Paper Citing NAMD - Abstract
Yakubovich, Alexander V.; Solov'yov, Andrey V.; Greiner, Walter
Conformational Changes in Polypeptides and Proteins
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 110:257-269, JAN 2010
We consider the process of alpha-helix <-> random coil transition in alanine polypeptides. For this, we suggest a novel theoretical method based on the statistical mechanics. We apply the developed formalism for the description of the thermodynamical properties of alanine polypeptides of different length. We analyze the essential thermodynamical properties of the system such as heat capacity, the phase transition temperature, and the latent heat of the phase transition. Alternatively, we have obtained same thermodynamical characteristics from the molecular dynamics simulations and compared the results with the results of statistical mechanics calculations. The comparison proves the validity of the statistical mechanics approach and establishes its accuracy. We extend the developed formalism for the description of the alpha-helix <-> random coil transition in the presence of the effects of solvent. The performed analysis explains prominent decrease of the phase transition temperature of the polypeptide in water solution. (C) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 110: 257-269, 2010
