3.3.3 Membrane Protein (M)
Non-synonymous mutations are also increasing in M protein, occurred in the whole coding region except position 50, 51, 72, 102, 103, 116, 118, 120, 159, 178, 179, and 187. However, the most common have been detected in NTD and CTD as compared with TM domains (Figure 5). The M is a glycoproteins, and most abundant in CoV particles [49]. It forms four main domains, NTD, triple transmembrane domain, consisting of three transmembrane helices (TMH), attached to CTD and N-linked glycosylated protein with conserved domain of 13 amino acids [50] (Figure 4). The M is present in two configurations; long (Endodomain) and compact form because it undergoes elongation and compression [51]. Although spikes are evenly present on both forms of M proteins but more likely to be present on long form, promoting S insertions. After being translated into the polysomes attached to the membrane of endoplasmic reticulum, M proteins are transported to the golgi complex.
The M protein facilitates in virion formation while interacting with E proteins in the golgi complex. Out of three TMH, the first one provides union of M protein, enhanced membrane affinity, and detention in golgi [52]. The M protein increase the virus transmission by blocking the Nuclear Factor Kappa B (NFkB), required for immune responses against pathogens [53]. The M protein of the SARS CoV also shows the activation of b interferons (IFN-b) in cell lines [54]. Such humoral responses are generated by the M protein and its antigenic epitopes have been found in the TM1 and TM2 region of protein. The M protein interacts with itself (homotypic) and other structural proteins like S, E, and N (heterotypic) helping in budding and formation of new virus particles. Homotypic interaction is possible with the help of residues present all along the M protein sequence also in TM regions while CTD is involve its heterotypic interactions with E and N protein. The M protein is also involved in the ribonucleoprotein packaging, and dileucine residues present at 219 and 220 positions (L219, L220) are essential for nucleocapsid packaging [55]. Variations in membrane protein may cause adverse effect as it is involved in regulating the virus life cycle. A large number of mutations has been seen in the CTD of the M protein, mostly from 142-209 amino acids. Some of the frequently seen mutations in M protein are A2V, A2S, D3G, L17I, H125S, T175M, and D209Y (Figure 4). However, what kind of effect these variants may produce is still unknown. The crystal structure of M is not available and neither there is any suitable template for homology modeling. We downloaded the 3D structure of M from I-TASSER (ID QHD43419) to compute the effect of common variants on M protein thermodynics.
The effect of common mutations on NTD of M structure is mainly seems stabilizing
We detected 627 in M protein mutations (S3), some of them with greater frequencies are listed in the table (Table 6). Mutations have seen in the residues required for nucleocapsid packaging (L219C (1), L219T (1), L220Y (2) and L220I (1)) respectively. These mutations can alter the ribonucleoprotein packaging which may result in lagging the virion particles formations. The M protein plays important role in viral circulation that suggests it to be a therapeutic drug target to retard the virion particles formations or reduce inflammations in the host cells.