α/310‐Helix transitions in α‐methylalanine homopeptides: Conformational transition pathway and potential of mean force

Publisher Website
Google Scholar
Abstract
The conformational transition between the α‐ and 310‐helical states of α‐methylalanine homopeptides is studied with molecular mechanics. Conformational transition pathways for Ace‐(MeA)n‐NMe withn= 7, 9, and 11 are obtained with the algorithms of Elber and co‐workers [R. Czerminski & R. Elber (1990)International Journal of Quantum Chemistry, Vol. 24, pp. 167–186; A. Ulitsky & R. Elber (1990)Journal of Chemical Physics, Vol. 92, pp. 1510–1511]. The free energy surface, or potential of mean force, for the conformational transition of Ace‐(MeA)9‐NMe is calculated from molecular dynamics simulations, and a method is presented for the decomposition of the free energy surface into the constituent energetic and entropic terms, via the calculation of the required temperature derivativesin situ. For the AMBER/OPLS model employed here, the conformational transition pathways each contain a single 310‐helical‐like transition state, and the transition state potential energy relative to the 310‐conformation is 3 kcal/mol, independent of peptide length. Entropic stabilization in the barrier region significantly lowers the activation free energies for the forward and reverse transitions from the estimates of the barrier heights based simply on potential energy alone. © 1994 John Wiley & Sons, Inc.