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Theoretical Chemistry Accounts

, Volume 130, Issue 4–6, pp 1169–1183 | Cite as

Ground-state properties of the retinal molecule: from quantum mechanical to classical mechanical computations of retinal proteins

  • Ana-Nicoleta BondarEmail author
  • Michaela Knapp-Mohammady
  • Sándor Suhai
  • Stefan Fischer
  • Jeremy C. SmithEmail author
Regular Article

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.

Keywords

Retinal Retinal proteins Quantum mechanical Force-field parameters 

Notes

Acknowledgments

This work has been supported in part by the Deutsche Krebsforschungszentrum and by the Deutsche Forschungsgemeinschaft (SM 63/7). J. C. S. was supported by a Laboratory-Directed Research and Development grant from the United States Department of Energy. A.-N. B. was supported in part by grants GM74637 and GM086685 from the National Institutes of General Medical Sciences (at UC Irvine) and by a Marie Curie International Reintegration Grant (FP7-PEOPLE-2010-RG 276920) at the Freie Universität Berlin. We thank the Norddeutscher Verbund für Hoch-und Höchstleistungsrechner (HLRN) for an Award of computing time (to A.-N. B).

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Ana-Nicoleta Bondar
    • 1
    • 2
    Email author
  • Michaela Knapp-Mohammady
    • 3
  • Sándor Suhai
    • 4
  • Stefan Fischer
    • 5
  • Jeremy C. Smith
    • 6
    • 7
    Email author
  1. 1.Theoretical Molecular Biophysics, Department of PhysicsFreie Universität BerlinBerlinGermany
  2. 2.Department of Physiology and Biophysics, School of MedicineUniversity of California at IrvineIrvineUSA
  3. 3.Molecular Biophysics Department and Division of Functional Genome AnalysisGerman Cancer Research CenterHeidelbergGermany
  4. 4.Molecular Biophysics DepartmentGerman Cancer Research CenterHeidelbergGermany
  5. 5.Computational Biochemistry, IWRUniversity of HeidelbergHeidelbergGermany
  6. 6.Oak Ridge National LaboratoryOak RidgeUSA
  7. 7.Department of Biochemistry and Molecular BiologyUniversity of TennesseeKnoxvilleUSA

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