BUSCADOR RECOLECTA

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., This work was supported by Grant PID2021-124297NB-C33
funded by MCIN/AEI/10.13039/501100011033 and, as
appropriate, by “ERDF A way of making Europe”, by the
“European Union” or the “European Union NextGenerationEU/PRTR”, and by the “Severo Ochoa” Program for Centers
of Excellence in R&D (CEX2019-000917-S) awarded to
ICMAB. The authors thank CESGA Supercomputing Center
for technical support and computer time at the supercomputers Finisterrae II and III. M.S. is supported by the
European Union Horizon 2020 research and innovation
programme under Marie Sklodowska-Curie Action Individual
Fellowship Grant Agreement No. 101026158., Peer reviewed

A prominent feature of the SARS-CoV-2 virus is the presence of a large glycoprotein spike protruding from the virus envelope. The spike determines the interaction of the virus with the environment and the host. Here, we used an all-atom molecular dynamics simulation method to investigate the interaction of up- and down-conformations of the S1 subunit of the SARS-CoV-2 spike with the (100) surface of Au, Ag, and Cu. Our results revealed that the spike protein is adsorbed onto the surface of these metals, with Cu being the metal with the highest interaction with the spike. In our simulations, we considered the spike protein in both its up-conformation Sup (one receptor binding domain exposed) and down-conformation Sdown (no exposed receptor binding domain). We found that the affinity of the metals for the up-conformation was higher than their affinity for the down-conformation. The structural changes in the spike in the up-conformation were also larger than the changes in the down-conformation. Comparing the present results for metals with those obtained in our previous MD simulations of Sup with other materials (cellulose, graphite, and human skin models), we see that Au induces the highest structural change in Sup, larger than those obtained in our previous studies., This work was supported by Grant PID2021-124297NB-C33 funded by MCIN/AEI/10.13039/501100011033 and, as appropriate, by “ERDF A way of making Europe”, by the “European Union” or by the “European Union NextGenerationEU/PRTR” and by the “Severo Ochoa” Program for Centers of Excellence in R&D (CEX2019-000917-S) awarded to ICMAB. We thank the Spanish national supercomputing network (BSC-RES) for the award of computer time at the Minotauro supercomputer. M .S. is supported by the European Union Horizon 2020 research and innovation programme under Marie Sklodowska-Curie Action Individual Fellowship grant agreement no. 101026158., With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000917-S)., Peer reviewed

Coordinates (input files and equilibrated structures) corresponding to the MD simulations reported in Sahihi and Faraudo, J. Chem. Inf. Model. 2022, 62, 16, 3814–3824 https://doi.org/10.1021/acs.jcim.2c00562 . Please cite this publication and the dataset in any use of the data.

The coordinate files in pdb format include fully glycosylated structures of the S1 subunit of SARS-CoV-2 spike protein (up and down confirmations) and a polystyrene slab., European Commission:
MAT4COVID - Interaction of SARS-CoV-2 virus with materials: a multi computational simulation study. (101026158), Peer reviewed