Intensity fluctuations of the copper site resonant vibrational modes as observed by MD simulation in single plastocyanin molecule

The bond distance of the copper–sulfur in the plastocyanin (PC) active site has been followed along the molecular dynamics (MD) simulation trajectory, in a single molecule configuration. The power spectrum of the bond distance fluctuations, calculated for different time intervals, qualitatively reproduces the main spectral features of the experimental resonance Raman spectra of PC. The peak intensities of the vibrational modes appear significantly fluctuate during the dynamical evolution of the system. Such a variability, even if it occurs at an enormously different time scale, is consistent with the fluctuations observed in the experimental Raman spectra of similar systems when the single molecule limit is approached.