3.3.2 Envelope Protein (E)
The E protein of is composed of 76 amino acids [40] weighing 8 to 12 kDa [41]. The E protein consists of NTD, hydrophobic domain and CTD [42]. These domains are arranged from NTD (aa1-9) to CTD (aa38-75), and hydrophobic region spreads from 10 to 37 (Figure 3) [43]. Ionic pores are formed across the membrane due to the arrangement of hydrophobic tail region. Structurally it shows pentameric configuration having 35 alpha helical regions and 40 looped ring regions formed by the hydrophobic tail. This pentameric configuration of hydrophobic tail can be affected by the interactions with in C terminal domain [44]. These pores act as ion channels that provide movements across the membrane and enhancing the pathogenicity of virus [45]. Some novel mutations that were seen in the E protein sequence, does not exist in already existing coronaviruses. In the E protein of CoV-2 at 69th arginine is mutated by isoleucine, threonine and lysine (R69I, R69T, and R69K). Moreover in amino acid sequence of CoV-2 at positions 55 and 56, serine and phenylalanine have been reported instead of threonine and valine [46].
Being the smallest structural protein (75aa) of CoV-2, all the residues positions of the E protein mutated with non-synonymous (S2). Most of these mutations have been detected in the ending sequence of E, including 68 to 73 amino acids. Some of the most frequently seen mutations in E protein are; T91, S68F, R691, P71L, P71S, and L73F (Figure 3). Some other E protein mutations have been listed in the table along with their amino acids (Table 4 and S2). Mutations in the CTD like, S55F (128), V62F (129), R69I (159) may affects the virus pathogenesis, altering the binding of E protein to tight junction, associated PALS1. The transmembrane variants, T9I (168), F20L (90), L21F (84), V24M (76) and T30I (72) may effects the homo pentameric configuration of the E protein [47]. The E protein may also be an effective drug target as it imparts equally in the pathogenicity and cytotoxicity of virus.
The E protein contributes viral pathogenicity, cytotoxicity, and also responsible for viral assembly and release. It forms viroporins which are hydrophobic in nature [48]. Proline residues facilitates in targeting Cis-Golgi complex by the hydrophobic tail, present in the cytoplasm. Through some golgi complex associating elements, NTD also helps tail region in targeting golgi complex as mutations in the tail region may affects its efficiency. The release of these virion particles are facilitated by the ionic gradient, present in the endoplasmic reticulum and golgi compartment by the E protein [40].
The CTD of E proteins has some common mutations whose stability was predicted. The DynaMut prediction outcome of L73F (ΔΔG: -0.417 kcal/mol), P71S (ΔΔG: -0.255 kcal/mol) exert a destabilizing effect. However, T9I (ΔΔG: 0.190 kcal/mol), P71L (ΔΔG: 0.012 kcal/mol), and S68F (ΔΔG: 0.362 kcal/mol) shows a stabilizing effect.