Concerted motions in the photoactive yellow protein.
Molecular dynamics simulations have been performed with the aim of identifying concerted backbone motions in the photoactive yellow protein. Application of the essential dynamics method revealed large, chromophore-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 which is part of the PAS domain motif, found in light perception proteins. The hinge points identified in these fluctuations correlate with the positions of evolutionary conserved glycines. The results derived from the simulations directly correlate with available experimental data, provide a framework for understanding the dynamic behaviour of the yellow protein and give clues to subsequent steps in the signal transduction pathway.
van Aalten
D M
DM
Department of Biochemistry and Molecular Biology, University of Leeds, UK.
Hoff
W D
WD
Findlay
J B
JB
Crielaard
W
W
Hellingwerf
K J
KJ
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D004396:Coloring Agents / Q000378:metabolism; D003198:Computer Simulation; D017124:Conserved Sequence; D003460:Crystallization; D005998:Glycine / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020283:Photoreceptors, Microbial; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D016415:Sequence Alignment; D013997:Time Factors
D001426:Bacterial Proteins; D004396:Coloring Agents; D008024:Ligands; D020283:Photoreceptors, Microbial; C050162:photoactive yellow protein, Bacteria; D005998:Glycine