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- Catalysis of the retinal subpicosecond photoisomerization pr...Catalysis of the retinal subpicosecond photoisomerization process in acid purple bacteriorhodopsin and some bacteriorhodopsin mutants by chloride ions
Biophysical Journal, Volume 71, Issue 3, 1 September 1996, Pages 1545-1553
S.L. Logunov, M.A. el-Sayed and J.K. Lanyi
AbstractThe dynamics and the spectra of the excited state of the retinal in bacteriorhodopsin (bR) and its K-intermediate at pH 0 was compared with that of bR and halorhodopsin at pH 6.5. The quantum yield of photoisomerization in acid purple bR was estimated to be at least 0.5. The change of pH from 6.5 to 2 causes a shift of the absorption maximum from 568 to 600 nm (acid blue bR) and decreases the rate of photoisomerization. A further decrease in pH from 2 to 0 shifts the absorption maximum back to 575 nm when HCl is used (acid purple bR). We found that the rate of photoisomerization increases when the pH decreases from 2 to 0. The effect of chloride anions on the dynamics of the retinal photoisomerization of acid bR (pH 2 and 0) and some mutants (D85N, D212N, and R82Q) was also studied. The addition of 1 M HCl (to make acid purple bR, pH 0) or 1 M NaCl to acid blue bR (pH 2) was found to catalyze the rate of the retinal photoisomerization process. Similarly, the addition of 1 M NaCl to the solution of some bR mutants that have a reduced rate of retinal photoisomerization (D85N, D212N, and R82Q) was found to catalyze the rate of their retinal photoisomerization process up to the value observed in wild-type bR. These results are explained by proposing that the bound Cl- compensates for the loss of the negative charges of the COO- groups of Asp85 and/or Asp212 either by neutralization at low pH or by residue replacement in D85N and D212N mutants.
Abstract | PDF (840 kb) - Molecular Dynamics Simulation of Bacteriorhodopsin's Photois...Molecular Dynamics Simulation of Bacteriorhodopsin's Photoisomerization Using Ab Initio Forces for the Excited Chromophore
Biophysical Journal, Volume 85, Issue 3, 1 September 2003, Pages 1440-1449
Shigehiko Hayashi, Emad Tajkhorshid and Klaus Schulten
AbstractRetinal proteins are photoreceptors found in many living organisms. They possess a common chromophore, retinal, that upon absorption of light isomerizes and thereby triggers biological functions ranging from light energy conversion to phototaxis and vision. The photoisomerization of retinal is extremely fast, highly selective inside the protein matrix, and characterized through optimal sensitivity to incoming light. This article describes the first report of an ab initio quantum mechanical description of the in situ isomerization dynamics of retinal in bacteriorhodopsin, a microbial retinal protein that functions as a light-driven proton pump. The description combines ab initio multi-electronic state molecular dynamics of a truncated retinal chromophore model (-methyl--methylpenta-2,4-dieniminium cation fragment) with molecular mechanics of the protein motion and unveils in complete detail the photoisomerization process. The results illustrate the essential role of the protein for the characteristic kinetics and high selectivity of the photoisomerization: the protein arrests inhomogeneous photoisomerization paths and funnels them into a single path that initiates the functional process. Supported by comparison with dynamic spectral modulations observed in femtosecond spectroscopy, the results identify the principal molecular motion during photoisomerization.
Abstract | Full Text | PDF (320 kb) - QM/MM Study of Energy Storage and Molecular Rearrangements D...QM/MM Study of Energy Storage and Molecular Rearrangements Due to the Primary Event in Vision
Biophysical Journal, Volume 87, Issue 5, 1 November 2004, Pages 2931-2941
Jose A. Gascon and Victor S. Batista
AbstractThe energy storage and the molecular rearrangements due to the primary photochemical event in rhodopsin are investigated by using quantum mechanics/molecular mechanics hybrid methods in conjunction with high-resolution structural data of bovine visual rhodopsin. The analysis of the reactant and product molecular structures reveals the energy storage mechanism as determined by the detailed molecular rearrangements of the retinyl chromophore, including rotation of the (C11–C12) dihedral angle from −11° in the 11- isomer to −161° in the all- product, where the preferential sense of rotation is determined by the steric interactions between Ala-117 and the polyene chain at the C13 position, torsion of the polyene chain due to steric constraints in the binding pocket, and stretching of the salt bridge between the protonated Schiff base and the Glu-113 counterion by reorientation of the polarized bonds that localize the net positive charge at the Schiff-base linkage. The energy storage, computed at the ONIOM electronic-embedding approach (B3LYP/6-31G*:AMBER) level of theory and the → electronic-excitation energies for the dark and product states, obtained at the ONIOM electronic-embedding approach (TD-B3LYP/6-31G*//B3LYP/6-31G*:AMBER) level of theory, are in very good agreement with experimental data. These results are particularly relevant to the development of a first-principles understanding of the structure-function relations in prototypical G-protein-coupled receptors.
Abstract | Full Text | PDF (441 kb) - …more
Copyright © 1996 The Biophysical Society. All rights reserved.
Biophysical Journal, Volume 70, Issue 6, 2875-2881, 1 June 1996
doi:10.1016/S0006-3495(96)79857-0
Research Article
Replacement effects of neutral amino acid residues of different molecular volumes in the retinal binding cavity of bacteriorhodopsin on the dynamics of its primary process
S.L. Logunov, M.A. el-Sayed and J.K. Lanyi
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta 30332–0400, USA.
Abstract
We have determined the rate and quantum yield of retinal photoisomerization, the spectra of the primary transients, and the energy stored in the K intermediate in the photocycle of some bacteriorhodopsin mutants (V49A, A53G, and W182F) in which residue replacements are found to change the Schiff base deprotonation kinetics (and thus the protein-retinal interaction). Because of their change in the local volume resulting from these individual replacements, these substitutions perturb the proton donor-acceptor relative orientation change and thus the Schiff base deprotonation kinetics. These replacements are thus expected to change the charge distribution around the retinal, which controls its photoisomerization dynamics. Subpicosecond transient spectroscopy as well as photoacoustic technique are used to determine the retinal photoisomerization rate, quantum yield, and the energy stored in the K-intermediate for these mutants. The results are compared with those obtained for wild-type bacteriorhodopsin and other mutants in which charged residues in the cavity are replaced by neutral ones. In some of the mutants the rate of photoisomerization is changed, but in none is the quantum yield or the energy stored in the K intermediate altered from that in the wild type. These results are discussed in terms of the shapes of the potential energy surfaces of the excited and ground states of retinal in the perpendicular configuration within the protein and the stabilization of the positive charge in the ground and the excited state of the electronic system of retinal.
