The investigation of the structures of peptides in different solvents by molecular dynamic simulation method.

In this study by using molecular dynamic simulation (MD) technique, the determination of possible three dimensional conformations of Salmon Calcitonin peptide (sCT) (pdb 2GLH) having secondary structures identified through experimental methods and recently used frequently in the production of protein-based drugs has been aimed. In addition to this, the effects of solvent and temperature on these conformations have been analyzed.For this purpose, the MD simulations have been run for five different solvent (SPC, TIP3p, TIP4p, TIP5p and METHANOL) under the conditions of constant temperature (300K) and pressure (1 atm). Then the possible three dimensional conformations of sCT peptide and the variations of their secondary structures during the simulations have been identified. The results have shown that the percentage-weighted secondary structures of peptide are observed as alpha-helix, random coil, turn and bend segments and, their percentages are dependant on the solvent used. It has been noticed that the results obtained from MD simulations are consistent with experimental results like those of nuclear magnetic resonance (NMR) and circular dichroisim (CD).Besides in order to investigate the effect of temperature on the secondary structures, the MD simulations ranging from 200 K to 500 K have been run under the same conditions in two different solvents. Accordingly, the results have indicated that the secondary structures of three dimensional conformations have turned into different secondary structures with the change in temperature and the type of this transformation depends on the solvent selected.