Classical Molecular Dynamics Simulation of the Photoinduced Electron Transfer Dynamics of Plastocyanin

TitleClassical Molecular Dynamics Simulation of the Photoinduced Electron Transfer Dynamics of Plastocyanin
Publication TypeJournal Article
Year of Publication1997
AuthorsUngar, LW, Scherer, NF, Voth, GA
JournalBiophys J
KeywordsBinding Sites Computer Simulation Copper Electron Transport Mathematics Models, Molecular Photochemistry Plastocyanin/*chemistry/*metabolism/radiation effects Probability *Protein Conformation

Classical molecular dynamics simulations are used to investigate the nuclear motions associated with photoinduced electron transfer in plastocyanin. The blue copper protein is modeled using a molecular mechanics potential; potential parameters for the copper-protein interactions are determined using an x-ray crystallographic structure and absorption and resonance Raman spectra. Molecular dynamics simulations yield a variety of information about the ground (oxidized) and optically excited (charge-transfer) states: 1) The probability distribution of the potential difference between the states, which is used to determine the coordinate and energy displacements, places the states well within the Marcus inverted region. 2) The two-time autocorrelation function of the difference potential in the ground state and the average of the difference potential after instantaneous excitation to the excited state are very similar (confirming linear response in this system); their decay indicates that vibrational relaxation occurs in about 1 ps in both states. 3) The spectral densities of various internal coordinates begin to identify the vibrations that affect the optical transition; the spectral density of the difference potential correlation function should also prove useful in quantum simulations of the back electron transfer. 4) Correlation functions of the protein atomic motions with the difference potential show that the nuclear motions are correlated over a distance of more than 20 A, especially along proposed electron transport paths.