All-atom molecular dynamics simulations of 400 tetrapeptide GXXG (XX stands for any two amino acid residues) have been carried out in water and octane by utilizing the AMBER99 and AMBER03 force fields. The total ~20 �s simulation (>=20 ns per simulation) data are used to analyze the conformational propensity of each amino acid and how it is affected by solvent environment, residue type and force field. In addition, the trajectories are mapped into a coarse grain (CG) representation based on our CG model of protein. The CG bond and bend distributions are analyzed and their correlations to peptide backbone conformation and solvent polarity are obtained. The study aims at investigating the effects of protein backbone conformation among other factors on CG internal parameters for proteins. Furthermore, the conformational propensity of the 20 amino acids provides valuable information on the performance of the employed force fields under polar and nonpolar environments.

Conformational propensity of the 20 amino acids from all-atom molecular dynamics simulations of 400 tetrapeptides (GXXG) and its implication on internal parameter optimization for coarse grain model of protein

244th National Meeting (2012)

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