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Ground-state properties of the retinal molecule: from quantum mechanical to classical mechanical computations of retinal proteins. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1054-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Watanabe HC, Mori Y, Tada T, Yokoyama S, Yamato T. Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin. Biophysics (Nagoya-shi) 2010; 6:67-68. [PMID: 21297892 PMCID: PMC3032607 DOI: 10.2142/biophysics.6.67] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The synergetic effects of multiple rhodopsin mutations on color tuning need to be completely elucidated. Systematic genetic studies and spectroscopy have demonstrated an interesting example of synergetic color tuning between two amino acid residues in conger rhodopsin's ancestral pigment (p501): -a double mutation at one nearby and one distant residue led to a significant λ(max) blue shift of 13 nm, whereas neither of the single mutations at these two sites led to meaningful shifts.To analyze the molecular mechanisms of this synergetic color tuning, we performed homology modeling, molecular simulations, and electronic state calculations. For the double mutant, N195A/A292S, in silico mutation analysis demonstrated conspicuous structural changes in the retinal chromophore, whereas that of the single mutant, A292S, was almost unchanged. Using statistical ensembles of QM/MM optimized structures, the excitation energy of retinal chromophore was evaluated for the three visual pigments. As a result, the λ(max) shift of double mutant (DM) from p501 was -8 nm, while that of single mutant (SM) from p501 was +1 nm. Molecular dynamics simulation for DM demonstrated frequent isomerization between 6-s-cis and 6-s-trans conformers. Unexpectedly, however, the two conformers exhibited almost identical excitation energy, whereas principal component analysis (PCA) identified the retinal-counterion cooperative change of BLA (bond length alternation) and retinal-counterion interaction lead to the shift.
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Affiliation(s)
- Hiroshi C Watanabe
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
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Sugihara M, Hufen J, Buss V. Origin and Consequences of Steric Strain in the Rhodopsin Binding Pocket. Biochemistry 2005; 45:801-10. [PMID: 16411756 DOI: 10.1021/bi0515624] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To study the origin and the effects of steric strain on the chromophore conformation in rhodopsin, we have performed quantum-mechanical calculations on the wild-type retinal chromophore and four retinal derivatives, 13-demethyl-, 10-methyl-13-demethyl-, 10-methyl-, and 9-demethylretinal. For the dynamics of the whole protein, a combined quantum mechanics/molecular mechanics method (DFTB/CHARMM) was used and for the calculation of excited-state properties the nonempirical CASSCF/CASPT2 method. After relaxation inside the protein, all chromophores show significant nonplanar distortions from C10 to C13, most strongly for 10-methylretinal and least pronounced for 9-demethylretinal. In all five cases, the dihedral angle of the C10-C11=C12-C13 bond is negative which attests to the strong chiral discrimination exerted by the protein pocket. The calculations show that the nonplanar distortion of the chromophore, including the sense of rotation, is caused by a combination of two effects: the fitting of both ends to the protein matrix which imposes a distance constraint and the bonding arrangement at the Schiff base terminus. With both the counterion Glu113 and Lys296 displaced off the plane of the chromophore, their binding to N16 exerts a torque on the chromophore. As a result, the polyene chain, from N16 to C13, is twisted in a clockwise manner against the remaining part of the chromophore, leading to a C11=C12 bond with the observed negative dihedral angle. Shifts of the absorption maxima are reproduced correctly, in particular, the red shift of the 10-methyl and the strong blue shift of the 9-demethyl analogue relative to the wild type. Calculated positive rotatory strengths of the alpha-CD bands are in agreement with the calculated absolute conformation of the mutant chromophores.
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Affiliation(s)
- Minoru Sugihara
- Institute of Theoretical Low-Temperature Physics, University of Duisburg-Essen, 47057 Duisburg, Germany.
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Hufen J, Sugihara M, Buss V. How the Counterion Affects Ground- and Excited-State Properties of the Rhodopsin Chromophore. J Phys Chem B 2004. [DOI: 10.1021/jp046147k] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julia Hufen
- Institute of Theoretical Chemistry and Institute of Theoretical Low-Temperature Physics, University of Duisburg-Essen, D47048 Duisburg, Germany
| | - Minoru Sugihara
- Institute of Theoretical Chemistry and Institute of Theoretical Low-Temperature Physics, University of Duisburg-Essen, D47048 Duisburg, Germany
| | - Volker Buss
- Institute of Theoretical Chemistry and Institute of Theoretical Low-Temperature Physics, University of Duisburg-Essen, D47048 Duisburg, Germany
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Sugihara M, Buss V, Entel P, Hafner J. The Nature of the Complex Counterion of the Chromophore in Rhodopsin. J Phys Chem B 2004. [DOI: 10.1021/jp0362786] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Minoru Sugihara
- Theoretical Low-Temperature Physics, University of Duisburg-Essen, 47048 Duisburg, Germany, Theoretical Chemistry, University of Duisburg-Essen, 47048 Duisburg, Germany, and Center for Computational Materials Science, University of Vienna, 1090 Vienna, Austria
| | - Volker Buss
- Theoretical Low-Temperature Physics, University of Duisburg-Essen, 47048 Duisburg, Germany, Theoretical Chemistry, University of Duisburg-Essen, 47048 Duisburg, Germany, and Center for Computational Materials Science, University of Vienna, 1090 Vienna, Austria
| | - Peter Entel
- Theoretical Low-Temperature Physics, University of Duisburg-Essen, 47048 Duisburg, Germany, Theoretical Chemistry, University of Duisburg-Essen, 47048 Duisburg, Germany, and Center for Computational Materials Science, University of Vienna, 1090 Vienna, Austria
| | - Jürgen Hafner
- Theoretical Low-Temperature Physics, University of Duisburg-Essen, 47048 Duisburg, Germany, Theoretical Chemistry, University of Duisburg-Essen, 47048 Duisburg, Germany, and Center for Computational Materials Science, University of Vienna, 1090 Vienna, Austria
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Sugihara M, Buss V, Entel P, Elstner M, Frauenheim T. 11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore. Biochemistry 2002; 41:15259-66. [PMID: 12484764 DOI: 10.1021/bi020533f] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory (DFT) calculations based on the self-consistent-charge tight-binding approximation have been performed to study the influence of the protein pocket on the 3-dimensional structure of the 11-cis-retinal Schiff base (SB) chromophore. Starting with an effectively planar chromophore embedded in a protein pocket consisting of the 27 next-nearest amino acids, the relaxed chromophore geometry resulting from energy optimization and molecular dynamics (MD) simulations has yielded novel insights with respect to the following questions: (i) The conformation of the beta-ionone ring. The protein pocket tolerates both conformations, 6-s-cis and 6-s-trans, with a total energy difference of 0.7 kcal/mol in favor of the former. Of the two possible 6-s-cis conformations, the one with a negative twist angle (optimized value: -35 degrees ) is strongly favored, by 3.6 kcal/mol, relative to the one in which the dihedral is positive. (ii) Out-of-plane twist of the chromophore. The environment induces a nonplanar helical deformation of the chromophore, with the distortions concentrated in the central region of the chromophore, from C10 to C13. The dihedral angle between the planes formed by the bonds from C7 to C10 and from C13 to C15 is 42 degrees. (iii) The absolute configuration of the chromophore. The dihedral angle about the C12-C13 bond is +170 degrees from planar s-cis, which imparts a positive helicity on the chromophore, in agreement with earlier considerations based on theoretical and spectroscopic evidence.
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Affiliation(s)
- Minoru Sugihara
- Institute of Theoretical Low-Temperature Physics, University of Duisburg, D47048 Duisburg, Germany.
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Creemers AFL, Kiihne S, Bovee-Geurts PHM, DeGrip WJ, Lugtenburg J, de Groot HJM. (1)H and (13)C 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 2002; 99:9101-6. [PMID: 12093898 PMCID: PMC123100 DOI: 10.1073/pnas.112677599] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2001] [Indexed: 11/18/2022] Open
Abstract
Rhodopsin is a member of the superfamily of G-protein-coupled receptors. This seven alpha-helix transmembrane protein is the visual pigment of the vertebrate rod photoreceptor cells that mediate dim light vision. In the active binding site of this protein the ligand or chromophore, 11-cis-retinal, is covalently bound via a protonated Schiff base to lysine residue 296. Here we present the complete (1)H and (13)C assignments of the 11-cis-retinylidene chromophore in its ligand-binding site determined with ultra high field magic angle spinning NMR. Native bovine opsin was regenerated with 99% enriched uniformly (13)C-labeled 11-cis-retinal. From the labeled pigment, (13)C carbon chemical shifts could be obtained by using two-dimensional radio frequency-driven dipolar recoupling in a solid-state magic angle spinning homonuclear correlation experiment. The (1)H chemical shifts were assigned by two-dimensional heteronuclear ((1)H-(13)C) dipolar correlation spectroscopy with phase-modulated Lee-Goldburg homonuclear (1)H decoupling applied during the t(1) period. The data indicate nonbonding interactions between the protons of the methyl groups of the retinylidene ionone ring and the protein. These nonbonding interactions are attributed to nearby aromatic acid residues Phe-208, Phe-212, and Trp-265 that are in close contact with, respectively, H-16/H-17 and H-18. Furthermore, binding of the chromophore involves a chiral selection of the ring conformation, resulting in equatorial and axial positions for CH(3)-16 and CH(3)-17.
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Affiliation(s)
- Alain F L Creemers
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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Lee HM, Kim J, Kim CJ, Kim KS. Ab initio study of the isomerization of retinal chromophore and its derivatives. J Chem Phys 2002. [DOI: 10.1063/1.1459705] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Zhou H, Tajkhorshid E, Frauenheim T, Suhai S, Elstner M. Performance of the AM1, PM3, and SCC-DFTB methods in the study of conjugated Schiff base molecules. Chem Phys 2002. [DOI: 10.1016/s0301-0104(01)00695-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Yamamoto S, Wasada H, Kakitani T, Yamato T. Ab initio MO study on the potential energy surfaces for twisting around C 15 N bond of protonated Schiff base of retinal. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(00)00842-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Buß V, Weingart O, Sugihara M. Schnelle Photoisomerisierung eines Rhodopsinmodells – eine Ab-initio-Moleküldynamikstudie. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/1521-3757(20000804)112:15<2895::aid-ange2895>3.0.co;2-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Yamamoto S, Wasada H, Kakitani T. Ab initio MO study on the potential energy surfaces of low-lying excited states of protonated Schiff base retinal. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(98)00168-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Buß V, Kolster K, Terstegen F, Vahrenhorst R. Absoluter Drehsinn der Verdrillung um die C12-C13-Bindung des Retinalchromophors von Rhodopsin – semiempirische und nichtempirische Berechnung chiroptischer Daten. Angew Chem Int Ed Engl 1998. [DOI: 10.1002/(sici)1521-3757(19980703)110:13/14<1997::aid-ange1997>3.0.co;2-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Terstegen F, Buβ V. Influence of DFT-calculated electron correlation on energies and geometries of retinals and of retinal derivatives related to the bacteriorhodopsin and rhodopsin chromophores. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(98)90243-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Terstegen F, Buß V. Geometries and interconversion pathways of free and protonated β-ionone Schiff bases. An ab initio study of photoreceptor chromophore model compounds. Chem Phys 1997. [DOI: 10.1016/s0301-0104(97)00194-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Tajkhorshid E, Paizs B, Suhai S. Conformational Effects on the Proton Affinity of the Schiff Base in Bacteriorhodopsin: A Density Functional Study. J Phys Chem B 1997. [DOI: 10.1021/jp971283t] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emadeddin Tajkhorshid
- Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, FRG
| | - Béla Paizs
- Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, FRG
| | - Sándor Suhai
- Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, FRG
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Froese RD, Komaromi I, Suzie Byun K, Morokuma K. Theoretical studies of protonated and non-protonated Schiff bases of retinal: ground state structures and energies of the all-trans, 13-cis, 11-cis, 9-cis, 6,7-cis, and 6-s-cis isomers. Chem Phys Lett 1997. [DOI: 10.1016/s0009-2614(97)00519-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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