Molecular dynamics simulation of entropy driven ligand escape process in heme pocket.
Molecular dynamics simulations were performed to investigate the gate effect of protein motion on the escape of O(2) from the heme pocket. The existing geometric entropy in a spherical cavity pushes the ligand toward the cavity surface, and then the ligand escape along the cavity surface is controlled by the gate size and gate modulation, i.e., protein dynamics regulate the gating behavior, which is an inherent feature of proteins such as myoglobin. Our simulation results confirm that the ligand escape process is basically entropy driven.
Sheu
Sheh-Yi
SY
Faculty of Life Sciences, Institute of Biochemistry, Institute of Bioinformatics, and Structural Biology Program, National Yang-Ming University, Taipei 112, Taiwan. sysheu@ym.edu.tw