Insights into the conformation changes of SARS-CoV-2 spike receptor-binding domain on graphene

Jianbin Du; Chunmei Yang; Xiangyun Ma; Qifeng Li

doi:10.1016/j.apsusc.2021.151934

Insights into the conformation changes of SARS-CoV-2 spike receptor-binding domain on graphene

Appl Surf Sci. 2022 Mar 15:578:151934. doi: 10.1016/j.apsusc.2021.151934. Epub 2021 Nov 27.

Authors

Jianbin Du^{1

2}, Chunmei Yang², Xiangyun Ma², Qifeng Li²

Affiliations

¹ College of Science, Langfang Normal University, Langfang 065000, China.
² School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely spread in the world, causing more than two million deaths and seriously threatening human life. Effective protection measures are important to prevent the infection and spreading of the virus. To explore the effects of graphene on the virus adsorption and its biological properties, the adsorption process of the receptor binding domain (RBD) of SARS-CoV-2 on graphene has been investigated by molecular dynamics simulations in this paper. The results show that RBD can be quickly adsorbed onto the surface of graphene due to $π - π$ stacking and hydrophobic interactions. Residue PHE486 with benzene ring has stronger adsorption force and the maximum contact area with graphene. Graphene significantly affects the secondary structure of RBD area, especially on the three key sites of binding with human ACE2, GLY476, PHE486 and ASN487. The binding free energy of RBD and graphene shows that the adsorption is irreversible. Undoubtedly, these changes will inevitably affect the pathogenicity of the virus. Therefore, this study provides a theoretical basis for the application of graphene in the protection of SARS-CoV-2, and also provides a reference for the potential application of graphene in the biomedical field.

Keywords: Graphene; Molecular dynamics; Protein adsorption; SARS-CoV-2; Secondary structure.