1
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Ammar A, Cavill R, Evelo C, Willighagen E. PSnpBind: a database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow. J Cheminform 2022; 14:8. [PMID: 35227289 PMCID: PMC8886843 DOI: 10.1186/s13321-021-00573-5] [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: 08/11/2021] [Accepted: 11/18/2021] [Indexed: 11/15/2022] Open
Abstract
A key concept in drug design is how natural variants, especially the ones occurring in the binding site of drug targets, affect the inter-individual drug response and efficacy by altering binding affinity. These effects have been studied on very limited and small datasets while, ideally, a large dataset of binding affinity changes due to binding site single-nucleotide polymorphisms (SNPs) is needed for evaluation. However, to the best of our knowledge, such a dataset does not exist. Thus, a reference dataset of ligands binding affinities to proteins with all their reported binding sites’ variants was constructed using a molecular docking approach. Having a large database of protein–ligand complexes covering a wide range of binding pocket mutations and a large small molecules’ landscape is of great importance for several types of studies. For example, developing machine learning algorithms to predict protein–ligand affinity or a SNP effect on it requires an extensive amount of data. In this work, we present PSnpBind: A large database of 0.6 million mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow. It provides a web interface to explore and visualize the protein–ligand complexes and a REST API to programmatically access the different aspects of the database contents. PSnpBind is open source and freely available at https://psnpbind.org.
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Affiliation(s)
- Ammar Ammar
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
| | - Rachel Cavill
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Chris Evelo
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
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2
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Krebs FS, Zoete V, Trottet M, Pouchon T, Bovigny C, Michielin O. Swiss-PO: a new tool to analyze the impact of mutations on protein three-dimensional structures for precision oncology. NPJ Precis Oncol 2021; 5:19. [PMID: 33737716 PMCID: PMC7973488 DOI: 10.1038/s41698-021-00156-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
Swiss-PO is a new web tool to map gene mutations on the 3D structure of corresponding proteins and to intuitively assess the structural implications of protein variants for precision oncology. Swiss-PO is constructed around a manually curated database of 3D structures, variant annotations, and sequence alignments, for a list of 50 genes taken from the Ion AmpliSeqTM Custom Cancer Hotspot Panel. The website was designed to guide users in the choice of the most appropriate structure to analyze regarding the mutated residue, the role of the protein domain it belongs to, or the drug that could be selected to treat the patient. The importance of the mutated residue for the structure and activity of the protein can be assessed based on the molecular interactions exchanged with neighbor residues in 3D within the same protein or between different biomacromolecules, its conservation in orthologs, or the known effect of reported mutations in its 3D or sequence-based vicinity. Swiss-PO is available free of charge or login at https://www.swiss-po.ch .
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Affiliation(s)
- Fanny S Krebs
- Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research Lausanne Branch, University of Lausanne, Lausanne, Switzerland
| | - Vincent Zoete
- Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research Lausanne Branch, University of Lausanne, Lausanne, Switzerland.
- Molecular Modelling Group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Maxence Trottet
- Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research Lausanne Branch, University of Lausanne, Lausanne, Switzerland
- Molecular Modelling Group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Timothée Pouchon
- Molecular Modelling Group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Christophe Bovigny
- Molecular Modelling Group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Olivier Michielin
- Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research Lausanne Branch, University of Lausanne, Lausanne, Switzerland.
- Molecular Modelling Group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
- Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland.
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3
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Visualizing protein structures - tools and trends. Biochem Soc Trans 2021; 48:499-506. [PMID: 32196545 DOI: 10.1042/bst20190621] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 02/06/2023]
Abstract
Molecular visualization is fundamental in the current scientific literature, textbooks and dissemination materials. It provides an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Tools for visual exploration of structural data have become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. This mini-review was written as a short and compact overview for scientists who need to visualize protein structures and want to make an informed decision which tool they should use. Here, we first describe a few 'Swiss Army knives' geared towards protein visualization for everyday use with an existing large user base, then focus on more specialized tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.
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4
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Segura J, Rose Y, Westbrook J, Burley SK, Duarte JM. RCSB Protein Data Bank 1D Tools and Services. Bioinformatics 2020; 36:5526-5527. [PMID: 33313665 PMCID: PMC8016458 DOI: 10.1093/bioinformatics/btaa1012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/14/2020] [Accepted: 11/23/2020] [Indexed: 11/17/2022] Open
Abstract
Motivation Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein and gene features and helping to understand biomolecular function. Results Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI and the UniProtKB data resources and visualize integrated data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate spaces and an interactive tool allows convenient visualization of the 1-dimensional data over the web. Availabilityand implementation https://1d-coordinates.rcsb.org and https://rcsb.github.io/rcsb-saguaro. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joan Segura
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, California, USA
| | - Yana Rose
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, California, USA
| | - John Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, California, USA.,Research Collaboratory for Structural Bioinformatics Protein Data Bank.,Institute for Quantitative Biomedicine
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, California, USA.,Research Collaboratory for Structural Bioinformatics Protein Data Bank.,Institute for Quantitative Biomedicine.,Department of Chemistry and Chemical Biology, The State University of New Jersey, New Jersey, USA.,Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Jersey, USA
| | - Jose M Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, California, USA
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5
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Liu J, Liu W, Li XL, Li Q, Dai W, Li YY. TGPred: a tumor gene prediction webserver for analyzing structural and functional impacts of variants. J Mol Cell Biol 2020; 12:556-558. [PMID: 32246141 PMCID: PMC7493032 DOI: 10.1093/jmcb/mjaa007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/20/2020] [Indexed: 11/16/2022] Open
Affiliation(s)
- Jixiang Liu
- Shanghai Center for Bioinformation Technology & Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute, Shanghai 201203, China
| | - Wei Liu
- Shanghai Center for Bioinformation Technology & Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute, Shanghai 201203, China
| | - Xue-Ling Li
- Shanghai Center for Bioinformation Technology & Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute, Shanghai 201203, China.,National Engineering Research Center for Nanotechnology, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
| | - Quanxue Li
- Shanghai Center for Bioinformation Technology & Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute, Shanghai 201203, China.,School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Wentao Dai
- Shanghai Center for Bioinformation Technology & Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute, Shanghai 201203, China.,Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology & Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute, Shanghai 201203, China.,Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
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6
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Stephenson JD, Laskowski RA, Nightingale A, Hurles ME, Thornton JM. VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations. Bioinformatics 2020; 35:4854-4856. [PMID: 31192369 PMCID: PMC6853667 DOI: 10.1093/bioinformatics/btz482] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/17/2019] [Accepted: 06/07/2019] [Indexed: 12/16/2022] Open
Abstract
Motivation Understanding the protein structural context and patterning on proteins of genomic variants can help to separate benign from pathogenic variants and reveal molecular consequences. However, mapping genomic coordinates to protein structures is non-trivial, complicated by alternative splicing and transcript evidence. Results Here we present VarMap, a web tool for mapping a list of chromosome coordinates to canonical UniProt sequences and associated protein 3D structures, including validation checks, and annotating them with structural information. Availability and implementation https://www.ebi.ac.uk/thornton-srv/databases/VarMap. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- James D Stephenson
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Roman A Laskowski
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
| | - Andrew Nightingale
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Janet M Thornton
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
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7
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Wang J, Sheridan R, Sumer SO, Schultz N, Xu D, Gao J. G2S: a web-service for annotating genomic variants on 3D protein structures. Bioinformatics 2019; 34:1949-1950. [PMID: 29385402 DOI: 10.1093/bioinformatics/bty047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 01/26/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants detected by recent large-scale sequencing efforts. There are several mapping resources currently available, but none of them provides a web API (Application Programming Interface) that supports programmatic access. Results We present G2S, a real-time web API that provides automated mapping of genomic variants on 3D protein structures. G2S can align genomic locations of variants, protein locations, or protein sequences to protein structures and retrieve the mapped residues from structures. G2S API uses REST-inspired design and it can be used by various clients such as web browsers, command terminals, programming languages and other bioinformatics tools for bringing 3D structures into genomic variant analysis. Availability and implementation The webserver and source codes are freely available at https://g2s.genomenexus.org. Contact g2s@genomenexus.org. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Juexin Wang
- Department of Electrical Engineering & Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Robert Sheridan
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - S Onur Sumer
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nikolaus Schultz
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dong Xu
- Department of Electrical Engineering & Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Jianjiong Gao
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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8
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Lev A, Simon AJ, Barel O, Eyal E, Glick-Saar E, Nayshool O, Birk O, Stauber T, Hochberg A, Broides A, Almashanu S, Hendel A, Lee YN, Somech R. Reduced Function and Diversity of T Cell Repertoire and Distinct Clinical Course in Patients With IL7RA Mutation. Front Immunol 2019; 10:1672. [PMID: 31379863 PMCID: PMC6650764 DOI: 10.3389/fimmu.2019.01672] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/04/2019] [Indexed: 01/01/2023] Open
Abstract
The alpha subunit of IL-7 receptor (IL7R7α) is critical for the differentiation of T cells, specifically for the development and maintenance of γδT cells. Mutations in IL7RA are associated with Severe Combined Immunodeficiency (SCID). Infants with IL7RA deficiency can be identified through newborn screening program. We aimed at defining the immunological and genetic parameters that are directly affected by the IL7RA mutation on the immune system of five unrelated patients which were identified by our newborn screening program for SCID. The patients were found to have a novel identical homozygote mutation in IL7RA (n.c.120 C>G; p.F40L). Both surface expression of IL7Rα and functionality of IL-7 signaling were impaired in patients compared to controls. Structural modeling demonstrated instability of the protein structure due to the mutation. Lastly the TRG immune repertoire of the patients showed reduced diversity, increased clonality and differential CDR3 characteristics. Interestingly, the patients displayed significant different clinical outcome with two displaying severe clinical picture of immunodeficiency and three had spontaneous recovery. Our data supports that the presented IL7RA mutation affects the IL-7 signaling and shaping of the TRG repertoire, reinforcing the role of IL7RA in the immune system, while non-genetic factors may exist that attribute to the ultimate clinical presentation and disease progression.
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Affiliation(s)
- Atar Lev
- The National Lab for Diagnosing SCID - The Israeli Newborn Screening Program, Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Sheba Medical Center, Edmond and Lily Safra Children's Hospital, Israel Ministry of Health, Tel HaShomer, Israel.,The Mina and Everard Goodman Faculty of Life Sciences, Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Amos J Simon
- Sheba Cancer Research Center and Institute of Hematology, Sheba Medical Center, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ortal Barel
- Sheba Cancer Research Center and Institute of Hematology, Sheba Medical Center, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eran Eyal
- Sheba Cancer Research Center and Institute of Hematology, Sheba Medical Center, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel HaShomer, Israel
| | - Efrat Glick-Saar
- Sheba Cancer Research Center and Institute of Hematology, Sheba Medical Center, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel HaShomer, Israel
| | - Omri Nayshool
- Sheba Cancer Research Center and Institute of Hematology, Sheba Medical Center, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel HaShomer, Israel
| | - Ohad Birk
- Soroka Medical Center, Genetics Institute, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tali Stauber
- The National Lab for Diagnosing SCID - The Israeli Newborn Screening Program, Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Sheba Medical Center, Edmond and Lily Safra Children's Hospital, Israel Ministry of Health, Tel HaShomer, Israel
| | - Amit Hochberg
- Department of Pediatrics, Hillel Yaffe Medical Center, Hadera, Israel
| | - Arnon Broides
- Faculty of Health Sciences, Soroka University Medical Center, Pediatric Immunology Clinic, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Shlomo Almashanu
- The National Center for Newborn Screening, Israel Ministry of Health, Tel HaShomer, Israel
| | - Ayal Hendel
- The Mina and Everard Goodman Faculty of Life Sciences, Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Yu Nee Lee
- The National Lab for Diagnosing SCID - The Israeli Newborn Screening Program, Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Sheba Medical Center, Edmond and Lily Safra Children's Hospital, Israel Ministry of Health, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raz Somech
- The National Lab for Diagnosing SCID - The Israeli Newborn Screening Program, Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Sheba Medical Center, Edmond and Lily Safra Children's Hospital, Israel Ministry of Health, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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9
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Konc J, Skrlj B, Erzen N, Kunej T, Janezic D. GenProBiS: web server for mapping of sequence variants to protein binding sites. Nucleic Acids Res 2019; 45:W253-W259. [PMID: 28498966 PMCID: PMC5570222 DOI: 10.1093/nar/gkx420] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/02/2017] [Indexed: 02/02/2023] Open
Abstract
Discovery of potentially deleterious sequence variants is important and has wide implications for research and generation of new hypotheses in human and veterinary medicine, and drug discovery. The GenProBiS web server maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein–protein, protein–nucleic acid, protein–compound, and protein–metal ion binding sites. The concept of a protein–compound binding site is understood in the broadest sense, which includes glycosylation and other post-translational modification sites. Binding sites were defined by local structural comparisons of whole protein structures using the Protein Binding Sites (ProBiS) algorithm and transposition of ligands from the similar binding sites found to the query protein using the ProBiS-ligands approach with new improvements introduced in GenProBiS. Binding site surfaces were generated as three-dimensional grids encompassing the space occupied by predicted ligands. The server allows intuitive visual exploration of comprehensively mapped variants, such as human somatic mis-sense mutations related to cancer and non-synonymous single nucleotide polymorphisms from 21 species, within the predicted binding sites regions for about 80 000 PDB protein structures using fast WebGL graphics. The GenProBiS web server is open and free to all users at http://genprobis.insilab.org.
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Affiliation(s)
- Janez Konc
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.,University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, 6000 Koper, Slovenia
| | - Blaz Skrlj
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Nika Erzen
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Tanja Kunej
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Dusanka Janezic
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, 6000 Koper, Slovenia
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10
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Leibovitch M, Reid NE, Victoria J, Hanic-Joyce PJ, Joyce PBM. Analysis of the pathogenic I326T variant of human tRNA nucleotidyltransferase reveals reduced catalytic activity and thermal stability in vitro linked to a conformational change. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:616-626. [PMID: 30959222 DOI: 10.1016/j.bbapap.2019.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/22/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
The I326T mutation in the TRNT1 gene encoding human tRNA nucleotidyltransferase (tRNA-NT) is linked to a relatively mild form of SIFD. Previous work indicated that the I326T variant was unable to incorporate AMP into tRNAs in vitro, however, expression of the mutant allele from a strong heterologous promoter supported in vivo CCA addition to both cytosolic and mitochondrial tRNAs in a yeast strain lacking tRNA-NT. To address this discrepancy, we determined the biochemical and biophysical characteristics of the I326T variant enzyme and the related variant, I326A. Our in vitro analysis revealed that the I326T substitution decreases the thermal stability of the enzyme and causes a ten-fold reduction in enzyme activity. We propose that the structural changes in the I326T variant that lead to these altered parameters result from a rearrangement of helices within the body domain of the protein which can be probed by the inability of the monomeric enzyme to form a covalent dimer in vitro mediated by C373. In addition, we confirm that the effects of the I326T or I326A substitutions are relatively mild in vivo by demonstrating that the mutant alleles support both mitochondrial and cytosolic CCA-addition in yeast.
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Affiliation(s)
- M Leibovitch
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada
| | - N E Reid
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada
| | - J Victoria
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada
| | - P J Hanic-Joyce
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada
| | - P B M Joyce
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada.
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11
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Kreft L, Turan D, Hulstaert N, Botzki A, Martens L, Vandermarliere E. Scop3D: Online Visualization of Mutation Rates on Protein Structure. J Proteome Res 2019; 18:765-769. [PMID: 30540477 DOI: 10.1021/acs.jproteome.8b00681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Scop3D is a tool that automatically annotates protein structure with sequence conservation starting from a set of protein sequence variants. We present a complete upgrade and rewrite of Scop3D. We have included a DNA module that allows the analysis of single nucleotide polymorphisms in relation to the structural context of the protein. Scop3D therefore forms a bridge between genomics and protein structure. Moreover, Scop3D is now also available through an intuitive web-interface that makes the tool highly user-friendly.
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Affiliation(s)
- Lukasz Kreft
- VIB Bioinformatics Core , VIB , Ghent 120-9052 , Belgium
| | - Demet Turan
- VIB-UGent Center for Medical Biotechnology , VIB , Ghent 9000 , Belgium.,Department of Biochemistry , Ghent University , Ghent 9000 , Belgium
| | - Niels Hulstaert
- VIB-UGent Center for Medical Biotechnology , VIB , Ghent 9000 , Belgium.,Department of Biochemistry , Ghent University , Ghent 9000 , Belgium
| | | | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology , VIB , Ghent 9000 , Belgium.,Department of Biochemistry , Ghent University , Ghent 9000 , Belgium
| | - Elien Vandermarliere
- VIB-UGent Center for Medical Biotechnology , VIB , Ghent 9000 , Belgium.,Department of Biochemistry , Ghent University , Ghent 9000 , Belgium.,VIB Headquarters , VIB , Ghent 120-9052 , Belgium
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12
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Rahman R, Sharma I, Gahlot LK, Hasija Y. DermaGene and VitmiRS: a comprehensive systems analysis of genetic dermatological disorders. BIOMEDICAL DERMATOLOGY 2018. [DOI: 10.1186/s41702-018-0028-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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13
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Iuso A, Wiersma M, Schüller HJ, Pode-Shakked B, Marek-Yagel D, Grigat M, Schwarzmayr T, Berutti R, Alhaddad B, Kanon B, Grzeschik NA, Okun JG, Perles Z, Salem Y, Barel O, Vardi A, Rubinshtein M, Tirosh T, Dubnov-Raz G, Messias AC, Terrile C, Barshack I, Volkov A, Avivi C, Eyal E, Mastantuono E, Kumbar M, Abudi S, Braunisch M, Strom TM, Meitinger T, Hoffmann GF, Prokisch H, Haack TB, Brundel BJ, Haas D, Sibon OC, Anikster Y. Mutations in PPCS, Encoding Phosphopantothenoylcysteine Synthetase, Cause Autosomal-Recessive Dilated Cardiomyopathy. Am J Hum Genet 2018; 102:1018-1030. [PMID: 29754768 DOI: 10.1016/j.ajhg.2018.03.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/22/2018] [Indexed: 01/25/2023] Open
Abstract
Coenzyme A (CoA) is an essential metabolic cofactor used by around 4% of cellular enzymes. Its role is to carry and transfer acetyl and acyl groups to other molecules. Cells can synthesize CoA de novo from vitamin B5 (pantothenate) through five consecutive enzymatic steps. Phosphopantothenoylcysteine synthetase (PPCS) catalyzes the second step of the pathway during which phosphopantothenate reacts with ATP and cysteine to form phosphopantothenoylcysteine. Inborn errors of CoA biosynthesis have been implicated in neurodegeneration with brain iron accumulation (NBIA), a group of rare neurological disorders characterized by accumulation of iron in the basal ganglia and progressive neurodegeneration. Exome sequencing in five individuals from two unrelated families presenting with dilated cardiomyopathy revealed biallelic mutations in PPCS, linking CoA synthesis with a cardiac phenotype. Studies in yeast and fruit flies confirmed the pathogenicity of identified mutations. Biochemical analysis revealed a decrease in CoA levels in fibroblasts of all affected individuals. CoA biosynthesis can occur with pantethine as a source independent from PPCS, suggesting pantethine as targeted treatment for the affected individuals still alive.
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Structural dynamics is a determinant of the functional significance of missense variants. Proc Natl Acad Sci U S A 2018; 115:4164-4169. [PMID: 29610305 PMCID: PMC5910821 DOI: 10.1073/pnas.1715896115] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Discrimination of clinically relevant mutations from neutral mutations is of paramount importance in precision medicine and pharmacogenomics. Our study shows that current computational predictions of pathogenicity, mostly based on analysis of sequence conservation, may be improved by considering the changes in the structural dynamics of the protein due to point mutations. We introduce and demonstrate the utility of a classifier that takes advantage of efficient evaluation of structural dynamics by elastic network models. Accurate evaluation of the effect of point mutations on protein function is essential to assessing the genesis and prognosis of many inherited diseases and cancer types. Currently, a wealth of computational tools has been developed for pathogenicity prediction. Two major types of data are used to this aim: sequence conservation/evolution and structural properties. Here, we demonstrate in a systematic way that another determinant of the functional impact of missense variants is the protein’s structural dynamics. Measurable improvement is shown in pathogenicity prediction by taking into consideration the dynamical context and implications of the mutation. Our study suggests that the class of dynamics descriptors introduced here may be used in conjunction with existing features to not only increase the prediction accuracy of the impact of variants on biological function, but also gain insight into the physical basis of the effect of missense variants.
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A missense mutation in MYH1 is associated with susceptibility to immune-mediated myositis in Quarter Horses. Skelet Muscle 2018; 8:7. [PMID: 29510741 PMCID: PMC5838957 DOI: 10.1186/s13395-018-0155-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 02/25/2018] [Indexed: 12/30/2022] Open
Abstract
Background The cause of immune-mediated myositis (IMM), characterized by recurrent, rapid-onset muscle atrophy in Quarter Horses (QH), is unknown. The histopathologic hallmark of IMM is lymphocytic infiltration of myofibers. The purpose of this study was to identify putative functional variants associated with equine IMM. Methods A genome-wide association (GWA) study was performed on 36 IMM QHs and 54 breed matched unaffected QHs from the same environment using the Equine SNP50 and SNP70 genotyping arrays. Results A mixed model analysis identified nine SNPs within a ~ 2.87 Mb region on chr11 that were significantly (Punadjusted < 1.4 × 10− 6) associated with the IMM phenotype. Associated haplotypes within this region encompassed 38 annotated genes, including four myosin genes (MYH1, MYH2, MYH3, and MYH13). Whole genome sequencing of four IMM and four unaffected QHs identified a single segregating nonsynonymous E321G mutation in MYH1 encoding myosin heavy chain 2X. Genotyping of additional 35 IMM and 22 unaffected QHs confirmed an association (P = 2.9 × 10− 5), and the putative mutation was absent in 175 horses from 21 non-QH breeds. Lymphocytic infiltrates occurred in type 2X myofibers and the proportion of 2X fibers was decreased in the presence of inflammation. Protein modeling and contact/stability analysis identified 14 residues affected by the mutation which significantly decreased stability. Conclusions We conclude that a mutation in MYH1 is highly associated with susceptibility to the IMM phenotype in QH-related breeds. This is the first report of a mutation in MYH1 and the first link between a skeletal muscle myosin mutation and autoimmune disease. Electronic supplementary material The online version of this article (10.1186/s13395-018-0155-0) contains supplementary material, which is available to authorized users.
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Leibovitch M, Hanic-Joyce PJ, Joyce PBM. In vitro studies of disease-linked variants of human tRNA nucleotidyltransferase reveal decreased thermal stability and altered catalytic activity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:527-540. [PMID: 29454993 DOI: 10.1016/j.bbapap.2018.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/09/2018] [Accepted: 02/14/2018] [Indexed: 11/15/2022]
Abstract
Mutations in the human TRNT1 gene encoding tRNA nucleotidyltransferase (tRNA-NT), an essential enzyme responsible for addition of the CCA (cytidine-cytidine-adenosine) sequence to the 3'-termini of tRNAs, have been linked to disease phenotypes including congenital sideroblastic anemia with B-cell immunodeficiency, periodic fevers and developmental delay (SIFD) or retinitis pigmentosa with erythrocyte microcytosis. The effects of these disease-linked mutations on the structure and function of tRNA-NT have not been explored. Here we use biochemical and biophysical approaches to study how five SIFD-linked amino acid substitutions (T154I, M158V, L166S, R190I and I223T), residing in the N-terminal head and neck domains of the enzyme, affect the structure and activity of human tRNA-NT in vitro. Our data suggest that the SIFD phenotype is linked to poor stability of the T154I and L166S variant proteins, and to a combination of reduced stability and altered catalytic efficiency in the M158 V, R190I and I223T variants.
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Affiliation(s)
- M Leibovitch
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada
| | - P J Hanic-Joyce
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada
| | - P B M Joyce
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada.
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