Water-Mediated Conformations of the Alanine Dipeptide as Revealed by Distributed Umbrella Sampling Simulations, Quantum Mechanics Based Calculations, and Experimental Data

Abstract

An exhaustive umbrella sampling simulation of the alanine dipeptide in solution is reported. The presence of stable Y conformations in solution is assessed by both quantum calculations and experimental data from X-ray and NMR protein-solved structures available in the protein coil library. The agreement between experimental and simulation Ramachandran plots of the dipeptide in solution is excellent. A suitable explanation of the stabilization of the Y conformation mediated by water for the alanine dipeptide is discussed on the basis of Car−Parrinello MD calculations of the dipeptide in water.