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Ghysbrecht S, Keller BG. Thermal isomerization rates in retinal analogues using Ab-Initio molecular dynamics. J Comput Chem 2024; 45:1390-1403. [PMID: 38414274 DOI: 10.1002/jcc.27332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/29/2024]
Abstract
For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is most accurate for small molecules in the gas phase. A wide range of alternative rate theories exist that can better capture reactions involving complex molecules and environmental effects. However, they require that the chemical reaction is sampled by molecular dynamics simulations. This is a formidable challenge since the accessible simulation timescales are many orders of magnitude smaller than typical timescales of chemical reactions. To overcome these limitations, rare event methods involving enhanced molecular dynamics sampling are employed. In this work, thermal isomerization of retinal is studied using tight-binding density functional theory. Results from transition state theory are compared to those obtained from enhanced sampling. Rates obtained from dynamical reweighting using infrequent metadynamics simulations were in close agreement with those from transition state theory. Meanwhile, rates obtained from application of Kramers' rate equation to a sampled free energy profile along a torsional dihedral reaction coordinate were found to be up to three orders of magnitude higher. This discrepancy raises concerns about applying rate methods to one-dimensional reaction coordinates in chemical reactions.
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Affiliation(s)
- Simon Ghysbrecht
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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2
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Demoulin B, El-Tahawy MMT, Nenov A, Garavelli M, Le Bahers T. Intramolecular photo-induced charge transfer in visual retinal chromophore mimics: electron density-based indices at the TD-DFT and post-HF levels. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1815-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Sproviero EM. Opsin Effect on the Electronic Structure of the Retinylidene Chromophore in Rhodopsin. J Chem Theory Comput 2015; 11:1206-19. [PMID: 26579769 DOI: 10.1021/ct500612n] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Direct examination of experimental NMR parameters combined with electronic structure analysis was used to provide a first-principle interpretation of NMR experiments and give a precise evaluation of how the electronic perturbation of the protein environment affects the electronic properties of the retinylidene chromophere in rhodopsin. To this end, we pursued a theoretical analysis using a combination of tools including quantum mechanics/molecular mechanics (QM/MM) at the Density Functional Theory (DFT) level, in conjunction with gauge independent atomic orbital (GIAO) calculations of (13)C NMR chemical shieldings and (1)J(CC) spin-spin coupling constants obtained with the Coupled Perturbed DFT (CPDFT) method. The opsin effect on the retinylidene chromophere is interpreted as an inductive effect of Glu-113 which readjusts the weighting factors of resonance substructures of the conjugated chain of the chromophere. These changes give a rationalization to the alternating effect of the (13)C chemical shifts magnitudes when comparing the retinylidene chromophere in the presence and absence of the protein environment. Conversely, perturbation of π orbitals has little to no effect over (1)J (13)C-(13)C spin-spin coupling constants, as they are mainly dominated by the Fermi contact term, and hence the counteraion effect is restricted to the vicinity of the perturbation. Thus, the apparent contradiction between experimental findings based on chemical shifts (deep penetration) and one-bond J-couplings (localized effects of the protonated Schiff base at the chain terminus) is in fact a consequence of different properties responding differently to the same external perturbation.
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Affiliation(s)
- Eduardo M Sproviero
- Department of Chemistry & Biochemistry, University of the Sciences in Philadelphia , 600 South 43rd Street, Philadelphia, Pennsylvania 19104-4495, United States
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Wolter T, Elstner M, Fischer S, Smith JC, Bondar AN. Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States. J Phys Chem B 2014; 119:2229-40. [DOI: 10.1021/jp505818r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Tino Wolter
- Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Stefan Fischer
- IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany
| | - Jeremy C. Smith
- Center for
Molecular
Biophysics, University of Tenessee, Oak Ridge National Laboratory, PO BOX 2008 MS6164, Oak Ridge, Tennessee 37831-6164, United States
| | - Ana-Nicoleta Bondar
- Theoretical
Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, Arnimallee 14, D-14195 Berlin, Germany
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Comparative study of spectroscopic properties of the low-lying electronic states of 2,4-pentadien-1-iminium cation and its N-substituted analogues. J CHEM SCI 2012. [DOI: 10.1007/s12039-012-0311-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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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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7
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Affiliation(s)
- Anniina Erkkilä
- Laboratory of Organic Chemistry, Department of Chemical Technology, Helsinki University of Technology, P.O. Box 6100, FI-02015 TKK, Finland
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Röhrig UF, Sebastiani D. NMR Chemical Shifts of the Rhodopsin Chromophore in the Dark State and in Bathorhodopsin: A Hybrid QM/MM Molecular Dynamics Study. J Phys Chem B 2008; 112:1267-74. [DOI: 10.1021/jp075662q] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ute F. Röhrig
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland, and Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Sebastiani
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland, and Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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9
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Röhrig UF, Guidoni L, Rothlisberger U. Solvent and Protein Effects on the Structure and Dynamics of the Rhodopsin Chromophore. Chemphyschem 2005; 6:1836-47. [PMID: 16110519 DOI: 10.1002/cphc.200500066] [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: 11/09/2022]
Abstract
The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol solution, and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid quantum mechanics/molecular mechanics (QM/MM) descriptions). Finite temperature effects are taken into account by molecular dynamics simulations. The different components that determine the structure and dynamics of the chromophore in the protein are dissected, both in the dark state and in the early photointermediates. In vacuum and in solution the chromophore displays a very high flexibility, which is significantly reduced by the protein environment. In the 11-cis chromophore, the bond-length alternation, which is correlated with the dipole moment, is found to be similar in solution and in the protein, while it differs greatly with respect to minimum-energy vacuum structures. In the model of the earliest protein photointermediate, the highly twisted chromophore shows a very reduced bond-length alternation.
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Affiliation(s)
- Ute F Röhrig
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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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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Touw SI, de Groot HJ, Buda F. DFT calculations of the 1H chemical shifts and 13C chemical shift tensors of retinal isomers. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Touw SIE, de Groot HJM, Buda F. Ab Initio Modeling of the Spatial, Electronic, and Vibrational Structure of Schiff Base Models for Visual Photoreceptors. J Phys Chem B 2004. [DOI: 10.1021/jp048734b] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Corni S, Cappelli C, Del Zoppo M, Tomasi J. Prediction of Solvent Effects on Vibrational Absorption Intensities and Raman Activities in Solution within the Polarizable Continuum Model: A Study on Push−Pull Molecules. J Phys Chem A 2003. [DOI: 10.1021/jp034960u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefano Corni
- INFM Center for nanoStructure and bioSystems at Surfaces (S3), Dipartimento di Fisica, Università di Modena e Reggio Emilia, via Campi 213/A, I-41100 Modena, Italy, Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, I-56126 Pisa, Italy, and Dipartimento di Chimica Materiali e Ingegneria Chimica, Politecnico di Milano, Piazza Leonardo Da Vinci 32, I-20133 Milano, Italy
| | - Chiara Cappelli
- INFM Center for nanoStructure and bioSystems at Surfaces (S3), Dipartimento di Fisica, Università di Modena e Reggio Emilia, via Campi 213/A, I-41100 Modena, Italy, Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, I-56126 Pisa, Italy, and Dipartimento di Chimica Materiali e Ingegneria Chimica, Politecnico di Milano, Piazza Leonardo Da Vinci 32, I-20133 Milano, Italy
| | - Mirella Del Zoppo
- INFM Center for nanoStructure and bioSystems at Surfaces (S3), Dipartimento di Fisica, Università di Modena e Reggio Emilia, via Campi 213/A, I-41100 Modena, Italy, Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, I-56126 Pisa, Italy, and Dipartimento di Chimica Materiali e Ingegneria Chimica, Politecnico di Milano, Piazza Leonardo Da Vinci 32, I-20133 Milano, Italy
| | - Jacopo Tomasi
- INFM Center for nanoStructure and bioSystems at Surfaces (S3), Dipartimento di Fisica, Università di Modena e Reggio Emilia, via Campi 213/A, I-41100 Modena, Italy, Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, I-56126 Pisa, Italy, and Dipartimento di Chimica Materiali e Ingegneria Chimica, Politecnico di Milano, Piazza Leonardo Da Vinci 32, I-20133 Milano, Italy
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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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Sergi A, Grüning M, Ferrario M, Buda F. Density Functional Study of the Photoactive Yellow Protein's Chromophore. J Phys Chem B 2001. [DOI: 10.1021/jp002270+] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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