ArticleProteins2022
Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic.
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Article in Proteins, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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31citing papers in PubMed, 1 pooled it
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review.Journal of infection and public health · 2022Pooled it
- Curcumin-Based Virtual Screening Identifies Inhibitors of SARS-CoV-2 Spike Protein and ACE2 Receptor Binding.Medicinal chemistry (Shariqah (United Arab Emirates)) · 2026Article
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- Bioinformatics approach for discovery of potential lead compound of NSP6 of SARS-CoV-2 using structure based virtual screening and molecular dynamics simulations.Scientific reports · 2025Article
- Proteomic strategies to interrogate the Fe-S proteome.Biochimica et biophysica acta. Molecular cell research · 2024Review
- Comprehensive proteomic analysis of HCoV-OC43 virions and virus-modulated extracellular vesicles.Journal of virology · 2024Article
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- Ligand- and Structure-Based Virtual Screening Identifies New Inhibitors of the Interaction of the SARS-CoV-2 Spike Protein with the ACE2 Host Receptor.Pharmaceutics · 2024Article
- Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia.Microorganisms · 2024Article
- Modeling of ACE2 and antibodies bound to SARS-CoV-2 provides insights into infectivity and immune evasion.JCI insight · 2023Article
- nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands.Nucleic acids research · 2023Article
- Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics.International journal of molecular sciences · 2023Review
- Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3.Scientific reports · 2023Article
- A comprehensive survey of coronaviral main protease active site diversity in 3D: Identifying and analyzing drug discovery targets in search of broad specificity inhibitors for the next coronavirus pandemic.bioRxiv : the preprint server for biology · 2023Article
- Article
- Integrative Bioinformatics Approaches Indicate a Particular Pattern of Some SARS-CoV-2 and Non-SARS-CoV-2 Proteins.Vaccines · 2022Article
- Hands-on training in structural biology, a tool for sustainable development in Africa series 4.Biology open · 2022Article
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- Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign.ACS chemical biology · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
Corrections and comments
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Authors and funding
64 authors.
Joseph H LubinInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Christine ZardeckiInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.ORCID https://orcid.org/0000-0002-4149-1745
Elliott M DolanInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Changpeng LuInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Zhuofan ShenInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Shuchismita DuttaInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
John D WestbrookInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Brian P HudsonInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
David S GoodsellInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Jonathan K WilliamsDepartment of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.ORCID https://orcid.org/0000-0002-7272-6885
Maria VoigtInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Vidur SarmaInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Lingjun XieInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Thejasvi VenkatachalamInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Steven ArnoldInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Luz Helena Alfaro AlvaradoGrinnell College, Grinnell, Iowa, USA.
Kevin CatalfanoUniversity of Notre Dame, Notre Dame, Indiana, USA.
Aaliyah KhanUniversity of Maryland Baltimore County, Baltimore, Maryland, USA.
Erika McCarthyStevens Institute of Technology, Hoboken, New Jersey, USA.
Sophia StaggersFrostburg State University, Frostburg, Maryland, USA.
Brea TinsleyYoungstown State University, Youngstown, Ohio, USA.
Alan TrudeauUniversity of Central Florida, Orlando, Florida, USA.
Jitendra SinghNew York City College of Technology, Brooklyn, New York, USA.
Lindsey WhitmoreHoward University, Washington, District of Columbia, USA.
Helen ZhengWatchung Hills Regional High School, Warren, New Jersey, USA.
Matthew BenedekXavier University, Cincinnati, Ohio, USA.
Jenna CurrierHope College, Holland, Michigan, USA.
Mark DreselDepartment of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Ashish DuvvuruHope College, Holland, Michigan, USA.
Britney DyszelUrsinus College, Collegeville, Pennsylvania, USA.
Emily FingarSUNY Oswego, Oswego, New York, USA.
Elizabeth M HennenRoger Williams University, Bristol, Rhode Island, USA.
Michael KirschSUNY Oswego, Oswego, New York, USA.
Ali A KhanSUNY Oswego, Oswego, New York, USA.
Charlotte Labrie-ClearySUNY Oswego, Oswego, New York, USA.
Stephanie LaporteBrandeis University, Waltham, Massachusetts, USA.
Evan LenkeitDepartment of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Kailey MartinUrsinus College, Collegeville, Pennsylvania, USA.
Marilyn OrellanaHope College, Holland, Michigan, USA.
Melanie Ortiz-Alvarez de la CampaUniversity of Puerto Rico-Rio Piedras, San Juan, Puerto Rico.
Isaac ParedesJohn Jay College, New York, New York, USA.
Baleigh WheelerGrand View University, Des Moines, Iowa, USA.
Allison RupertGrand View University, Des Moines, Iowa, USA.
Andrew SamDepartment of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Katherine SeeRochester Institute of Technology, Rochester, New York, USA.
Santiago Soto ZapataSUNY Oswego, Oswego, New York, USA.
Paul A CraigRochester Institute of Technology, Rochester, New York, USA.
Bonnie L HallGrand View University, Des Moines, Iowa, USA.
Jennifer JiangInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Julia R KoeppeSUNY Oswego, Oswego, New York, USA.
Stephen A MillsXavier University, Cincinnati, Ohio, USA.
Michael J PikaartHope College, Holland, Michigan, USA.
Rebecca RobertsUrsinus College, Collegeville, Pennsylvania, USA.
Yana BrombergDepartment of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA.
J Steen HoyerDepartment of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA.
Siobain DuffyDepartment of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA.
Jay TischfieldDepartment of Genetics, Rutgers, The State University of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, New Jersey, USA.
Francesc X RuizCenter for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Eddy ArnoldDepartment of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Jean BaumDepartment of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Jesse SandbergCenter for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, New Jersey, USA.
Grace BranniganCenter for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, New Jersey, USA.
Sagar D KhareInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.ORCID https://orcid.org/0000-0002-2255-0543
Stephen K BurleyInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Funding
NIMH Center Repository Supporting Stem Cell ResearchU24MH068457 · NIMH · RUTGERS THE ST UNIV OF NJ NEW BRUNSWICK · PI BRZUSTOWICZ, LINDA M, KNOWLES, JAMES A · 2003 to 2024
$213.8MPDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICSR01GM133198 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI BURLEY, STEPHEN K · 2019 to 2023
$19.3MThe NINDS Human Cell and Data Repository (U24 renewal)U24NS095914 · NINDS · RUTGERS, THE STATE UNIV OF N.J. · PI Azadeh Jadali, JAMES A KNOWLES · 2015 to 2026
$15.9MSTRUCTURES OF HIV REVERSE TRANSCRIPTASE WITH SUBSTRATESR37AI027690 · NIAID · RUTGERS THE ST UNIV OF NJ NEW BRUNSWICK · PI ARNOLD, EDWARD · 1999 to 2018
$14.4MUMDNJ TRAINING GRANT IN BIOTECHNOLOGYT32GM008339 · NIGMS · RUTGERS THE ST UNIV OF NJ NEW BRUNSWICK · PI YARMUSH, MARTIN L · 1989 to 2019
$6.1MRutgers Biotechnology Training ProgramT32GM135141 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI ANN M. STOCK, Martin L Yarmush · 2020 to 2026
$3.5MRutgers Helium Recovery System for High Field NMRR35GM136431 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI BAUM, JEAN S · 2020 to 2024
$3.3MPrinciples for Designing Stimulus-Responsive EnzymesR01GM132565 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI KHARE, SAGAR D · 2019 to 2022
$1.8MPredoctoral Training Program in Biological Data Science at Brown UniversityT32GM128596 · NIGMS · BROWN UNIVERSITY · PI RAMACHANDRAN, SOHINI, SANDSTEDE, BJORN · 2018 to 2022
$1.5MNIAID NIH HHS R37 AI027690NIGMS NIH HHS R01 GM132565NIGMS NIH HHS R01 GM133198NIGMS NIH HHS R35 GM136431NIGMS NIH HHS T32 GM008339NIGMS NIH HHS T32 GM128596NIGMS NIH HHS T32 GM135141NIMH NIH HHS U24 MH068457NINDS NIH HHS U24 NS095914
Abstract
Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein-protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein-protein and protein-nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
Indexed as
COVID-19PandemicsAmino AcidsHumansProspective StudiesProteomeSARS-CoV-2Viral ProteinsAmino AcidsProteomeViral ProteinscoronavirusCOVID-19databasesevolutionmolecularpandemicsproteinSARS-CoV-2viral proteins
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