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Comparison of the binding characteristics of SARS-CoV and SARS-CoV-2 RBDs to ACE2 at different temperatures by MD simulations.
Yan, Fang-Fang; Gao, Feng.
  • Yan FF; Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.
  • Gao F; Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.
Brief Bioinform ; 22(2): 1122-1136, 2021 03 22.
Article in English | MEDLINE | ID: covidwho-1352120
ABSTRACT
Temperature plays a significant role in the survival and transmission of SARS-CoV (severe acute respiratory syndrome coronavirus) and SARS-CoV-2. To reveal the binding differences of SARS-CoV and SARS-CoV-2 receptor-binding domains (RBDs) to angiotensin-converting enzyme 2 (ACE2) at different temperatures at atomic level, 20 molecular dynamics simulations were carried out for SARS-CoV and SARS-CoV-2 RBD-ACE2 complexes at five selected temperatures, i.e. 200, 250, 273, 300 and 350 K. The analyses on structural flexibility and conformational distribution indicated that the structure of the SARS-CoV-2 RBD was more stable than that of the SARS-CoV RBD at all investigated temperatures. Then, molecular mechanics Poisson-Boltzmann surface area and solvated interaction energy approaches were combined to estimate the differences in binding affinity of SARS-CoV and SARS-CoV-2 RBDs to ACE2; it is found that the binding ability of ACE2 to the SARS-CoV-2 RBD was stronger than that to the SARS-CoV RBD at five temperatures, and the main reason for promoting such binding differences is electrostatic and polar interactions between RBDs and ACE2. Finally, the hotspot residues facilitating the binding of SARS-CoV and SARS-CoV-2 RBDs to ACE2, the key differential residues contributing to the difference in binding and the interaction mechanism of differential residues that exist at all investigated temperatures were analyzed and compared in depth. The current work would provide a molecular basis for better understanding of the high infectiousness of SARS-CoV-2 and offer better theoretical guidance for the design of inhibitors targeting infectious diseases caused by SARS-CoV-2.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Angiotensin-Converting Enzyme 2 / SARS-CoV-2 Type of study: Prognostic study Limits: Humans Language: English Journal: Brief Bioinform Journal subject: Biology / Medical Informatics Year: 2021 Document Type: Article Affiliation country: Bib

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Angiotensin-Converting Enzyme 2 / SARS-CoV-2 Type of study: Prognostic study Limits: Humans Language: English Journal: Brief Bioinform Journal subject: Biology / Medical Informatics Year: 2021 Document Type: Article Affiliation country: Bib