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Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: multireference ab initio quantum mechanics/molecular mechanics studies.

ABSTRACT: We have investigated photoabsorption spectra of bovine rhodopsin and its mutants (E122Q and E113Q) by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations as well as retinal in vacuo by pure QM calculations, employing multireference (MR) ab initio and TD-B3LYP methods. The sophisticated MR-SORCI+Q and MRCISD+Q methods extrapolated with respect to adopted approximations can reproduce the experimental absorption maxima of retinal very well. The relatively inexpensive MR-DDCI2+Q method gives absorption maxima blue-shifted by ca. 65 nm from experimental values; however, this error is systematic and thus MR-DDCI2+Q can be used to estimate spectral shifts. In MR calculations, the ground-state energy of retinal at B3LYP geometry is significantly lower than that at CASSCF geometry. Therefore, B3LYP geometry is more reliable than CASSCF geometry, which has a blue-shift error as large as 100 nm in the gas phase. The effect of ground-state geometry on the excitation energies is less critical in the polarizing field of protein environments. At the B3LYP geometry, there is no significant charge transfer upon vertical excitation to the S1 excited-state either from Glu1 13 to retinal or from Schiff-base terminal to beta-ionone ring through the polyene chain. All-trans to 11-cis isomerization of retinal in the gas phase has no influence on the calculated S1 absorbing state, in agreement with experiment. The shoulder of the experimental absorption spectrum of retinal in vacuo at the S1 absorbing band appears to be the second electronic transition (S2) in our calculations, contrary to previous tentative assignment to vibrational state of S1 or to the S1 band of a retinal isomer.

SUBMITTER: Altun A

PROVIDER: S-EPMC2669894 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature

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Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: multireference ab initio quantum mechanics/molecular mechanics studies.

Altun Ahmet A Yokoyama Shozo S Morokuma Keiji K

The journal of physical chemistry. B 20081201 51

We have investigated photoabsorption spectra of bovine rhodopsin and its mutants (E122Q and E113Q) by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations as well as retinal in vacuo by pure QM calculations, employing multireference (MR) ab initio and TD-B3LYP methods. The sophisticated MR-SORCI+Q and MRCISD+Q methods extrapolated with respect to adopted approximations can reproduce the experimental absorption maxima of retinal very well. The relatively inexpensive MR-DDCI2+Q meth ...[more]

PMID: 19367945

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Project description:Reliable studies of enzymatic reactions by combined quantum mechanics/molecular mechanics (QM/MM) approaches, with an ab initio description of the quantum region, presents a major challenge to computational chemists. The main problem is the need for a very large computer time for the evaluation of the QM energy, which in turn makes it extremely challenging to perform proper configurational sampling. A seemingly reasonable alternative is to perform energy minimization studies of the type used in gas-phase ab initio studies. However, it is hard to see why such an approach should give reliable results in protein active sites. To examine the problems with energy minimization QM/MM approaches, we chose the hypothetical reaction of a metaphosphate ion with water in the Ras.GAP complex. This hypothetical reaction served as a simple benchmark reaction. The possible problems with the QM/MM minimization were explored by generating several protein configurations from long MD simulations and using energy minimization and scanning of the reaction coordinates to evaluate the corresponding potential energy surfaces of the reaction for each of these different protein configurations. Comparing these potential energy surfaces, we found major variations of the corresponding minima. Furthermore, the reaction energies and activation energies also varied significantly even for similar protein configurations. The specific coordination of a magnesium ion, present in the active center of the protein complex, turned out to influence the energetics of the reaction in a major way, where a direct coordination to the reactant leads to an increase of the activation energy by 17 kcal/mol. Apparently, using energy minimization to generate potential surfaces for an enzymatic reaction, while starting from a single protein structure, could lead to major errors in calculations of activation free energies and binding free energies. Thus we believe that extensive samplings of the configurational space of the protein are essential for meaningful determination of the energetics of enzymatic reactions. The possible relevance of our conclusion with regard to a recent study of the RasGAP reaction is discussed.

Dataset Information

Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: multireference ab initio quantum mechanics/molecular mechanics studies.

Publications

Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: multireference ab initio quantum mechanics/molecular mechanics studies.

Similar Datasets

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