Comparison of the SARS-CoV-2 (2019-nCoV) M protein with its counterparts of SARS-CoV and MERS-CoV species

Abstract

Coronaviruses M proteins are well-represented in the major protein component of the viral envelope. During the viral assembly, they play an important role by association with all other viral structural proteins. Despite their crucial functions, very little information regarding the structures and functions of M proteins is available. Here we utilize bioinformatic tools from available sequences and 3D structures of SARS-CoV, SARS-CoV2, and MERS-CoV M proteins in order to predict potential B-cell epitopes and assessing antibody binding affinity. Such study aims to aid finding more effective vaccines and recognize neutralizing antibodies. we found some rather exciting differences between SARS-COV-2, SARS-Cov and MERS-CoV M proteins. Two SARS-CoV-2 peptides with significant antigen presentation scores for human cell surface proteins have been identified. The results reveal that N-terminal domains of M proteins of SARS-CoV and SARS-CoV2 are translocated (outside) whereas it is inside (cytoplasmic side) in MERS-CoV.

Keywords: B-cell epitopes; M protein; MERS-CoV; SARS-CoV; SARS-CoV-2; Structural proteins.

Fig. 1

Hydropathy profile and prediction of TMD of M protein (a) Hydropathy profile for M proteins of SARS-CoV-2, SARS-CoV and MERS-CoV. The positive values state hydrophobic and negative values state hydrophilic regions in the protein. (b) The plot shows the posterior probability of inside/outside/ TMD for MERS-CoV M protein. (c) For SARS-CoV M protein. (d) For SARS-CoV-2 M protein.

Fig. 2

The multiple sequence alignment of the M protein produced by using CLUSTALX 2.1 program. The conserved proline is spotted (green), cysteine (blue) and dileucine (LL) motif (orange). The prediction of transmembrane helices is indicated in brown box.

Fig. 3

Phylogenetic analysis of M protein sequences from 29 orthologues. The M protein sequences were aligned using MUSCLE alignment (Edgar, 2004). The Neighbor-joining tree was generated based on the alignment. The tree was rooted using Bat-CoV HKU9-5 M protein sequence as the outgroup. The highly related betacoronaviruses MERS-CoV are highlighted (blue color), SARS-CoV (red color), and SARS-CoV2 (green color). Number at nodes indicates bootstrap support (1000 replicates), and the scale bar 2 represents the estimated number of substitutions per site. Accession numbers of sequences used in the analyses are shown next each species.

Fig. 4

Secondary structures and possible topological transmembrane models of M protein (a) Secondary structure of SARS-CoV2 M protein. (b) Secondary structure of SARS-CoV M protein. (c) Secondary structure of MERS-CoV M protein. The yellow bars at the terminal ends of each sequences indicate possible disordered regions. (d) Topological transmembrane model of SARS-CoV2 M protein. (e) Topological transmembrane model of SARS-CoV Mprotein. (f) Topological transmembrane model of MERS-CoV M protein.

Fig. 5

Intrinsic disorder prediction of M proteins, (a) SARS-CoV2 M protein. (b) SARS-CoV M protein. (c) MERS-CoV M protein. The disorder profiles generated using three predictors: PONDR® VSL2 (purple line), PONDR® VL-XT (red line), PONDR® XL1-XT (orange line).

Fig. 6

BepiPred linear epitope prediction of M proteins, (a) for MERS-CoV M protein. (b) for SARS-CoV M protein. (c) SARS-CoV2 M protein. The desired epitope residue showed in yellow color. The red horizontal line indicates surface accessibility threshold (0.55). The x-axis and y-axis represent the position and score, respectively. The highest peak region indicates the most effective B-cell epitope. (d) 3D presents linear epitopes on the MERS-CoV M protein surface. (e) for SARS-CoV M protein. (f) for SARS-CoV2 M protein.