Molecular dynamics of cis-trans isomerization in rhodopsin

Birge, Robert R.; Hubbard, Lynn M.

doi:10.1021/ja00527a008

Cited by 175 publications

(118 citation statements)

References 29 publications

(43 reference statements)

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“…This intersection point shows a geometrical displacement consistent with those of the reported CI-Rh intersection (14). The computed high crossing probability is also consistent with previous studies including the related system bR (5,6,20). According to the result above the linear momentum of Fig.…”

Section: Resultssupporting

confidence: 90%

Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry

Frutos

Andruniów²,

Santoro³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

272

420

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The primary event that initiates vision is the photoinduced isomerization of retinal in the visual pigment rhodopsin (Rh). Here, we use a scaled quantum mechanics/molecular mechanics potential that reproduces the isomerization path determined with multiconfigurational perturbation theory to follow the excited-state evolution of bovine Rh. The analysis of a 140-fs trajectory provides a description of the electronic and geometrical changes that prepare the system for decay to the ground state. The data uncover a complex change of the retinal backbone that, at Ϸ60-fs delay, initiates a space saving ''asynchronous bicycle-pedal or crankshaft'' motion, leading to a conical intersection on a 110-fs time scale. It is shown that the twisted structure achieved at decay features a momentum that provides a natural route toward the photoRh structure recently resolved by using femtosecond-stimulated Raman spectroscopy.photoisomerization ͉ rhodopsin ͉ vision T he visual pigment rhodopsin (Rh) (1, 2) is a G protein-coupled receptor containing a 11-cis retinal chromophore (PSB11) bounded to a lysine residue (Lys-296) via a protonated Schiff base linkage (see Fig. 1). While the biological activity of Rh is triggered by the light-induced 11-cis all-trans isomerization of PSB11, this reaction owes its efficiency (e.g., short time scale and high quantum yields) to the protein cavity (1). Recently, the mechanism of the isomerization of retinal in Rh has been investigated by using femtosecond-stimulated Raman spectroscopy (FSRS) (3). Kukura et al. (3) have reported on experimentally derived structures of photoRh and bathoRh, namely the first and second ground-state intermediates of the Rh photocycle.While such progress has provided information on the structural changes achieved 200 fs after light absorption, the faster structural changes prompting the excited-state decay of PSB11 (i.e., the central event of the isomerization mechanism) remain to be established. Indeed, it has been suggested that such decay may occur on a 60-fs time scale through fast hydrogen out-ofplane (HOOP) motion (3), whereas the traditional view points to a slower Ϸ150-fs decay driven by cis-trans isomerization motion (4). In principle, molecular dynamics simulations featuring a quantum chemical description of the chromophore can be used to address such issues. This fact was shown by Warshel (5) using semiempirical quantum chemistry to describe PSB11 and geometrical constraints to account for the protein environment. Later, Birge and Hubbard (6) reported a different semiempirical study of an explicit chromophore-counterion pair evolving along a single coordinate. While the first simulation of the retinal photoisomerization using a full atomic-level protein model (7) was reported for the related receptor bacterio-Rh (bR), attempts to simulate the PSB11 excited-state motion in a complete Rh model are more recent (8-10). On the other hand, a quantitative evaluation of the isomerization coordinate and time scale requires, as a prerequisite, an accurate excited-st...

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Section: Resultssupporting

confidence: 90%

Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry

Frutos

Andruniów²,

Santoro³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

272

420

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“…An interesting difference in the charge alternation pattern has been observed upon rotating the chromophore around the C1 1-C12 "double bond" in excited state (16). The INDO-CISD calculations for the excited state predict an extra polarization at 90" of rotation around the Cl l-C12 bond.…”

Section: Charge Distributionmentioning

confidence: 99%

“…In Fig. 5 we have collected some previous INDO-CISD and MNDOC results from the literature (16,20). The charges obtained by the SLG wave function (cf.…”

Section: Charge Distributionmentioning

confidence: 99%

Effect of protonation on the ground state properties of retinal analogs: an ab-initio study

Poirier¹,

Yadav²,

Śurján³

1987

Can. J. Chem.

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. Can. J. Chem. 65, 892 (1987). The ground state properties (bond lengths, bond orders, net atomic charge distribution) of various cis and trans isomers of retinal analogs have been studied at ab initio SCF and correlated levels. The effect of protonation on the properties of the retinal Schiff base analogs has also been studied. Convergence in various properties has been observed with increasing chain length justifying the use of smaller analogs mimicking retinal. Convergence is, however, slower for the protonated retinal Schiff base analogs. The protonated retinal Schiff base analogs show an increased conjugation reflected in the bond orders, bond lengths, and in the decrease in the HOMO-LUMO gap. The nodal characteristics of the HOMO of the protonated retinal Schiff base analog also indicate a strong conjugation in the vicinity of the protonated nitrogen. Based on the results of calculations at the correlated level, the sudden polarization charge transfer mechanism is shown to be an artifact of HF-based methods used in the calculations. Utilisant des mCthodes ab initio en champ auto-cohhent et a des niveaux permettant d'Ctablir une corrtlation, on a CtudiC les propriCtCs a 1'Ctat fondamental (longueurs des liaisons, ordres des liaisons, distributions des charges atomiques nettes) des divers isomkres cis et trans d'analogues du retinal. On a aussi CtudiC l'effet de la protonation sur les propriCtts d'analogues des bases de Schiff du rCtinal. On a observk une convergence des diverses proprittts avec une augmentation de la longueur de la chaine et cette observation justifie l'utilisation d'analogues plus petits qui reproduisent les proprittCs du rCtinal; toutefois, la convergence est plus lente pour les analogues protonCs des bases de Schiff du retinal. Les analogues protones des bases de Schiff du rCtinal prksentent une plus grande conjugaison qui se rkflkte dans les ordres et les longueurs des liaisons et par une diminution de la diffkrence entre la haute occupCe et la basse vacante. Les caracttristiques nodales de la haute occupte de I'analogue proton6 de la base de Schiff du rttinal suggkrent qu'il existe une forte conjugaison au voisinage de I'azote protont. En se basant sur les rCsultats de ces calculs aux niveaux oh l'on peut ttablir une corrklation, on dCmontre que la polarisation soudaine dans le mkcanisme de transfert de charge n'a pas de signification physique et qu'elle est inhCrente aux mkthodes basCes sur HF qui sont utilistes dans les calculs.[Traduit par la revue]

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“…For example, when only one rotational degree of freedom is included [12], rhodopsin cannot isomerize quickly because the moment of inertia is too Methyl-hydrogen steric interactions break the planarity of the molecule and contribute to ultrafast photoisomerization. great.…”

Section: Introductionmentioning

confidence: 99%

A vision for ultrafast photoisomerization

Aalberts

Stabenau

2010

Physica A: Statistical Mechanics and its Applications

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We propose a simple physical mechanism to explain the ultrafast first step of vision, a photoinduced cis to trans rotation of retinal. In the ground state, the torsional stability of π bonds is countered by Coulomb interactions acting between the π lobes; the torsional dependence for Coulomb interactions is absent in the often-used Ohno approximation, but restored with our formula. After photoexcitation, the bonding weakens causing the destabilizing terms to dominate. The twist in the ground state due to steric interactions surrounding the 11-cis bond increases the initial torque and thus the speed of the reaction.

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Molecular dynamics of cis-trans isomerization in rhodopsin

Cited by 175 publications

References 29 publications

Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry

Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry

Effect of protonation on the ground state properties of retinal analogs: an ab-initio study

A vision for ultrafast photoisomerization

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