Molecular dynamics simulations of Echovirus1

Abstract

Covalently attaching thiol-functionalized gold nanoclusters to virus surfaces could provide new visualization method for tracking viruses with TEM [1]. This type of imaging could provide better resolution images and shed light, e.g., on virus infection pathways [1]. The controllable binding of these nanoclusters would be essential, and this requires atomic scale information on potential binding sites. In addition atomic scale structural information on virus-nanocluster complexes and their dynamics are needed. Both types of information are potentially obtainable from an all-atom simulation. The aim of this work was to construct a valid model system and set up simulation for full Echovirus 1 capsid in salt solution. A model system of the full Echovirus 1 in salt solution is proposed and simulated up to 200 ns. Also comparative systems with different ligands are proposed and simulated. Based on the simulation the validity of the model is assessed and established in terms of convergence of energy terms, structure and relations to experiments. More detailed look is given considering behavior of potential binding sites, hydrophobic pocket and different pocket factors and cysteine residues. The recognized points of interest to be studied in further simulations are discussed. The proposed model then lays foundation for more extensive studies of this virus with molecular dynamics simulations.