MD simulation of echovirus capsid: atomic charges of pocket factors by multiconformational RESP

Abstract

Molecular dynamics simulation of the complex of the capsid of echovirus 1 and a pocket factor, i.e. palmitic acid (PLM), was performed under rotational symmetry boundary conditions, using the APRICOT program. Echovirus belongs to the picornavirus family, and are frequently responsible for febrile illness and viral meningitis. A milistic acid (MYR) is bound to the N terminal of VP4 of the capsid. The atomic charges of PLM and MYR were determined by the restrained electrostatic potential fit (RESP fit), using the electrostatic potential calculated at the HF/6-31G* level using Gaussian03. The protonation states of the 22 histidine residues in the X-ray structure (pdb-ID:1EV1) were determined by considering the neighbor atoms and by calculation with the protonate3D program of the modeling software MOE. Atomic fluctuations calculated from the simulation were compared with the temperature factor of the X-ray analysis of the capsid of a homologous echovirus 11, because temperature factors are not reported in 1EV1.