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Keywords:

  • protein;
  • hydration water;
  • solvation free energy;
  • molecular dynamics simulation

Abstract

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. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012