Binding affinity and mechanisms of SARS-CoV-2 variants

Yanqiang Han, Zhilong Wang, Zhiyun Wei*, Igor Schapiro, Jinjin Li

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


During the rapid worldwide spread of SARS-CoV-2, the viral genome has been undergoing numerous mutations, especially in the spike (S) glycoprotein gene that encode a type-I fusion protein, which plays an important role in the infectivity and transmissibility of the virus into the host cell. In this work, we studied the effect of S glycoprotein residue mutations on the binding affinity and mechanisms of SARS-CoV-2 using molecular dynamics simulations and sequence analysis. We quantitatively determined the degrees of binding affinity caused by different S glycoprotein mutations, and the result indicated that the 501Y.V1 variant yielded the highest enhancements in binding affinity (increased by 36.8%), followed by the N439K variant (increased by 29.5%) and the 501Y.V2 variant (increased by 19.6%). We further studied the structures, chemical bonds, binding free energies (enthalpy and entropy), and residue contribution decompositions of these variants to provide physical explanations for the changes in SARS-CoV-2 binding affinity caused by these residue mutations. This research identified the binding affinity differences of the SARS-CoV-2 variants and provides a basis for further surveillance, diagnosis, and evaluation of mutated viruses.

Original languageAmerican English
Pages (from-to)4184-4191
Number of pages8
JournalComputational and Structural Biotechnology Journal
StatePublished - Jan 2021

Bibliographical note

Publisher Copyright:
© 2021 The Authors


  • Binding affinity
  • Coronavirus variant
  • Residue mutation
  • SARS‐CoV‐2
  • Spike glycoprotein


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