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

A new formalism is developed that enables us to analyze reorganization ener gy of the protein electron transfer reaction from a classic molecular dynam ics trajectory with special emphasis on structural and frequency signature. In particular, energy contributions are divided into those from interactio ns of donor or acceptor sites with surrounding protein or water environment s. This formalism is applied to cytochrome c. The protein environment is fo und to be soft as the water environment and, therefore, contributes similar ly to the reorganization energy.