CONCERTED MOTIONS IN THE PHOTOACTIVE YELLOW PROTEIN

Molecular dynamics simulations have been performed with the aim of ide ntifying concerted backbone motions in the photoactive yellow protein. Application of the essential dynamics method revealed large, chromoph ore-linked fluctuations of the protein in the ground state, as well as in a form containing the isomerized chromophore. Various loops become more mobile upon isomerization of the chromophore, including a loop w hich is part of the PAS domain moth, found in light perception protein s. The hinge points identified in these fluctuations correlate with th e positions of evolutionary conserved glycines. The results derived fr om the simulations directly correlate with available experimental data , provide a framework for understanding the dynamic behaviour of the y ellow protein and give clues to subsequent steps in the signal transdu ction pathway.