Study on the effect of cosolvent in peptide solution and the electrostatic effect of protein conformation

Abstract

We have performed molecular dynamics (MD) simulations at 300 K on the tricomponent solution containing tripeptide, cosolvent and water molecules to investigate the structural and energetic effects of cosolvents on the peptide and water molecules. We use the glycerol or urea molecule as cosolvent and Gly-Ala-Phe (GAF) as tripeptide in each simulation. The concentration of cosolvent is adjusted to 6~7V% of water. We have also carried out the MD simulations on the two component solution without tripeptide (GAF), i.e., only urea or glycerol molecules, to compare with the above system. We analyze the structural and dynamic change of the tripeptide by the torsional angle distribution and the root-mean-square (RMS) fluctuation. The interactions between all constituent molecules are analyzed by their hydrogen-bonding characteristics. We examine the water structure through hydrogen-bond, the distribution of energies and hydrogen-bonded circular networks, ring. Cosolvent-induced conformational changes occur in the Ala residue in urea solution. The residue, Ala, interacts with urea molecules substituted for water molecules through hydrogen-bond. The water structure around the peptide is slightly more ordered in glycerol solution where glycerol is excluded in the vicinity of peptide. In order to examine in detail the effect of ionizable residues on the stability of α-helical structure, we have performed molecular dynamics simulation on melittin under the controlled pH with macroscopic dielectric model. We simulate at +3-charged, +6-charged and totally uncharged states of melittin, respectively. From these calculations, we obtain various conformational properties such as helical contents, torsion angle trajectories, temperature factors and end-to-end distance. +3-charged state correponding to basic pH range shows the most stable structure. Our analysis conclude that helix is least stable at neutral pH including six positively charged residues and helicity increases as pH ap...