The Stability of Protein Secondary Structures in Aqueous Solution

Abstract

In this article we review the results of our applications of MD simulations with specialized sampling techniques to the study of secondary structural stability in solution. We present free energy surfaces as functions of conformational reaction coordinates which correspond to the folding (and unfolding) of several model secondary structures: an isolated amide hydrogen bond, reverse turns in blocked di‐amino acids, α helices in blocked tri‐ and tetra‐amino acids, and an antiparallel β sheet formed by two blocked amino acids. The free energy surfaces allow us to identify stable structures along the reaction coordinates and, in some cases, to estimate the timescales for the interconversion of these structures. Furthermore, we use thermodynamic decompositions of free energy differences taken from the surfaces to understand the differences of the relative stabilities of various folded and unfolded structures in terms peptide‐peptide and peptide‐solvent interactions. The results presented herein should be usefu...