Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface

Abstract

A prominent feature of coronaviruses is the presence of a large glycoprotein spike (S) protruding from the viral particle. The specific interactions of a material with S determine key aspects such as its possible role for indirect transmission or its suitability as a virucidal material. Here, we consider all-atom molecular dynamics simulations of the interaction between a polymer surface (polystyrene) and S in its up and down conformations. Polystyrene is a commonly used plastic found in electronics, toys, and many other common objects. Also, previous atomic force microscopy (AFM) experiments showed substantial adhesion of S over polystyrene, stronger than in other common materials. Our results show that the main driving forces for the adsorption of the S protein over polystyrene were hydrophobic and π–π interactions with S amino acids and glycans. The interaction was stronger for the case of S in the up conformation, which exposes one highly flexible receptor binding domain (RBD) that adjusts its conformation to interact with the polymer surface. In this case, the interaction has similar contributions from the RBD and glycans. In the case of S in the down conformation, the interaction with the polystyrene surface was weaker and it was dominated by glycans located near the RBD. We do not find significant structural changes in the conformation of S, a result which is in deep contrast to our previous results with another hydrophobic surface (graphite). Our results suggest that SARS-CoV-2 virions may adsorb strongly over plastic surfaces without significantly affecting their infectivity.

Investigation of the effects of N-Acetylglucosamine on the stability of the spike protein in SARS-CoV-2 by molecular dynamics simulations

“…In another MD study [109] it was also found that the RBD region of spike displays a RMSD of 0.5 nm. In another MD study by Sahihi and Faraudo [110] , the average RMSD values without glycans of S protein were found to be about 4.96 ± 0.19 Å for down conformations (corresponds to our S-without-GlcNAc system)”. Both of our systems reach stability after the first 20 ns of the simulation ( Figure 4 a).…”

Effect of surfactants on SARS-CoV-2: Molecular Dynamics Simulations

“…Our MD simulations indicate that the virus spikes can be attached to sebaceous human skin without any deformation or alteration and retain their hydration 10 . Also, our simulations indicate that they can remain adsorbed with a high affinity over common plastics without any substantial deformation 11 . Only some materials such as metals 12 or carbon based materials 13 seem to be able to have a substantial impact on the adsorbed virus spikes.…”

“…The force-field employed in the simulations was CHARMM36 33,34 as in 31 and as in our previous simulations of the SARS-CoV-2 Spike glycoprotein 10,11,13 . The force field also includes an appropiate parametrization for the surfactants.…”

On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study

“…On the other hand, Faraudo et al investigated the spike protein interactions with the surfaces of different materials including cellulose, graphite, and polystyrene. − Their obtained results indicated that the properties of the surfaces can affect the dynamical features of the spike protein. Moreover, in the structure of the spike protein, the RBD part plays a more important role in the corresponding interactions with the surfaces.…”

“…To have a comprehensive insight into the dynamical behavior of the RBD on the surface of different materials, the obtained results were compared with the previous studies. 19 , 38 , 39 , 73 − 75 In the previous study, we also compared the RBD interactions with the graphene and phosphorene nanosheet. 19 Our obtained results indicated that the phosphorene nanosheet can be a better candidate for coronavirus detection than the graphene nanostructure.…”