Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages

Abstract

Motivation: Charged amino acid residues on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to influence its binding to different cell surface receptors, its non-specific electrostatic interactions with the environment, and its structural stability and conformation. It is therefore important to obtain a good understanding of amino acid mutations that affect the total charge on the spike protein which have arisen across different SARS-CoV-2 lineages during the course of the virus' evolution.

Results: We analyse the change in the number of ionizable amino acids and the corresponding total charge on the spike proteins of almost 2200 SARS-CoV-2 lineages that have emerged over the span of the pandemic. Our results show that the previously observed trend toward an increase in the positive charge on the spike protein of SARS-CoV-2 variants of concern has essentially stopped with the emergence of the early omicron variants. Furthermore, recently emerged lineages show a greater diversity in terms of their composition of ionizable amino acids. We also demonstrate that the patterns of change in the number of ionizable amino acids on the spike protein are characteristic of related lineages within the broader clade division of the SARS-CoV-2 phylogenetic tree. Due to the ubiquity of electrostatic interactions in the biological environment, our findings are relevant for a broad range of studies dealing with the structural stability of SARS-CoV-2 and its interactions with the environment.

Availability and implementation: The data underlying the article are available in the Supplementary material.

Figure 1.

(a) Evolution of the number of ionizable amino acids on the S protein with the divergence of SARS-CoV-2 lineages. Amino acids in the first column (ARG, LYS, and HIS) take on a positive charge, while amino acids in the second column (ASP, GLU, and TYR) take on a negative charge. Each point represents the average value over the sequences from a single lineage, its colour corresponding to the first recorded date of its emergence. (b) Heatmap of the relative change in the number of ionizable amino acids compared to the WT (lineage B), arranged according to lineage divergence [Equation (3)]. Ticks along the y-axis mark select VOCs and VBMs, also listed in Table 2.

Figure 2.

Centroids of the eight clusters obtained by k-means clustering of the relative changes in the number of ionizable amino acids $\overline{\delta }(\text{AA})$ on the S proteins of 2174 SARS-CoV-2 lineages (Fig. 1b). ASP, GLU, and TYR take on a negative charge while ARG, LYS, and HIS take on a positive charge. Next to the numbered label of each cluster is the number of lineages in the dataset that belong to it. The centroids are further hierarchically ordered as shown by the dendrogram on the left side.

Figure 3.

Average total charge on the S proteins of 2174 different SARS-CoV-2 lineages at three different values of pH (pH 5, 7, 9) as a function of average lineage divergence. Individual lineages are coloured according to one of the eight clusters of their relative change in the number of ionizable amino acids to which they belong (cf. Fig. 2). Black symbols show the total charge according to the centroid of each cluster and are positioned at the mean divergence of the cluster.

Figure 4.

Placement of the 2174 SARS-CoV-2 lineages analysed in this work on the phylogenetic tree of all SARS-CoV-2 lineages as provided by Nextclade (Aksamentov et al. 2021). Only a single sequence of each analysed lineage is shown for clarity, and the tree is annotated with the major Nextstrain clades (Hadfield et al. 2018). Individual lineages are coloured according to one of the eight clusters of their relative change in the number of ionizable amino acids to which they belong (cf. Fig. 2).

Figure 5.

(a–d) Electrostatic surface potential on the S proteins of four different SARS-CoV-2 variants: (a) WT [PDB: 7FB0], delta [PDB: 7TUO], omicron BA.2 [PDB: 7UB6], and omicron BA.2.75 [PDB: 8GS6]. The electrostatic potential was determined at pH 7 using APBS and PDB2PQR software (Jurrus et al. 2018). (e) Characteristic mutations of ionizable amino acids on the S proteins of different SARS-CoV-2 variants, each variant belonging to one of the eight charge clusters identified in this work (Fig. 2; cluster index is noted in parentheses next to the variant name). The variant-characteristic mutations were obtained from cov-spectrum.org, and only those mutations occurring in at least 70% of the sequences were retained. Mutations are marked as $+1$ if the change is from a negatively charged amino acid to a neutral one or from a neutral one to a positively charged one; as $-1$ if the charge is from a positively charged amino acid to a neutral one or from a neutral one to a negatively charged one; and as $\pm 2$ if the change is from a negatively charged amino acid to a positively charged one or vice versa. The positions of the mutations on the S protein amino acid sequence are annotated with some of the most important regions of the S protein (Jackson et al. 2022): NTD, N-terminal domain; RBD, receptor-binding domain; S1/S2, furin cleavage site; S2’, S2’ cleavage site; FP, fusion peptide and fusion-peptide proximal region; HR, hexad repeat; TM, transmembrane anchor.