Abstract
The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.
Publication types
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Research Support, U.S. Gov't, Non-P.H.S.
MeSH terms
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Angiotensin-Converting Enzyme 2
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Betacoronavirus / chemistry
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Betacoronavirus / metabolism*
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Betacoronavirus / physiology
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Binding Sites
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COVID-19
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Coronavirus Infections / metabolism
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Cytochrome P-450 Enzyme System / chemistry
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Cytochrome P-450 Enzyme System / metabolism
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Host-Pathogen Interactions
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Humans
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Models, Molecular
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Molecular Docking Simulation
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Pandemics
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Peptidyl-Dipeptidase A / chemistry
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Peptidyl-Dipeptidase A / metabolism*
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Pneumonia, Viral / metabolism
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Protein Binding
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Protein Domains
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SARS-CoV-2
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Severe Acute Respiratory Syndrome / metabolism
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Severe acute respiratory syndrome-related coronavirus / chemistry
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Severe acute respiratory syndrome-related coronavirus / metabolism*
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Severe acute respiratory syndrome-related coronavirus / physiology
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Software*
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Spike Glycoprotein, Coronavirus / chemistry
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Spike Glycoprotein, Coronavirus / metabolism*
Substances
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Spike Glycoprotein, Coronavirus
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spike protein, SARS-CoV-2
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Cytochrome P-450 Enzyme System
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Peptidyl-Dipeptidase A
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ACE2 protein, human
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Angiotensin-Converting Enzyme 2