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Ground-state properties of the retinal molecule: from quantum mechanical to classical mechanical computations of retinal proteins |
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| Authors: | Ana-Nicoleta Bondar Michaela Knapp-Mohammady S��ndor Suhai Stefan Fischer Jeremy C Smith |
| Institution: | 1. Theoretical Molecular Biophysics, Department of Physics, Freie Universit?t Berlin, Arnimallee 14, 14195, Berlin, Germany 2. Department of Physiology and Biophysics, School of Medicine, University of California at Irvine, Med. Sci. I, D374, Irvine, CA, 92697-4560, USA 3. Molecular Biophysics Department and Division of Functional Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany 4. Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany 5. Computational Biochemistry, IWR, University of Heidelberg, Speyerstrasse 6, room H304, 69115, Heidelberg, Germany 6. Oak Ridge National Laboratory, PO Box 2008 MS6164, Oak Ridge, TN, 37831-6164, USA 7. Department of Biochemistry and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Ave, Knoxville, TN, 37996, USA |
| Abstract: | Retinal proteins are excellent systems for understanding essential physiological processes such as signal transduction and ion pumping. Although the conjugated polyene system of the retinal chromophore is best described with quantum mechanics, simulations of the long-timescale dynamics of a retinal protein in its physiological, flexible, lipid-membrane environment can only be performed at the classical mechanical level. Torsional energy barriers are a critical ingredient of the classical force-field parameters. Here we review briefly current retinal force fields and discuss new quantum mechanical computations to assess how the retinal Schiff base model and the approach used to derive the force-field parameters may influence the torsional potentials. |
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