Solvation effect on the structural change of a globular protein: A molecular dynamics study

摘要

To investigate the relationship between structural change and the solvation effect, we estimated the solvation free energy or excess chemical potential (ECP) of a globular protein by the energy representation method for the protein structure obtained by a molecular dynamic simulation. A large fluctuation of ECP was detected. The estimated ECP along the first principal component axis of protein fluctuation was accompanied with "open-close" structural change, which indicated a smooth and progressive change in ECP. By performing a global water density analysis in the grid space, the water density at the hydration site had a strong correlation with the ECP.