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Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

  • Conference paper
Quantum Mechanical Simulation Methods for Studying Biological Systems

Part of the book series: Centre de Physique des Houches ((LHWINTER,volume 4))

Abstract

A combination of molecular dynamics and quantum chemistry techniques have been employed to study the electronic excitation and conformational potential surface of retinal in the binding site of bacteriorhodopsin (bR). The CASSCF(6,9)/6–31G level of “ab initio” calculations (within Gaussian92) has been used for the treatment of both the ground (SO) and excited (S1) states of retinal. Charges of all atoms in the protein are represented by spherical Gaussians and explicitly included in the electronic Hamiltonian of retinal. Spectral properties have been analyzed for the native bR pigment as well as for its D85N mutant. The calculated relative shift in the absorption maxima between the two pigments is in better agreement with experiment than the computed absolute parameters of the absorption line shapes. The dark adaptation processes in bacteriorhodopsin (which involves rotation around the 13–14 and the 15-N retinal double bonds) has been modelled by following the pre-defined reaction coordinate. Our simulations support the notion that the isomerization process is catalyzed by the protonation of an aspartic acid (Asp85) side group of bacteriorhodopsin.

This work was supported by grants from the National Institutes of Health (PHS 5 P41 RR05969-04), the National Science Foundation (BIR-9318159), and the Roy J. Carver Charitable Trust.

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Authors and Affiliations

  1. Beckman Institute and Departments of Physics and Biophysics, University of Illinois at Urbana-Champaign, 405 North Matthews, Urbana, Illinois, 61801, USA

    I. Logunov & K. Schulten

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  1. I. Logunov
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  2. K. Schulten
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  1. Institut de Biologie Structurale, Laboratoire de Dynamique Molculaire, 41 avenue des Martyrs, 38027, Grenoble Cedex 1, France

    Dominique Bicout  & Martin Field  & 

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© 1996 Springer-Verlag Berlin Heidelberg

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Logunov, I., Schulten, K. (1996). Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin. In: Bicout, D., Field, M. (eds) Quantum Mechanical Simulation Methods for Studying Biological Systems. Centre de Physique des Houches, vol 4. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-09638-3_10

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  • DOI: https://doi.org/10.1007/978-3-662-09638-3_10

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