Molecular dynamics simulation study on the high-pressure behaviour of an AK16 peptide

Abstract

While most proteins unfold under high-pressure conditions, some high-pressure experiments suggest that an AK16 peptide forms more helical structures. In order to understand this abnormality, 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. It was 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 behaviour under high-pressure conditions is consistent with the experimental results. The radius of gyration of highly helical structures decreases with increasing pressure. Moreover, interatomic distances of AK16 become shorter at high pressure than at low pressure. These behaviours indicate that the helical structures are squeezed by high pressure.

Keywords::

• helical peptide
• pressure dependence
• partial molar volume
• generalised-ensemble algorithm
• simulated tempering

Acknowledgements

Some of the computations were performed on the supercomputers at the Research Center for Computational Science, Institute for Molecular Science. This work was supported, in part, by Grants-in-Aid for JSPS Fellows.