Water-Peptide Dynamics during Conformational Transitions.
Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions and the dynamical correlations of water with the peptide's configurational motions indicate that the water molecules represent an integral part of the molecular system during the conformational changes, in contrast with the metastable periods when water and peptide dynamics are essentially decoupled.
†Nonlinearity and Complexity Research Group, Aston University, Birmingham, B4 7ET, United Kingdom.
Dmitry
D
Nerukh
‡School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom.
Sergey
S
Karabasov
conformational dynamics; conformational transitions; peptide conformations; water dynamics