Computer Simulations of the interaction between SARS-CoV-2 spike glycoprotein and different surfaces

Abstract

A prominent feature of coronaviruses is the presence of a large glycoprotein spike protruding from a lipidic membrane. This glycoprotein spike determines the interaction of coronaviruses with the environment and the host. In this paper, we perform all atomic Molecular Dynamics simulations of the interaction between the SARS-CoV-2 trimeric glycoprotein spike and surfaces of materials. We considered a material with high hydrogen bonding capacity (cellulose) and a material capable of strong hydrophobic interactions (graphite). Initially, the spike adsorbs to both surfaces through essentially the same residues belonging to the receptor binding subunit of its three monomers. Adsorption onto cellulose stabilizes in this configuration, with the help of a large number of hydrogen bonds developed between cellulose and the three receptor binding domains (RBD) of the glycoprotein spike. In the case of adsorption onto graphite, the initial adsorption configuration is not stable and the surface induces a substantial deformation of the glycoprotein spike with a large number of adsorbed residues not pertaining to the binding subunits of the spike monomers.

Structural behavior of monomer of SARS-CoV-2 spike protein during initial stage of adsorption on graphene

“…As can be seen, the secondary structure of the S-protein is not subject to substantial changes during its relaxation in water but also during its adsorption on graphene. Similar behavior was reported in the study of the spike glycoprotein adsorption on the graphite and cellulose [ 33 ]. The S1 subunit is dominated by β-sheets while the S2 subunit is rich in α-helices.…”

“…The ratio λ 1 : λ 2 : λ 3 is changed to 2.78 : 1.39: 1 and 2.15 : 1.16: 1, respectively, for the relaxed free S-protein and the S-protein adsorbed on the graphene. Striking deformation of the spike glycoprotein adsorbed on the graphite was also observed in other molecular dynamics study [ 33 ].…”

“…In the glycosylated RBD, this amino acid residue is slightly removed from the graphene. However, it has been shown that the glycan moieties are only marginally involved into the contact with interacting surface and they occupy the lateral regions of the adsorbed spike glycoprotein [ 33 ]. The interactions of individual residues with the graphene do not seem to be mediated by water molecules; the water molecules in the first hydration layer, however, affect the orientation of those residues which do not possess some stacking interactions with graphene.…”

“…The intra- and intermolecular interactions of S-protein and graphene were described by the CHARMM force field [ 29 ]. Water molecules were represented by the TIP3P model [ 30 , 31 ] Using the non-polarizable force fields for the representation of graphene carbon atoms is quite common in the graphene-protein-water systems [ 32 , 33 ]. Inclusion of polarization effects may influence the adsorption energies and relative strength of adsorption of the individual amino acids residues but it adds more interaction sites which makes simulations more time demanding.…”

SARS-CoV-2 virion physicochemical characteristics pertinent to abiotic substrate attachment

“…One of the exemptions represents Ref. [ 41 ] where the all atom MD modeling was used to determine the interactions of the SARS-CoV-2 trimeric spike protein with cellulose (assumed to be capable of forming strong hydrogen bonding) and graphite, a hydrophobic material. The protein with total charge of -23 e (corresponding to pH 7) was inserted in a water droplet, while the substrate was neutral and not hydrated.…”