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.