Theoretical study on the effect of hydration in several conformers in AcAlaNHMe

Abstract

It is a well-known fact that the water plays an important role in deter mining the tertiary structures of proteins. To study this role of water, di or tripeptide systems are selected frequently for its simplicity. For the case of AlaDipeptide(AcAlaNHMe), those studies revealed that $C_7$ conformation was dominant in vacuo or in non-polar solvents and that $\alpha_R$ and $P_{II}$ conformations were equally dominant in aqueous solvents. However, some other studies showed different results. In this study, energy minimization technique, called Va10a a Quasi-Newton algorithm, have been applied to trace the effect of hydration on the transitions between several conformers of Ala-dipeptide, specially the transition from $C_7$ to $\alpha_R$ and $C_7$ to $P_{II}$, varying the number of waters. The result showed apparant stabilization for $\alpha_R$ and $P_{II}$ structures in comparison to $C_7$ and $C_5$ structures, Empirical potential energy function, consists of torsional energy, non-bonded energy, electrostatic interaction, and hydrogen bonded energy, and central force ST2 model proposed by Stillinger and Rahman, for description of water, have been used.