Autoimmune diseases

Covid-19 Spike protein: structure and functions.

Covid-19 (coronavirus) spike protein mediates the entry of corona virus into the host cell. It is a multifunctional molecular machine that mediates coronavirus entry into host cells by binding to the receptor on the host cell surface through its S1 subunit, and then fuses viral and host membranes through its S2 subunit.

The coronavirus spike is composed of three segments, ahich are a large ectodomain, a single-pass transmembrane anchor, and a short intracellular tail. The ectodomain consists of a receptor-binding subunit S1 and a membrane-fusion subunit S2. The spike is a clove-shaped trimer with three S1 heads and a trimeric S2 stalk. During virus entry, the S1 binds to a receptor on the host cell surface for viral attachment, while S2 fuses the host and viral membranes, allowing viral genomes to enter host cells. The binding to receptor and subsequent membrane fusion are the initial and critical steps in the infection cycle of coronavirus. These also are the critical therapeutic targets.


The SARS-CoV-2 uses human angiotensin-converting enzyme 2 (ACE-2) as receptor to gain entrance into its host cells. This is done through the formation of non-aggregated homotrimers by the SARS-CoV-2 spike proteins Recombinant overexpressed SARS-CoV-2 spike proteins, which then specifically bind to human ACE-2.

The alphacoronavirus HCoV-NL63 and the betacoronavirus SARS-CoV both recognize a zinc peptidase angiotensin-converting enzyme 2. However, within the alphacoronavirus group, HCoV-NL63 and other alphacoronaviruses recognize different receptors; while HCoV-NL63 recognizes ACE-2, other alphacoronaviruses such as TGEV, PEDV, and PRCV recognize another zinc peptidase, aminopeptidase N (APN). In the same way, SARS-CoV and other betacoronaviruses recognize different receptors; MERS-CoV and HKU4 recognize a serine peptidase, dipeptidyl peptidase 4 (DPP4), MHV recognizes a cell adhesion molecule, carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), while BCoV and OC43 recognize sugar instead of human ACE-2.


The SARS-CoV S1-CTD is composed of two subdomains: a core structure and a receptor-binding motif (RBM). The core structure is a five-stranded antiparallel β-sheet, while the RBM exhibits a gently concave outer surface to bind ACE2. The base of this concave surface is a short, two-stranded antiparallel β-sheet, and two ridges are formed by loops. The ectodomain of ACE2 contains a membrane-distal peptidase domain and a membrane-proximal collectrin domain. During the virus binding and entry into host cells, SARS-CoV binding does not interfere with the enzymatic activity of ACE2; conversely, enzymatic activity of ACE2 does not play any role in SARS-CoV entry.

There are two virus-binding hot spots on human ACE2, both of which consist of a salt bridge buried in a hydrophobic environment and contribute significantly to virus-receptor binding. These binding hotsports are ACE2 residues Lys31 and Lys 353. In order to bind with the host receptor, residues 479 and 487 in SARS-CoV S1-CTD must interact closely with these hot spots. However, SARS-CoV S1-CTD are under selective pressure to mutate. Two naturally selected viral mutations, K479N and S487T, strengthened the hot spot structures and enhanced the binding affinity of S1-CTD for human ACE2, and consequently played important roles in the civet-to-human and human-to-human transmissions of SARS-CoV during the SARS epidemic.


When compared to human ACE2, rat ACE2 contains two different residues that resist SARS-CoV binding: His353 disturbs the hot spot structure centering on Lys353, whereas Asn82 introduces an N-linked glycan, presenting steric interference with SARS-CoV binding. Mouse ACE2 also contains His353 but does not have the N-linked glycan at the 82 position. These make rat ACE2 resistant to SARS-CoV, whereas mouse ACE2 is a poor receptor. Consequently, SARS-CoV does not infect rat cells, and it infects mouse cells inefficiently.

Structurally divergent viral RBDs may recognize the same protein receptor

The binding of alphacoronavirus HCoV-NL63 S1-CTD, and SARS-CoV with human ACE2 gives us the example of two structurally divergent viral RBDs which recorgnize the same protein receptor. HCoV-NL63 S1-CTD contains a core structure, which is a β-sandwich consisting of two three-stranded antiparallel β-sheets, and three RPM loops. This differs from the core structure of SARS-CoV S1-CTD, which consists of a single-layer, five-stranded β-sheet. The RBMs of HCoV-NL63 S1-CTD are three short, discontinuous loops. They differ from the RBM of SARS-CoV S1-CTD, which is a long, continuous subdomain. Despite their different structures, however, HCoV-NL63 and SARS-CoV S1-CTDs bind to the same VBMs on human ACE2.

This phenomenon is also seen in the binding of both the alphacoronavirus and betacoronavirus to human ACE2. Although alpha- and betacoronavirus S1-CTDs share a divergent core structures; which are a β-sandwich and a single-layer β-sheet, respectively, they share the same structural topology, suggesting a common evolutionary origin, and supporting the similarity of binding receptor.

Structurally similar viral RBDs may recognise different protein receptor

A comparison between the structure of alphacoronavirus PRCV and that of HCoV-NL63 presents an example of how two similar coronavirus RBDs can bind to different protein receptors. Both HCoV-NL63 S1-CTD, and PRCV S1-CTD possess a β-sandwich core structure and three RBM loops. The core structures of PRCV and HCoV-NL63 S1-CTDs are similar to each other, but their RBMs are not, leading to different receptor specificities. While HCoV-NL63 S1-CTDs recorgnizes human and mouse ACE2s, PRCV S1-CTD binds to porcine APN as its receptor.



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Chidubem Olovo is a biochemist, researcher and a content writer.

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