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Protein Surface Printer for Exploring Protein Domains.
Li, Yang; Qiao, Baofu; Olvera de la Cruz, Monica.
  • Li Y; Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60201, United States.
  • Qiao B; Department of Material Science and Engineering, Northwestern University, Evanston, Illinois 60201, United States.
  • Olvera de la Cruz M; Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60201, United States.
J Chem Inf Model ; 60(10): 5255-5264, 2020 10 26.
Article in English | MEDLINE | ID: covidwho-733547
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.
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / Peptidyl-Dipeptidase A / Severe acute respiratory syndrome-related coronavirus / Spike Glycoprotein, Coronavirus / Betacoronavirus Type of study: Prognostic study Limits: Humans Language: English Journal: J Chem Inf Model Journal subject: Medical Informatics / Chemistry Year: 2020 Document Type: Article Affiliation country: Acs.jcim.0c00582

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / Peptidyl-Dipeptidase A / Severe acute respiratory syndrome-related coronavirus / Spike Glycoprotein, Coronavirus / Betacoronavirus Type of study: Prognostic study Limits: Humans Language: English Journal: J Chem Inf Model Journal subject: Medical Informatics / Chemistry Year: 2020 Document Type: Article Affiliation country: Acs.jcim.0c00582