Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding

Abstract

Novel Coronavirus or SARS-CoV-2 has received worldwide attention due to the COVID-19 pandemic, which originated in Wuhan, China leading to thousands of deaths to date. The SARS-CoV-2 Spike glycoprotein protein is one of the main focus of COVID-19 related research as it is a structural protein that facilitates its attachment, entry, and infection to the host cells. We have focused our work on mutations in two of the several functional domains in the virus spike glycoprotein, namely, receptor-binding domain (RBD) and heptad repeat 1 (HR1) domain. These domains are majorly responsible for the stability of spike glycoprotein and play a key role in the host cell attachment and infection. In our study, several mutations like R408I, L455Y, F486L, Q493N, Q498Y, N501T of RBD (319-591), and A930V, D936Y of HR1 (912-984) have been studied to examine its role on the spike glycoprotein native structure. Comparisons of MD simulations in the WT and mutants revealed a significant de-stabilization effect of the mutations on RBD and HR1 domains. We have investigated the impact of mapped mutations on the stability of the spike glycoprotein, before binding to the receptor, which may be consequential to its binding properties to the receptor and other ligands.

Communicated by Ramaswamy H. Sarma

Keywords:

• COVID-19
• SARS-CoV-2 spike glycoprotein
• RBD and HR1 domain
• deleterious mutations
• MD simulations

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

SA is thankful for the Research Associate Fellowship by the Indian Council of Medical Research (ICMR), India, Project ID: (2019-6039 File No. ISRM/11(83)/2019). HK is the recipient of DBT-BioCARe women scientist fellowship awarded by the Department of Biotechnology, India (No.BT/PR31715/BIC/101/1233/2019). DG acknowledges the funding by the Department of Biotechnology, Government of India (Grant No. BT/BI/25/001/2006).