Ab initio, tight-binding and QM/MM calculations of the rhodopsin chromophore in its binding pocket

Phase Transitions

Volumn 77, Issue 1-2, 2004, Pages 31-45

  Sugihara, M ^a   Buss, V ^a   Entel, P ^a   Hafner, J ^b   Bondar, A N ^c   Elstner, M ^d   Frauenheim, T ^d  

^a UNIVERSITY OF DUISBURG ESSEN   (Germany)

^b UNIVERSITY OF VIENNA   (Austria)

^c UNIVERSITY OF HEIDELBERG   (Germany)

^d UNIVERSITY OF PADERBORN   (Germany)

Author keywords

Ab initio molecular dynamics and force field simulations; Rhodopsin

Indexed keywords

AMINO ACIDS; COMPUTER SIMULATION; CONFORMATIONS; ISOMERIZATION; MOLECULAR DYNAMICS; PROTEINS;

AB INITIO MOLECULAR DYNAMICS AND FORCE FIELD SIMULATIONS; RHODOPSIN; SCHIFF BASE; STRUCTURE DATA;

CHROMOPHORES;

EID: 4644221934     PISSN: 01411594     EISSN: None     Source Type: Journal    
DOI: 10.1080/1411590310001621564     Document Type: Conference Paper

References (47)

1. Al-Jandal, N., Farrar, G.J., Kiang, A.S., Humphres, M.M., et al. (1999). A novel mutation within the rhodopsin gene (Thr-94-Ile) causing autosomal dominant congenital stationary night blindness. Hum. Mutat., 13, 75.
2. Baldwin, J., Schertler, G.F.X. and Unger, V.M. (1997). An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. J. Mol. Biol., 272 144.
3. Birge, R.R. (1990). Nature of the primary photochemical events in rhodopsin and bacteriorhodopsin. Biochem. Biophys. Acta., 1016, 293.
4. Birge, R.R., Murray, L.R., Peierce, B.M., Akita, H., et al. (1985). Two-photon spectroscopy of locked-11 -cis-rhodopsin: evidence for a protonated Schiff base in a neutral protein binding site. Proc. Natl. Acad. Sci. U.S.A., 82, 4117.
5. Borhan, B., Souto, M.L., Imai, H., Shichda, Y., et al. (2000). Movement of retinal along the visual transduction path. Science, 288, 2209.
6. Buss, V. (2002). Inherent chirality of the retinal chromophore in rhodopsin-a nonempirical theoretical analysis of chiroptical data. Chirality, 13, 13.
7. Buss, V., Kolster, K., Terstegen, F. and Vahrenhorst, R. (1998). Absolute sense of twist of the C12-C13 bond of the retinal chromophore in rhodopsin - semiempirical and nonempirical calculations of chiroptical data. Angew. Chem. Int. Ed. Engl., 37, 1893.
8. Cohen, G.B., Yang, T., Robinson, P.R. and Oprian, D.D. (1993). Constitutive activation of opsin: Influence of charge at position 134 and size at position 296. Biochemistry, 296, 6111.
9. 13C MAS NMR evidence for pronounced ligand-protein interactions involving the ionone ring of the retinylidene chromophore in rhodopsin. Proc. Natl. Acad. Sci. U.S.A., 99, 9101.
10. Cui, Q., Elstner, M., Kaxiras, E., Frauenheim, T., et al. (2001). AQ m/mm implementation of the self-consistent charge density functional tight-binding (SCC-DFTB) method. J. Phys. Chem. B, 105, 569.
11. Doukas, A.G., Callender, R.H. and Ebrey, T.G. (1978). Resonance Raman studies of bovine metarhodopsin I and metarhodopsin II. Biochemistry, 17, 2430.
12. Elstner, M., Porezag, D., Elsner, J., Haugk, M., et al. (1998). Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties. Phys. Rev. B, 58, 7260.
13. Fahmy, K., Jäger, F., Beck, M., Zvyaga, T.A., et al. (1993). Protonation states of membrane-embedded carboxylic acid groups in rhodopsin and metarhodopsin II: a Fourier-transform infrared spectroscopy study of site-directed mutants. Proc. Natl. Acad. Sci. U.S.A., 90, 10206.
14. Feng, X., Verdegem, P.J.E., Lee, Y.K., Sandström, D., et al. (1997). Direct determination of a molecular torsional angle in the membrane protein rhodopsin by solid-state NMR. J. Am. Chem. Soc., 119, 6853.
15. Fujimoto, Y., Fishkin, N., Pescitelli, G., Decatur, J., et al. (2002). Solution and biologically relevant conformations of enantiomeric 11-cis-locked cyclopropyl retinals. J. Am. Chem. Soc., 124, 7294.
16. Garriga, P. and Manyosa, J. (2002). The eye photoreceptor protein rhodopsin. Structural implications for retinal disease. FEBS Letters, 528, 17.
17. Glusker, J.P. (1998). Directional aspects of intermolecular interactions. Top. Curr. Chem., 198, 1.
18. Gröbner, G., Burnett, I.J., Glaubitz, C., Choi, G., et al. (2000). Observations of light-induced structural changes of retinal within rhodopsin. Nature, 405, 810.
19. Han, M. and Smith, S.O. (1995). NMR constraints of the location of the retinal chromophore in rhodopsin and bathorhodopsin. Biochemistry, 34, 1425.
20. Han, M., DeDecker, B.S., and Smith, S.O. (1993). Localization on the retinal protonated Schiff base counterion in rhodopsin. Biophys. J., 65, 899.
21. Hofmann, K.P. (2000). Late photoproducts and signaling state of bovine rhodopsin. In: Stavenga, D.G., DeGrip, W.J. and Pugh, E.N. Jr. (Eds.), Handbook of Biological Physics, Vol. 3, Chapter 3, p. 91. Elsevier, Amsterdam.
22. Hug, S.J., Lewis, J.W., Einterz, C.M., Thorgeirsson, T.E., et al. (1990). Nanosecond photolysis of rhodopsin: Evidence for a new, blue-shifted- intermediate. Biochemistry, 29, 1475.
23. Kim, J.E., McCamant, D.W., Zhu, L. and Mathies, R.A. (2001). Resonance Raman structural evidence that the cis-trans isomerization in rhodopsin occurs in femtosectonds. J. Phys. Chem. B, 105, 1240.
24. Kresse, G. and Furthmüller, J. (1996). Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. Rev. B, 54, 11169.
25. Mathies, R.A. and Lugtenburg, J. (2000). The primary photoreaction of rhodopsin. In: D.G. Stavenga, W.J. DeGrip and Pugh E.N. Jr. (Eds.), Handbook of Biological Physics, Vol. 3, Chap. 2, p. 55. Elsevier, Amsterdam.
26. Okada, T., Fujiyohi, Y., Silow, M., Navarro, J., et al. (2002). Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography. Proc. Natl. Acad. Sci. U.S.A., 99, 5982.
27. Okada, T., Ernst, O.P. and Palczewski, K. (2001). Crystal structure of rhodopsin: Implications for vision and beyond. Current Opinion Struct. Biol., 11, 420.
28. Okada, T., Palczewski, K. and Hofmann, K.P. (2001). Activation of rhodopsin: new insights from structural and biochemical studies. Trends Biochem. Sci., 26, 318.
29. Okada, T., Trong, I.L., Fox, B.A., Behnke, C.A., et al. (2000). X-ray diffraction analysis of three-dimensional crystals of bovine rhodopsin obtained from mixed micelles. J. Struct. Biol., 130, 73.
30. Palczewski, K., Kumasaka, T., Hori, T., Behnke, C.A., et al. (2000). Crystal structure of rhodopsin: AG protein-coupled receptor. Science, 289, 739.
31. Röhrig, U.F., Guidoni, L. and Rothlisberger, U. (2002). Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations. Biochemistry, 41, 10799.
32. Schertler, G.F.X. and Hargrave, P.A. (1995). Projection structure of frog rhodopsin in two crystal forms. Proc. Natl. Acad. Sci. U.S.A., 92, 11578.
33. Schertler, G.F.X., Villa, C. and Henderson, R. (1993). Projection structure of rhodopsin. Nature, 362, 770.
34. Schoenlein, R.W., Peteanu, L.A., Mathies, R.A. and Shank, C.V. (1991). The first step in vision: Femtosecond isomerization of rhodopsin. Science, 254, 412.
35. Spooner, P.J.R., Sharples, J.M., Verhoeven, M.A., Lugtenburg, J., et al. (2002). Relative orientation between the β-ionone ring and the polyene chain for the chromophore of rhodopsin in native membranes. Biochemistry, 41, 7549.
36. Sugihara, M., Bondar, A.N., Buss, V., Entel, P., et al. (2003a). QM/MM study of the chromophore in rhodopsin and in the first intermediate, (in preparation).
37. Sugihara, M., Buss, V., Entel, P. and Hafner, J. (2003b). The nature of the complex counterion of the chromophore in rhodopsin. J. Phys. Chem. B., (to be submitted).
38. Sugihara, M., Buss, V., Entel, P., Elstner, M., et al. (2002) 11-cis-retinal protonated Schiff base: Influence of the protein environment on the geometry of the rhodopsin chromophore. Biochemistry, 41, 15259.
39. Sugihara, M., Entel, P., Meyer, H., Buss, V., et al. (2000). A molecular-dynamics study of the rhodopsin chromophore using ultrasoft pseudopotentials. Prog. Theor. Phys. Suppl., 138, 107.
40. Tang, L., Ebrey, T.G. and Subramaniam, S. (1995). Sequences and structures of retinal protein. Israel Jour. Chem., 35, 193.
41. Teller, D.C., Okada, T., Behnke, C.A., Palczewki, K., et al. (2001). Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs). Biochemistry, 40, 7761.
42. Terstegen, F. and Buss, V. (1996). All-trans and 11-cis-retinal, their N-methyl Schiff base and N-methyl protonated Schiff base derivatives: A comparative ab initio study, J. Mol. Struct. (Theochem), 369, 53.
43. Terstegen, F. and Buss, V. (1998). Influence of DFT-calculated electron correlation on energies and geometries of retinals and of reinal derivatives related to the bacteriorhodopsin and rhodopsin chromophores. J. Mol. Struct. (Theochem), 430, 209.
44. Unger, V.M., Hargrave, P.A., Baldwin, J.M. and Schertler, G.F.X. (1997). Arrangement of rhodopsin transmembrane α-helices. Nature, 389, 203.
45. 13C-labeling and 1-D rotational resonance MAS NMR. Biochemistry, 38, 11316.
46. Wald, G. (1968). Molecular basis of visual excitation. Science, 162, 230.
47. Yan, E.C.Y., Kazmi, M.A., De, S., Chang, B.S.W., et al. (2002). Function of extracellular loop 2 in rhodopsin: Glutamic acid 181 modulates stability and absorption wavelength of metarhodopsin II. Biochemistry, 41, 3620.