Paper Citing NAMD - Abstract
Mori, Yoshiharu; Okumura, Hisashi
Molecular dynamics of the structural changes of helical peptides induced by pressure
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2970-2981, NOV 2014
An AK16 peptide and a C-peptide analog are experimentally known to form more helical structures under high-pressure conditions than those at atmospheric pressure, even though most proteins usually unfold at high pressure. To understand the pressure-induced structural changes of the two peptides, molecular dynamics simulations with the simulated tempering method for the isobaric-isothermal ensemble were performed in a wide pressure range from 0.1 MPa to 1.4 GPa. We found that the fraction of the folded state decreases once and then increases with increasing pressure for both peptides. The partial molar volume change of both peptides from the folded state to the unfolded state increases monotonically from a negative value to a positive value as pressure increases. By calculating the radius of gyration and interatomic distances of the AK16 peptide and the C-peptide analog, we found that these peptides are compressed under high-pressure conditions, which causes the folded state to be more stable at high pressure. Furthermore, we found that the salt bridge of the C-peptide analog is broken under high pressure. Proteins 2014; 82:2970-2981. (c) 2014 Wiley Periodicals, Inc.
