Molecular dynamics study of the M412 intermediate of bacteriorhodopsin

Biophysical Journal
D XuK Schulten

Abstract

Molecular dynamics simulations have been carried out to study the M412 intermediate of bacteriorhodopsin's (bR) photocycle. The simulations start from two simulated structures for the L550 intermediate of the photocycle, one involving a 13-cis retinal with strong torsions, the other a 13,14-dicis retinal, from which the M412 intermediate is initiated through proton transfer to Asp-85. The simulations are based on a refined structure of bR568 obtained through all-atom molecular dynamics simulations and placement of 16 waters inside the protein. The structures of the L550 intermediates were obtained through simulated photoisomerization and subsequent molecular dynamics, and simulated annealing. Our simulations reveal that the M412 intermediate actually comprises a series of conformations involving 1) a motion of retinal; 2) protein conformational changes; and 3) diffusion and reconfiguration of water in the space between the retinal Schiff base nitrogen and the Asp-96 side group. (1) turns the retinal Schiff base nitrogen from an early orientation toward Asp-85 to a late orientation toward Asp-96; (2) disconnects the hydrogen bond network between retinal and Asp-85 and tilts the helix F of bR, enlarging bR's cytoplasmic channel; ...Continue Reading

Citations

Dec 26, 2002·Journal of Molecular Recognition : JMR·Günther H Peters, Robert P Bywater
Jan 1, 1996·Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology : Official Publication of the International Retrovirology Association·L DelamarreM C Dokhélar
Mar 17, 1999·Proceedings of the National Academy of Sciences of the United States of America·A DérP Ormos
Jun 6, 1998·Proceedings of the National Academy of Sciences of the United States of America·V RéatG Zaccai
Dec 20, 2015·Biophysical Journal·Marian BreuerJochen Blumberger
Sep 11, 2010·Physical Chemistry Chemical Physics : PCCP·Kazuhiro J FujimotoJun-Ya Hasegawa
Sep 14, 2000·Biochimica Et Biophysica Acta·S P Balashov
Sep 8, 1999·Microbiology and Molecular Biology Reviews : MMBR·G SchäferV Müller

❮ Previous
Next ❯

Related Concepts

Related Feeds

Cardiac Conduction System

The cardiac conduction system is a specialized tract of myocardial cells responsible for maintaining normal cardiac rhythm. Discover the latest research on the cardiac conduction system here.