A molecular dynamics study for the structure determination of the signaling state in the photocycle of photoactive yellow protein.
The structure of the putative signaling state in the photocycle of photoactive yellow protein, pB, is investigated by molecular dynamics (MD), steered MD, and free energy calculations. The present work suggests that the structural change toward pB involves a translational displacement of the N-terminal region. The structural rearrangement around alpha3, which is induced by the water molecular migration to the interior part of the protein during the formation of pB', makes the joint region between beta1 and the N-terminal domain flexible and induces the structural displacement of beta1 and the N-terminal domain.
Kamiya
Motoshi
M
Chemistry Department, Nagoya University, 1, Furocho, Chikusa-ku, Nagoya, Japan 464-8602. kamo@chem.nagoya-u.ac.jp
Ohmine
Iwao
I
D001426:Bacterial Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D020283:Photoreceptors, Microbial / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D001426:Bacterial Proteins; D020283:Photoreceptors, Microbial; C050162:photoactive yellow protein, Bacteria; D014867:Water