Paper Citing NAMD - Abstract
Mori, Yoshiharu; Okumura, Hisashi
Pressure-Induced Helical Structure of a Peptide Studied by Simulated Tempering Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4:2079-2083, JUN 20 2013
It is known experimentally that an AK16 peptide forms more alpha-helix, structures with increasing pressure while proteins unfold in general. In order to understand this abnormality, molecular dynamics (MD) simulations with the simulated tempering method for the isobaric-isothermal ensemble were performed in a wide pressure range from 1.0 X 10(-4) GPa to 1.4 GPa. From the results of the simulations, it is found that the fraction of the folded state decreases once and increases after that with increasing pressure. The partial molar volume change from the folded state to unfolded state increases monotonically from a negative value to a positive value with pressure. The behavior under high pressure conditions is consistent with the experimental results. The radius of gyration of highly helical structures decreases with increasing pressure, which indicates that the helix structure shrinks with pressure. This is the reason why the fraction of the folded state increases as pressure increases.
