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Molecular Dynamics Investigation of Primary Photoinduced Eventsin the Activation of Rhodopsin

By Jan Saam, Emad Tajkhorshid, Shigehiko Hayashi and Klaus Schulten


AbstractRetinal cis-trans isomerization and early relaxation steps have been studied in a 10-ns molecular dynamics simulation of a fully hydrated model of membrane-embedded rhodopsin. The isomerization, induced by transiently switching the potential energy function governing the C11C12 dihedral angle of retinal, completes within 150 fs and yields a strongly distorted retinal. The most significant conformational changes in the binding pocket are straightening of retinal's polyene chain and separation of its β-ionone ring from Trp-265. In the following 500ps, transition of 6s-cis to 6s-trans retinal and dramatic changes in the hydrogen bonding network of the binding pocket involving the counterion for the protonated Schiff base, Glu-113, occur. Furthermore, the energy initially stored internally in the distorted retinal is transformed into nonbonding interactions of retinal with its environment. During the following 10ns, increased mobilities of some parts of the protein, such as the kinked regions of the helices, mainly helix VI, and the intracellular loop I2, were observed, as well as transient structural changes involving the conserved salt bridge between Glu-134 and Arg-135. These features prepare the protein for major structural transformations achieved later in the photocycle. Retinal's motion, in particular, can be compared to an opening turnstile freeing the way for the proposed rotation of helix VI. This was demonstrated by a steered molecular dynamics simulation in which an applied torque enforced the rotation of helix VI

Publisher: The Biophysical Society. Published by Elsevier Inc.
Year: 2002
DOI identifier: 10.1016/S0006-3495(02)75314-9
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