Specifics of the coronavirus protein and receptor

Membrane Protein Structures of S Protein and ACE2 Receptor

S protein is a homotrimer classified as a type I transmembrane protein and a class I viral fusion protein (Huang et al. 2020; Pillay 2020). S consists of two main subunits, S1 and S2. The globular head contains the S1 N-terminal RBD which is used in the recognition and binding to the host ACE2 receptor while the stem contains the S2 C-terminal membrane fusion domain to mediate cell membrane fusion of SARS-CoV-2 with the host cell (Huang et al. 2020). S is oriented with a long extracellular N-terminus and a short intracellular C-terminus anchored by a single transmembrane (TM) domain (see Figure 4A) (Huang et al. 2020). S exists in a metastable conformation but undergoes significant conformational changes upon binding and interacting with ACE2 (Huang et al. 2020). The binding of S1 exposes a cleavage site within the S2 domain that is acted on by proteases such as TMPRSS2 (Pillay 2020).

There are several post-translational modifications in the S protein (Pillay 2020). The outer surface of S is heavily glycosylated with heterogeneous N-linked glycans, which likely play a role in mediating host attachment, influencing priming by host proteases and antibody recognition (Pillay 2020). There are also several cysteine residues found in the cytosolic tail of the protein, which undergo palmitoylation (Pillay 2020). Their likely role is to mediate the protein-protein interactions between S and the ACE2 receptor when binding.

The cleavage of the S1/S2 domains is important for the function of S. The cleavage site located between the S1 and S2 domains contains several basic arginine amino acid residues (Arg-Arg-Ala-Arg at residues 682-685) (Pillay 2020). Positively charged amino acids are likely useful in positioning the protease for cleavage via electrostatic interactions (Law et al. 2006).

ACE2 is a dipeptidyl carboxypeptidase classified as a type I transmembrane protein, with a single TM domain (see Figure 4B) and a zinc- and chlorine-binding domain (Pillay 2020). It is oriented with an extracellular N-terminus and intracellular C-terminus, like S (Pillay 2020). ACE2 is expressed most in nasal pathways as well as organs such as the lungs, intestine, and heart (Jin et al. 2020).

As seen with the S protein, there are also several post-translational modifications in ACE2. A study done by Sun et al. (2020) identified multiple hydroxyproline and methylated sites in the human ACE2 receptor. These methylated sites result in a loss of charge and thus increases their hydrophobicity (Sun et al. 2020). Methylated sites may also have some role in elevating gene expression (Misra et al. 2020). The hydroxyl groups in the hydroxyproline sites are likely meant to increase the hydrophilicity of proline in its extracellular region on ACE2. Other common post-translational modifications such as phosphorylation, acetylation, or fatty acid acylation were not identified (Sun et al. 2020).

Biochemistry of a SARS-CoV-2 Variant: B.1.1.7

The SARS-CoV-2 virus variant strain B.1.1.7 belongs to a lineage that was first identified and isolated in December 2020 in United Kingdom (Galloway et al. 2021). It soon became a variant of concern (VOC) due to its rapid spread in the UK and its arrival to the US.

B.1 is one of the earlier parent variants of SARS-CoV-2, from which B.1.1.7 arises. The B.1 strain developed a fixed mutation D614G (amino acid change from Asp to Gly at the 614th position in the RBD of S protein), which binds to the human ACE2 receptor more efficiently (UniProt 2021b). When cultured in human epithelial cells, the mutation aids in the production of infectious particles while causing no shift in the viruses’ inherent neutralization properties (UniProt 2021b).

On top of the D614G mutation, there are two other main amino acid mutations in the S protein, which are E484K (Glu to Lys at position 484) and N501Y (Asn to Tyr at position 501). The E484K mutation reduces neutralization by affecting the binding of serum polyclonal neutralising antibodies, while the N501Y mutation has been shown to enhance affinity to the human ACE2 receptor (Galloway et al. 2021; Jangra et al. 2021). Results from a paper published by Santos and Passos (2021) indicated through experimentation that the mutant N501Y established stronger interactions with residues Y41 and K535 on the ACE2 receptor. A combination of these mutations allows for enhanced and more efficient viral entry into the host cell, the overall resistance to antibodies, the latter of which raised concern over the efficacy of existing COVID-19 vaccines. Several other amino acid mutations such as A570D, P681H, T716I, S982A, D1118H target the S protein; however, they have not been extensively studied (Galloway et al. 2021).

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