Molecular dynamics simulation of the M intermediate of photoactive yellow protein in the crystalline state

For the M intermediate (putative signaling state) of photoactive yellow protein, there are serious disagreements between the crystalline structure based on time-resolved Laue diffraction analysis and the solution-structure obtained from various spectroscopic studies. Here, to explore the origin of such disagreements, molecular dynamics (MD) simulation for the crystalline state is performed and the results are compared with those from MD simulation for the solution state reported previously.