Study on the thermostability of rubredoxin from pyrococcus furiosus using molecular dynamics simulations

Abstract

The hyperthermostable protein, rubredoxin from Pyrococcus furiosus(RdPf) is 53-residue protein with a three-stranded anti-parallel β-sheet and several loops. The origin of the stability of the protein has been discussed in terms of electrostatic interactions by date. In this paper, the hydrophobic interaction of residues of the surface of the protein was investigated as well as electrostatic interactions. To investigate the effect of changes of electrostatic and hydrophobic interactions on the structure and dynamic property of RdPf, molecular dynamics simulations in solution were performed. Glu 14 has a backbone hydrogen bond with N-terminal and multiple electrostatic interactions with Ala 1, Trp 3, and Phe 29. The multiple electrostatic interactions have the thermal motion of Glu 14 reduced and the hydrogen bond between Glu 14 and Ala 1 remain at higher temperature. In the middle of the β-sheet, three hydrophobic residues, Val 4, Ile 11, and Leu 51 makes a cluster binding three strands of the β-sheet. This cluster aggregates more tightly with increasing temperature to stabilize the β-sheet and furthermore screens the hydrophobic core from the external thermal perturbation. These interactions are considered as important factors among the factors of the hyperthermostability which are not yet known perfectly.