Reorganization energy of protein electron transfer reaction: Study with structural and frequency signature

A new formalism is developed that enables us to analyze reorganization energy of the protein electron transfer reaction from a classic molecular dynamics trajectory with special emphasis on structural and frequency signature. In particular, energy contributions are divided into those from interactions of donor or acceptor sites with surrounding protein or water environments. This formalism is applied to cytochrome c. The protein environment is found to be soft as the water environment and, therefore, contributes similarly to the reorganization energy.