Regensburg 2022 – scientific programme
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BP: Fachverband Biologische Physik
BP 7: Poster 1
BP 7.16: Poster
Monday, September 5, 2022, 18:00–20:00, P1
Characterizing flexibility and mobility in the natural mutations of the SARS-CoV-2 spikes — James Panayis1, Dom Bellini2, and •Rudolf A. Römer1 — 1Department of Physics, University of Warwick, Coventry, CV4 7AL, UK — 2MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
We perform in-silico modelling of the SARS-CoV-2 spike protein and its mutations, using structures from the Protein Data Bank (PDB), to ascertain their dynamics, flexibility and rigidity. Identifying the precise nature of the dynamics for the spike proteins enables, in principle, the use of further in-silico design methods to quickly screen both existing and novel drugs that may hinder these natural dynamics. We use a recent protein flexibility modelling approach, combining methods for deconstructing a protein structure into a network of rigid and flexible units with a method that explores the elastic modes of motion of this network, and a geometric modelling of flexible motion. We also conduct this analysis on synthetic structures of some newer variants (α, β, γ, δ, λ, o) for some of which structure files are not yet available from the PDB. All proteins are thermalised for at least 1ns with NAMD to human body temperature before the flexibility analysis.