Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity

Abstract

The recognition of ACE2 by the receptor-binding domain (RBD) of spike protein mediates host cell entry. The objective of the work is to identify SARS-CoV2 spike variants that emerged during the pandemic and evaluate their binding affinity with ACE2. Evolutionary analysis of 2178 SARS-CoV2 genomes identifies RBD variants that are under selection bias. The binding efficacy of these RBD variants to the ACE2 has been analyzed by using protein-protein docking and binding free energy calculations. Pan-proteomic analysis reveals 113 mutations among them 33 are parsimonious. Evolutionary analysis reveals five RBD variants A348T, V367F, G476S, V483A, and S494P are under strong positive selection bias. Variations at these sites alter the ACE2 binding affinity. A348T, G476S, and V483A variants display reduced affinity to ACE2 in comparison to the Wuhan SARS-CoV2 spike protein. While the V367F and S494P population variants display a higher binding affinity towards human ACE2. Reorientation of several crucial residues at the RBD-ACE2 interface facilitates additional hydrogen bond formation for the V367F variant which enhances the binding energy during ACE2 recognition. On the other hand, the enhanced binding affinity of S494P is attributed to strong interfacial complementarity between the RBD and ACE2.

Keywords: ACE2; Binding free energy; Population variants; Selection; Spike glycoprotein.

Fig. 1

(A) Distribution of mutational sites over the entire spike protein. (B) RBM alignment of SARS-CoV2 variants. (C) Conserved and variable regions on the monomeric spike protein in the prefusion trimeric complex are shown. Detailed identification of variable residues within the RBD domain is highlighted within the square.

Fig. 2

(A) Distribution of relative rate on each residue of SARS-CoV2 spike protein (B) The relative rate value for the substitution of an amino acid to another one calculated from the maximum likelihood analysis. (C) Identification of the SARS-CoV2 S gene under positive selection bias by using the codon-based test. The probability of rejecting the null hypothesis of strict-neutrality in favor of the alternative hypothesis for positive selection is shown in different colors. (D) Selection site analysis of SARS-CoV2 spike protein under the positive selection bias. Corresponding alignment at the particular codon position (indicated by ∗) under high positive selection bias is shown. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3

(A) Scatter plot of the calculated RBD-ACE2 interfacial area and the binding free energy for wild-type and spike variants are shown. (B) The structural alignment of the crystal structure of the RBD-ACE2 complex (blue and red) with the refined complex (light blue and light red) is shown. (C) The binding regions of the RBD-ACE2 complex for wild-type and different spike variants are shown. RBD and ACE2 are shown as transparent cartoons with pink and cyan color, respectively. Residues that contribute significantly to the binding free energy are shown as green sticks. Residues that contribute differently for each spike variant in comparison to Wuhan SARS-CoV2 spikes are labeled. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4

Variations of root mean square deviation (RMSD) (A), Distribution of RBD-ACE2 distances (B), Distribution of RBD-ACE2 interfacial area (C), number of hydrogen bonds (D), van der Waals interaction energy (E), and electrostatic interactions energy (F) between RBD and ACE2 obtained from the molecular dynamics simulations for wild-type, V367F and S494P variant of RBD are shown.