Quantum Chemistry:  Molecular Dynamics Study of the Dark-Adaptation Process in Bacteriorhodopsin

Logunov, Ilya; Schulten, Klaus

doi:10.1021/ja953091m

Cited by 52 publications

(53 citation statements)

References 75 publications

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“…They reflect the changes due to the vibrationally hot dynamics in the ground state after the initial product assignment was made. This is also manifested by the large number of structures that could not be assigned to one of the types of (20) 25 (25) torsional motion at the end of the dynamics since at least one of the dihedral angles was located between 60 and 120°, that is, far away from planarity. Because of the large number of undetermined motions it is difficult to distinguish trends in the product formation.…”

Section: Resultsmentioning

confidence: 99%

“…These photoisomerization processes 8,9 belong to the fastest photochemical reactions in nature 1 and have been studied extensively in experimental [10][11][12][13] and theoretical investigations. [14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31] The large size of RPSB and the multireference character of the electronic wave function make high level accurate calculations very difficult to perform, especially when dynamics simulations are intended. Because of this limitation, the photochemical properties of RPSB have been studied theoretically mostly by simulation of model systems.…”

Section: Introductionmentioning

confidence: 99%

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Is the Photoinduced Isomerization in Retinal Protonated Schiff Bases a Single- or Double-Torsional Process?

2009

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Nonadiabatic photodynamical simulations are presented for the all-trans and 5-cis isomers of the hepta-3,5,7-trieniminium cation (PSB4) with the goal of characterizing the types of torsional modes occurring in the cis-trans isomerization processes in retinal protonated Schiff base (RPSB), the rhodopsin and bacteriorhodopsin chropomhore. Steric hindrance of these processes due to environmental effects have been modeled by imposing different sets of mechanical restrictions on PSB4 and studying its response in the photodynamics. Both the mechanism toward the conical intersection and the initial phase of the hot ground state dynamics has been studied in detail. A total of 600 trajectories have been computed using a complete active space self-consistent field wave function. Careful comparison with higher level methods has been made in order to verify the accuracy of the results. The most important mechanism driving restricted PSB4 isomerization in the excited state is characterized by two concerted twist motions (bipedal and closely related to it nonrigid bipedal) from which only one torsion tends to be continued during the relaxation into the ground state. The one-bond-flip is found to be important for the trans isomer as well. The main isomerization trend is a torsion around C(5)C(6) (equivalent to C(11)C(12) in RPSB) in the case of the cis isomer and around C(3)C(4) (C(13)C(14) in RPSB) in the case of the trans isomer. The simulations show an initial 70 fs relaxation into twisted regions and give an average internal conversion time of 130-140 fs, timings that are fully compatible with the general picture described by femtosecond transient absorption spectroscopic studies.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Is the Photoinduced Isomerization in Retinal Protonated Schiff Bases a Single- or Double-Torsional Process?

2009

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“…Given this centrality of function, the accessibility switch has been extensively explored in structural [9]–[12], spectroscopic [13]–[17], and computational studies [18]–[21]. Hypotheses regarding the molecular determinants of the accessibility switches have implicated the retinal/SB configuration [9], [16], [18]–[20], [22], changes in protein structure [13], [14], [23], [24], or a combination of multiple factors including water molecules [15], [25]–[29] as contributors to the switch function.…”

Section: Introductionmentioning

confidence: 99%

Schiff Base Switch II Precedes the Retinal Thermal Isomerization in the Photocycle of Bacteriorhodopsin

2013

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In bacteriorhodopsin, the order of molecular events that control the cytoplasmic or extracellular accessibility of the Schiff bases (SB) are not well understood. We use molecular dynamics simulations to study a process involved in the second accessibility switch of SB that occurs after its reprotonation in the N intermediate of the photocycle. We find that once protonated, the SB C15 = NZ bond switches from a cytoplasmic facing (13-cis, 15-anti) configuration to an extracellular facing (13-cis, 15-syn) configuration on the pico to nanosecond timescale. Significantly, rotation about the retinal’s C13 = C14 double bond is not observed. The dynamics of the isomeric state transitions of the protonated SB are strongly influenced by the surrounding charges and dielectric effects of other buried ions, particularly D96 and D212. Our simulations indicate that the thermal isomerization of retinal from 13-cis back to all-trans likely occurs independently from and after the SB C15 = NZ rotation in the N-to-O transition.

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“…Subsequent time-resolved experiments 3,8-13 observed a photoisomerization time of ∼100-200 fs for rhodopsin and bR, which is in the range of the theoretical prediction. Several simulation studies of the photoisomerization process in rhodopsin and bR were reported 1,[14][15][16][17][18][19] since the early work of ref 6. However, these instructive studies left major questions open. The studies of Birge and co-workers 14,15,20 used basically a onedimensional model, assuming the rate of the vibrational relaxation rather than calculating it (see section III).…”

Section: Introductionmentioning

confidence: 99%

Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event

2001

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The quantum dynamics of the primary photoisomerization event in bacteriorhodopsin is studied by a semiclassical trajectory approach. The relevant surface crossing probability is evaluated from the wave functions and potential surfaces of a hybrid quantum mechanical/molecular mechanics (QM/MM) Hamiltonian of the complete chromophore-protein-solvent system. The QM/MM model combines consistently the quantum mechanical Hamiltonian of the chromophore with the microscopic electric field of the ionized groups and induced dipoles of the protein-solvent system. The QCFF/PI Hamiltonian of the chromophore is adjusted to reproduce relevant ab initio results. The nonadiabatic coupling term <ψ 1 |∂ψ 0 /∂t> is calculated numerically from the corresponding wave functions. The simulations are performed by combining the ENZYMIX and QCFF/PI molecular modeling programs. The effect of the protein on the absorption spectrum of the chromophore is examined. It is found that this spectrum reflects the effect of the protein permanent dipoles, ionized residues, water molecules (in and around the protein), and the induced dipoles of the protein plus water system. Next, we probe the motion along the excited state surface. It is demonstrated, in agreement with our early study and more recent works, that the motion starts with bond vibrations and evolves to a torsional motion. It is also found that we are dealing with an overdumped motion. Major emphasis is placed on the nature of the surface crossing process. In particular, we try to examine the origin of the very large probability of crossing in the π/2 region. A large crossing probability was obtained first in our early simulation (Warshel, A. Nature 1976, 260, 679), but its origin was not explored in details. Such large crossing probabilities can be obtained by passing through strict conical intersections (where the two surfaces "touch" each other) or by passing through regions with large nonadiabatic coupling and small energy gap (such regions are usually close to conical intersections). It is found that some trajectories pass through strict conical intersections, whereas others cross through regions with nonzero energy gap and a large nonadiabatic coupling. This feature helps probably to ensure the stability of the photobiological process with regards to various mutations. The average surface crossing probability and our previously derived expression (Weiss, R. M.; Warshel, A. J. Am. Chem. Soc. 1979, 101, 6131) appear to provide an excellent approximation for the calculated quantum yield. Furthermore, the calculated quantum yield reproduces the corresponding observed value. Finally, we examine the behavior of trajectories that cross to the ground state before the π/2 region. Our finding that these trajectories are deflected backward allow us to exclude models where the surface crossing occurs before the π/2 region.

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Quantum Chemistry: Molecular Dynamics Study of the Dark-Adaptation Process in Bacteriorhodopsin

Cited by 52 publications

References 75 publications

Is the Photoinduced Isomerization in Retinal Protonated Schiff Bases a Single- or Double-Torsional Process?

Is the Photoinduced Isomerization in Retinal Protonated Schiff Bases a Single- or Double-Torsional Process?

Schiff Base Switch II Precedes the Retinal Thermal Isomerization in the Photocycle of Bacteriorhodopsin

Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event

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