Pressure-Induced Helical Structure of a Peptide Studied by Simulated Tempering Molecular Dynamics Simulations.
It is known experimentally that an AK16 peptide forms more α-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 × 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.
†Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan.
Yoshiharu
Y
Mori
‡Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan.|§Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan.
Hisashi
H
Okumura
AK16 peptide; generalized-ensemble algorithm; high pressure structure; partial molar volume; pressure dependence