Effect of solvents on short peptides structure: A molecular dynamics study

“The effect of (i) Methanol, (ii) Water and (iii) Glycerol on the stability and flexibility of (i) Polylysine, (ii) Polytryptophan and (iii) Ribonuclease A speptide was studied. Appropriate models for all the solvents were used to avoid unrealistic and abnormal behavior of the peptides solvated in them. GROMACS Software was used to perform all the simulations, generate the trajectory followed by the atoms and finally to analyze the results. All the peptides were first equilibrated and simulated for about 500ps in vacuum and then in different solvents and solvent mixtures for about 350ps. The equilibration simulations were stopped when the potential energy oscillated about a mean value and when the charge was equally distributed across the box. Data was stored after every 0.2ps, for the last 50ps for analyzing both the solvent and the peptide structures. Hydrogen bonding, radial densities, correlation functions and Ramachandran plots are reported. The simulation results indicate that the type of solvent largely affects the structure and flexibility of a peptide. The chemical nature of the polypeptide strongly affects its interaction with the solvent. Further work needs to be done to determine the effect of the presence of different solvents on the secondary structures by studying longer peptides”--Abstract, page iii