiple templates during modelling process. Moreover, by comparing with the available papain model, structural analysis provides an insight on how pro-peptide functions as a scaffold in fruit bromelain folding and contributing to inactivation of mature protein. The structural analysis also disclosed the similarities and differences between these models. Lastly, thermal stability of fruit bromelain was studied. Molecular dynamics simulation of fruit bromelain structures at several selected temperatures demonstrated how fruit bromelain responds to elevation of temperature.
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Affiliation(s)
- Wei Cheng Pang
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Aizi Nor Mazila Ramli
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia. .,Bio Aromatic Research Centre of Excellence, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia.,Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
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Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases. Int J Mol Sci 2020; 21:ijms21041352. [PMID: 32079302 PMCID: PMC7072860 DOI: 10.3390/ijms21041352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 02/07/2023] Open
Abstract
The life cycles of retroviruses rely on the limited proteolysis catalyzed by the viral protease. Numerous eukaryotic organisms also express endogenously such proteases, which originate from retrotransposons or retroviruses, including DNA damage-inducible 1 and 2 (Ddi1 and Ddi2, respectively) proteins. In this study, we performed a comparative analysis based on the structural data currently available in Protein Data Bank (PDB) and Structural summaries of PDB entries (PDBsum) databases, with a special emphasis on the regions involved in dimerization of retroviral and retroviral-like Ddi proteases. In addition to Ddi1 and Ddi2, at least one member of all seven genera of the Retroviridae family was included in this comparison. We found that the studied retroviral and non-viral proteases show differences in the mode of dimerization and density of intermonomeric contacts, and distribution of the structural characteristics is in agreement with their evolutionary relationships. Multiple sequence and structure alignments revealed that the interactions between the subunits depend mainly on the overall organization of the dimer interface. We think that better understanding of the general and specific features of proteases may support the characterization of retroviral-like proteases.
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46
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Holm L. DALI and the persistence of protein shape. Protein Sci 2020; 29:128-140. [PMID: 31606894 PMCID: PMC6933842 DOI: 10.1002/pro.3749] [Citation(s) in RCA: 452] [Impact Index Per Article: 113.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 12/30/2022]
Abstract
DALI is a popular resource for comparing protein structures. The software is based on distance-matrix alignment. The associated web server provides tools to navigate, integrate and organize some data pushed out by genomics and structural genomics. The server has been running continuously for the past 25 years. Structural biologists routinely use DALI to compare a new structure against previously known protein structures. If significant similarities are discovered, it may indicate a distant homology, that is, that the structures are of shared origin. This may be significant in determining the molecular mechanisms, as these may remain very similar from a distant predecessor to the present day, for example, from the last common ancestor of humans and bacteria. Meta-analysis of independent reference-based evaluations of alignment accuracy and fold discrimination shows DALI at top rank in six out of 12 studies. The web server and standalone software are available from http://ekhidna2.biocenter.helsinki.fi/dali.
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Affiliation(s)
- Liisa Holm
- Institute of Biotechnology, Helsinki Institute of Life Sciences and Research Program of Evolutionary and Organismal BiologyFaculty of Biosciences, University of HelsinkiHelsinkiFinland
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Deng L, Zhong G, Liu C, Luo J, Liu H. MADOKA: an ultra-fast approach for large-scale protein structure similarity searching. BMC Bioinformatics 2019; 20:662. [PMID: 31870277 PMCID: PMC6929402 DOI: 10.1186/s12859-019-3235-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 01/22/2023] Open
Abstract
Background Protein comparative analysis and similarity searches play essential roles in structural bioinformatics. A couple of algorithms for protein structure alignments have been developed in recent years. However, facing the rapid growth of protein structure data, improving overall comparison performance and running efficiency with massive sequences is still challenging. Results Here, we propose MADOKA, an ultra-fast approach for massive structural neighbor searching using a novel two-phase algorithm. Initially, we apply a fast alignment between pairwise structures. Then, we employ a score to select pairs with more similarity to carry out a more accurate fragment-based residue-level alignment. MADOKA performs about 6–100 times faster than existing methods, including TM-align and SAL, in massive alignments. Moreover, the quality of structural alignment of MADOKA is better than the existing algorithms in terms of TM-score and number of aligned residues. We also develop a web server to search structural neighbors in PDB database (About 360,000 protein chains in total), as well as additional features such as 3D structure alignment visualization. The MADOKA web server is freely available at: http://madoka.denglab.org/ Conclusions MADOKA is an efficient approach to search for protein structure similarity. In addition, we provide a parallel implementation of MADOKA which exploits massive power of multi-core CPUs.
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Affiliation(s)
- Lei Deng
- School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Guolun Zhong
- School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Chenzhe Liu
- School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Judong Luo
- Department of Radiation Oncology, the Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China.
| | - Hui Liu
- Lab of Information Management, Changzhou University, Changzhou, 213164, China.
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48
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McCoy MD, Shivakumar V, Nimmagadda S, Jafri MS, Madhavan S. SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants. BMC Bioinformatics 2019; 20:171. [PMID: 30943891 PMCID: PMC6448223 DOI: 10.1186/s12859-019-2774-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/22/2019] [Indexed: 01/18/2023] Open
Abstract
Background Molecular simulations are used to provide insight into protein structure and dynamics, and have the potential to provide important context when predicting the impact of sequence variation on protein function. In addition to understanding molecular mechanisms and interactions on the atomic scale, translational applications of those approaches include drug screening, development of novel molecular therapies, and targeted treatment planning. Supporting the continued development of these applications, we have developed the SNP2SIM workflow that generates reproducible molecular dynamics and molecular docking simulations for downstream functional variant analysis. The Python workflow utilizes molecular dynamics software (NAMD (Phillips et al., J Comput Chem 26(16):1781-802, 2005), VMD (Humphrey et al., J Mol Graph 14(1):33-8, 27-8, 1996)) to generate variant specific scaffolds for simulated small molecule docking (AutoDock Vina (Trott and Olson, J Comput Chem 31(2):455-61, 2010)). Results SNP2SIM is composed of three independent modules that can be used sequentially to generate the variant scaffolds of missense protein variants from the wildtype protein structure. The workflow first generates the mutant structure and configuration files required to execute molecular dynamics simulations of solvated protein variant structures. The resulting trajectories are clustered based on the structural diversity of residues involved in ligand binding to produce one or more variant scaffolds of the protein structure. Finally, these unique structural conformations are bound to small molecule ligand libraries to predict variant induced changes to drug binding relative to the wildtype protein structure. Conclusions SNP2SIM provides a platform to apply molecular simulation based functional analysis of sequence variation in the protein targets of small molecule therapies. In addition to simplifying the simulation of variant specific drug interactions, the workflow enables large scale computational mutagenesis by controlling the parameterization of molecular simulations across multiple users or distributed computing infrastructures. This enables the parallelization of the computationally intensive molecular simulations to be aggregated for downstream functional analysis, and facilitates comparing various simulation options, such as the specific residues used to define structural variant clusters. The Python scripts that implement the SNP2SIM workflow are available (SNP2SIM Repository. https://github.com/mccoymd/SNP2SIM, Accessed 2019 February ), and individual SNP2SIM modules are available as apps on the Seven Bridges Cancer Genomics Cloud (Lau et al., Cancer Res 77(21):e3-e6, 2017; Cancer Genomics Cloud [www.cancergenomicscloud.org; Accessed 2018 November]).
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Affiliation(s)
- Matthew D McCoy
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, 2115 Wisconsin Avenue, NW, Suite 110, Washington, D.C., 20007, USA.
| | - Vikram Shivakumar
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, 2115 Wisconsin Avenue, NW, Suite 110, Washington, D.C., 20007, USA
| | - Sridhar Nimmagadda
- Radiology and Radiological Science, Johns Hopkins University, 1550 Orleans St, #492, Cancer Research Building II, Baltimore, MD, 21287, USA
| | - Mohsin Saleet Jafri
- School of Systems Biology, George Mason University, 4461 Rockfish Creek Lane, MS 2A1, Fairfax, VA, 22030, USA
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, 2115 Wisconsin Avenue, NW, Suite 110, Washington, D.C., 20007, USA
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Ma J, Benitez JA, Li J, Miki S, Ponte de Albuquerque C, Galatro T, Orellana L, Zanca C, Reed R, Boyer A, Koga T, Varki NM, Fenton TR, Nagahashi Marie SK, Lindahl E, Gahman TC, Shiau AK, Zhou H, DeGroot J, Sulman EP, Cavenee WK, Kolodner RD, Chen CC, Furnari FB. Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair. Cancer Cell 2019; 35:504-518.e7. [PMID: 30827889 PMCID: PMC6424615 DOI: 10.1016/j.ccell.2019.01.020] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 11/10/2018] [Accepted: 01/28/2019] [Indexed: 11/21/2022]
Abstract
Ionizing radiation (IR) and chemotherapy are standard-of-care treatments for glioblastoma (GBM) patients and both result in DNA damage, however, the clinical efficacy is limited due to therapeutic resistance. We identified a mechanism of such resistance mediated by phosphorylation of PTEN on tyrosine 240 (pY240-PTEN) by FGFR2. pY240-PTEN is rapidly elevated and bound to chromatin through interaction with Ki-67 in response to IR treatment and facilitates the recruitment of RAD51 to promote DNA repair. Blocking Y240 phosphorylation confers radiation sensitivity to tumors and extends survival in GBM preclinical models. Y240F-Pten knockin mice showed radiation sensitivity. These results suggest that FGFR-mediated pY240-PTEN is a key mechanism of radiation resistance and is an actionable target for improving radiotherapy efficacy.
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Affiliation(s)
- Jianhui Ma
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Jorge A Benitez
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Jie Li
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Shunichiro Miki
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Claudio Ponte de Albuquerque
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Thais Galatro
- Department of Neurology, Laboratory of Molecular and Cellular Biology, LIM15, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Laura Orellana
- Science for Life Laboratory, 17121 Stockholm, Sweden; Theoretical and Computational Biophysics, Department of Theoretical Physics, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden; Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 114 18 Stockholm, Sweden
| | - Ciro Zanca
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Rachel Reed
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Antonia Boyer
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Tomoyuki Koga
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Nissi M Varki
- Department of Pathology, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Suely Kazue Nagahashi Marie
- Department of Neurology, Laboratory of Molecular and Cellular Biology, LIM15, School of Medicine, University of São Paulo, São Paulo, Brazil; Center for Studies of Cellular and Molecular Therapy (NAP-NETCEM-NUCEL), University of São Paulo, São Paulo, Brazil
| | - Erik Lindahl
- Science for Life Laboratory, 17121 Stockholm, Sweden; Theoretical and Computational Biophysics, Department of Theoretical Physics, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden; Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 114 18 Stockholm, Sweden
| | - Timothy C Gahman
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Andrew K Shiau
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Huilin Zhou
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - John DeGroot
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erik P Sulman
- Departments of Radiation Oncology, Translational Molecular Pathology, and Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Webster K Cavenee
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA; School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Richard D Kolodner
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Clark C Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Frank B Furnari
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pathology, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA.
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50
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RUPEE: A fast and accurate purely geometric protein structure search. PLoS One 2019; 14:e0213712. [PMID: 30875409 PMCID: PMC6420038 DOI: 10.1371/journal.pone.0213712] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/27/2019] [Indexed: 11/19/2022] Open
Abstract
Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. Despite their maturity, existing protein structure searches either use simplifying assumptions or compromise between fast response times and quality of results. These limitations can prevent the easy and efficient exploration of relationships between protein structures, which is the norm in other areas of inquiry. To address these limitations we have developed RUPEE, a fast and accurate purely geometric structure search combining techniques from information retrieval and big data with a novel approach to encoding sequences of torsion angles. Comparing our results to the output of mTM, SSM, and the CATHEDRAL structural scan, it is clear that RUPEE has set a new bar for purely geometric big data approaches to protein structure searches. RUPEE in top-aligned mode produces equal or better results than the best available protein structure searches, and RUPEE in fast mode demonstrates the fastest response times coupled with high quality results. The RUPEE protein structure search is available at https://ayoubresearch.com. Code and data are available at https://github.com/rayoub/rupee.
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