Charging effects on the conformation of protein

Abstract

We describe the contribution of charged residue on global structure of protein. In this paper, we use the Molecular Dynamics simulation and adopt the X-ray structure of melittin as a strarting conformation, at 300 K. The simulation was carried out by adopting Consistent Valence Force field in DISCOVER force field libraries fixed dielectric constant=5 as continuum model. Comparison between Molecular Dynamics simulation of protein and expreiment are in substantial agreement; Analysis of helical content showed the dependence of helical conformation on charged-state of protein. Also, torsion angle trajectories and various conformational properties such as temperature factors indicated that the distribution of charged residues in protein helices reflects the helixstabilizing propensity of those residue. In addition, the simulation reasonably represent the hinge bending flexibility of melittin. By this study, we confirmed that the electriostatic interaction is among the most important factors in determining the structure and function of protein.