Constant-pH molecular dynamics in AWSEM coarse-grained model

ERNESTO A. ROMAN; FRANCO TAVELLA

Ciudad Autónoma de Buenos Aires

Simposio; Protein Biophysics at the End of the World v2.0; 2017

Protein Biophysics at the End of the World

In this work we implement a coarse-grained molecular dynamic simulation to predict the shifted pKa of three model proteins: NTL9, HEWL and BBL. Given that such shifts come from electrostatic interactions we modified the current code of the AWSEM force field to change dynamically the charge of residues (Asparagine, Glutamic acid, Lysine, Histidine, N-C terminals and Arginine) and take in account for the effects of the solution pH. Moreover we use a Debye-Huckel form of the interaction to model the effects of salt concentrations in the solution. The sampling of the state space is made by a Metropolis Monte Carlo criterion. Our results show that the AWSEM representation of the protein improves previous results found in literature about coarse-grained constant pH molecular dynamics for non buried residues  and suggests that we need another considerations for buried ones.