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Mao J, Jin X, Shi M, Heidenreich D, Brown LJ, Brown RCD, Lelli M, He X, Glaubitz C. Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins. SCIENCE ADVANCES 2024; 10:eadj0384. [PMID: 38266078 PMCID: PMC10807816 DOI: 10.1126/sciadv.adj0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Proteorhodopsins are widely distributed photoreceptors from marine bacteria. Their discovery revealed a high degree of evolutionary adaptation to ambient light, resulting in blue- and green-absorbing variants that correlate with a conserved glutamine/leucine at position 105. On the basis of an integrated approach combining sensitivity-enhanced solid-state nuclear magnetic resonance (ssNMR) spectroscopy and linear-scaling quantum mechanics/molecular mechanics (QM/MM) methods, this single residue is shown to be responsible for a variety of synergistically coupled structural and electrostatic changes along the retinal polyene chain, ionone ring, and within the binding pocket. They collectively explain the observed color shift. Furthermore, analysis of the differences in chemical shift between nuclei within the same residues in green and blue proteorhodopsins also reveals a correlation with the respective degree of conservation. Our data show that the highly conserved color change mainly affects other highly conserved residues, illustrating a high degree of robustness of the color phenotype to sequence variation.
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Affiliation(s)
- Jiafei Mao
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - David Heidenreich
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Lynda J. Brown
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
| | - Richard C. D. Brown
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
| | - Moreno Lelli
- Department of Chemistry “Ugo Schiff” and Magnetic Resonance Center (CERM), University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Italy
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Italy
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- New York University–East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
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2
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O'Connor MS, Bragg ZT, Dearworth JR, Hendrickson HP. Quantum Mechanics/Molecular mechanics calculations predict A1, not A2, is present in melanopsin (Opn4m) of red-eared slider turtles (Trachemys scripta elegans). Vision Res 2023; 209:108245. [PMID: 37290221 DOI: 10.1016/j.visres.2023.108245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 06/10/2023]
Abstract
Melanopsin is a photopigment that plays a role in non-visual, light-driven, cellular processes such as modulation of circadian rhythms, retinal vascular development, and the pupillary light reflex (PLR). In this study, computational methods were used to understand which chromophore is harbored by melanopsin in red-eared slider turtles (Trachemys scripta elegans). In mammals, the vitamin A derivative 11-cis-retinal (A1) is the chromophore, which provides functionality for melanopsin. However, in red-eared slider turtles, a member of the reptilian class, the identity of the chromophore remains unclear. Red-eared slider turtles, similar to other freshwater vertebrates, possess visual pigments that harbor a different vitamin A derivative, 11-cis-3,4-didehydroretinal (A2), making their pigments more sensitive to red-light than blue-light, therefore, suggesting the chromophore to be the A2 derivative instead of the A1. To help resolve the chromophore identity, in this work, computational homology models of melanopsin in red-eared slider turtles were first constructed. Next, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to compare how A1 and A2 derivatives bind to melanopsin. Time dependent density functional theory (TDDFT) calculations were then used to determine the excitation energy of the pigments. Lastly, calculated excitation energies were compared to experimental spectral sensitivity data from responses by the irises of red-eared sliders. Contrary to what was expected, our results suggest that melanopsin in red-eared slider turtles is more likely to harbor the A1 chromophore than the A2. Furthermore, a glutamine (Q622.56) and tyrosine (Y853.28) residue in the chromophore binding pocket are shown to play a role in the spectral tuning of the chromophore.
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Affiliation(s)
- Michael S O'Connor
- Department of Chemistry, Lafayette College, Easton, PA 18042, United States
| | - Zoey T Bragg
- Department of Chemistry, Lafayette College, Easton, PA 18042, United States
| | - James R Dearworth
- Department of Biology, Lafayette College, Easton, PA 18042, United States
| | - Heidi P Hendrickson
- Department of Chemistry, Lafayette College, Easton, PA 18042, United States.
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3
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Fujimoto KJ, Minowa F, Nishina M, Nakamura S, Ohashi S, Katayama K, Kandori H, Yanai T. Molecular Mechanism of Spectral Tuning by Chloride Binding in Monkey Green Sensitive Visual Pigment. J Phys Chem Lett 2023; 14:1784-1793. [PMID: 36762971 DOI: 10.1021/acs.jpclett.2c03619] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The visual pigments of the cones perceive red, green, and blue colors. The monkey green (MG) pigment possesses a unique Cl- binding site; however, its relationship to the spectral tuning in green pigments remains elusive. Recently, FTIR spectroscopy revealed the characteristic structural modifications of the retinal binding site by Cl- binding. Herein, we report the computational structural modeling of MG pigments and quantum-chemical simulation to investigate its spectral redshift and physicochemical relevance when Cl- is present. Our protein structures reflect the previously suggested structural changes. AlphaFold2 failed to predict these structural changes. Excited-state calculations successfully reproduced the experimental red-shifted absorption energies, corroborating our protein structures. Electrostatic energy decomposition revealed that the redshift results from the His197 protonation state and conformations of Glu129, Ser202, and Ala308; however, Cl- itself contributes to the blueshift. Site-directed mutagenesis supported our analysis. These modeled structures may provide a valuable foundation for studying cone pigments.
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Affiliation(s)
- Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - Fumika Minowa
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - Michiya Nishina
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - Shunta Nakamura
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
| | - Sayaka Ohashi
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
| | - Takeshi Yanai
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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Pedraza-González L, Barneschi L, Padula D, De Vico L, Olivucci M. Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol. Top Curr Chem (Cham) 2022; 380:21. [PMID: 35291019 PMCID: PMC8924150 DOI: 10.1007/s41061-022-00374-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/29/2022] [Indexed: 10/27/2022]
Abstract
In recent years, photoactive proteins such as rhodopsins have become a common target for cutting-edge research in the field of optogenetics. Alongside wet-lab research, computational methods are also developing rapidly to provide the necessary tools to analyze and rationalize experimental results and, most of all, drive the design of novel systems. The Automatic Rhodopsin Modeling (ARM) protocol is focused on providing exactly the necessary computational tools to study rhodopsins, those being either natural or resulting from mutations. The code has evolved along the years to finally provide results that are reproducible by any user, accurate and reliable so as to replicate experimental trends. Furthermore, the code is efficient in terms of necessary computing resources and time, and scalable in terms of both number of concurrent calculations as well as features. In this review, we will show how the code underlying ARM achieved each of these properties.
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Affiliation(s)
- Laura Pedraza-González
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy. .,Department of Chemistry and Industrial Chemistry, University of Pisa, Via Moruzzi 13, 56124, Pisa, Italy.
| | - Leonardo Barneschi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Daniele Padula
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy.
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy. .,Department of Chemistry, Bowling Green State University, Bowling Green, OH, 43403, USA.
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6
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Prentice JCA. Efficiently Computing Excitations of Complex Systems: Linear-Scaling Time-Dependent Embedded Mean-Field Theory in Implicit Solvent. J Chem Theory Comput 2022; 18:1542-1554. [PMID: 35133827 PMCID: PMC9082505 DOI: 10.1021/acs.jctc.1c01133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Quantum embedding schemes have the
potential to significantly reduce
the computational cost of first-principles calculations while maintaining
accuracy, particularly for calculations of electronic excitations
in complex systems. In this work, I combine time-dependent embedded
mean field theory (TD-EMFT) with linear-scaling density functional
theory and implicit solvation models, extending previous work within
the ONETEP code. This provides a way to perform multilevel calculations
of electronic excitations on very large systems, where long-range
environmental effects, both quantum and classical in nature, are important.
I demonstrate the power of this method by performing simulations on
a variety of systems, including a molecular dimer, a chromophore in
solution, and a doped molecular crystal. This work paves the way for
high accuracy calculations to be performed on large-scale systems
that were previously beyond the reach of quantum embedding schemes.
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Affiliation(s)
- Joseph C A Prentice
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
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7
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Scholz L, Neugebauer J. Protein Response Effects on Cofactor Excitation Energies from First Principles: Augmenting Subsystem Time-Dependent Density-Functional Theory with Many-Body Expansion Techniques. J Chem Theory Comput 2021; 17:6105-6121. [PMID: 34524815 DOI: 10.1021/acs.jctc.1c00551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We investigate the possibility of describing protein response effects on a chromophore excitation by means of subsystem time-dependent density-functional theory (sTDDFT) in combination with a many-body expansion (MBE) approach. While sTDDFT is in principle intrinsically able to include such contributions, addressing cofactor excitations in protein models or entire proteins with full environment-response treatments is currently out of reach. Taking different model structures of the green fluorescent protein (GFP) and bovine rhodopsin as examples, we demonstrate that an embedded-MBE approach based on sTDDFT in its simplest version leads to a good agreement of the predicted protein response effect already at second order. To reproduce reference response effects from nonsubsystem TDDFT calculations quantitatively (error ≤ 5%), however, a third- or even fourth-order MBE may be required. For the latter case, we explore a selective inclusion of fourth-order terms that drastically reduces the computational burden. In addition, we demonstrate how this sTDDFT-MBE treatment can be utilized as an analysis tool to identify residues with dominant response contributions. This, in turn, can be employed to arrive at smaller structural models for light-absorbing proteins, which still feature all of the main characteristics in terms of photoresponse properties.
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Affiliation(s)
- Linus Scholz
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
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8
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Fujimoto KJ. Electronic Couplings and Electrostatic Interactions Behind the Light Absorption of Retinal Proteins. Front Mol Biosci 2021; 8:752700. [PMID: 34604313 PMCID: PMC8480471 DOI: 10.3389/fmolb.2021.752700] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
The photo-functional chromophore retinal exhibits a wide variety of optical absorption properties depending on its intermolecular interactions with surrounding proteins and other chromophores. By utilizing these properties, microbial and animal rhodopsins express biological functions such as ion-transport and signal transduction. In this review, we present the molecular mechanisms underlying light absorption in rhodopsins, as revealed by quantum chemical calculations. Here, symmetry-adapted cluster-configuration interaction (SAC-CI), combined quantum mechanical and molecular mechanical (QM/MM), and transition-density-fragment interaction (TDFI) methods are used to describe the electronic structure of the retinal, the surrounding protein environment, and the electronic coupling between chromophores, respectively. These computational approaches provide successful reproductions of experimentally observed absorption and circular dichroism (CD) spectra, as well as insights into the mechanisms of unique optical properties in terms of chromophore-protein electrostatic interactions and chromophore-chromophore electronic couplings. On the basis of the molecular mechanisms revealed in these studies, we also discuss strategies for artificial design of the optical absorption properties of rhodopsins.
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Affiliation(s)
- Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
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Varadharajan V, Arumugam GS, Shanmugam S. Isatin-based virtual high throughput screening, molecular docking, DFT, QM/MM, MD and MM-PBSA study of novel inhibitors of SARS-CoV-2 main protease. J Biomol Struct Dyn 2021; 40:7852-7867. [PMID: 33764269 DOI: 10.1080/07391102.2021.1904003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a rapidly growing health care emergency across the world. One of the viral proteases called main protease or Mpro, plays a crucial role in the replication of SARS-CoV-2. As the structure of Mpro of SARS-CoV-2 is similar to the Mpro of SARS-CoV-1 (responsible for SARS outbreak between 2002 and 2004), we hypothesize that the inhibitors of SARS-CoV-1 Mpro can also inhibit the Mpro of SARS-CoV-2. To test this hypothesis, a total of 79 isatin derivatives, which inhibited Mpro activity under in vitro conditions, were selected from the literature, and then screened through AutoDock Vina. The chemical features of the top 5 isatin derivatives with low binding energies (-8.5 to -8.2 kcal/mol) were used to screen similar types of compounds from several small-molecule libraries containing 15856508 compounds. A total of 1,609 compounds with similarity score ≥ 6 were screened and then subjected to docking as well as ADME analysis. Among the compounds screened, 4 ligands form Zinc drug-like library (ZINC000008848565, ZINC000009513563, ZINC000036759789 and ZINC000046053855) showed good ADMET properties, low binding energy (-8.4 to -8.6 kcal/mol), low interaction energy (-72.62 to -50.01 kcal/mol) and high structural stability with Mpro. Hence, the selected ligands might serve as the lead candidates for further wet laboratory validation, optimization and development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Sethupathi Shanmugam
- Department of Biopharmaceutical Development, Syngene International Ltd, Bangalore, India
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10
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Corbo JC. Vitamin A 1/A 2 chromophore exchange: Its role in spectral tuning and visual plasticity. Dev Biol 2021; 475:145-155. [PMID: 33684435 DOI: 10.1016/j.ydbio.2021.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/01/2021] [Indexed: 01/20/2023]
Abstract
Vertebrate rod and cone photoreceptors detect light via a specialized organelle called the outer segment. This structure is packed with light-sensitive molecules known as visual pigments that consist of a G-protein-coupled, seven-transmembrane protein known as opsin, and a chromophore prosthetic group, either 11-cis retinal ('A1') or 11-cis 3,4-didehydroretinal ('A2'). The enzyme cyp27c1 converts A1 into A2 in the retinal pigment epithelium. Replacing A1 with A2 in a visual pigment red-shifts its spectral sensitivity and broadens its bandwidth of absorption at the expense of decreased photosensitivity and increased thermal noise. The use of vitamin A2-based visual pigments is strongly associated with the occupation of aquatic habitats in which the ambient light is red-shifted. By modulating the A1/A2 ratio in the retina, an organism can dynamically tune the spectral sensitivity of the visual system to better match the predominant wavelengths of light in its environment. As many as a quarter of all vertebrate species utilize A2, at least during a part of their life cycle or under certain environmental conditions. A2 utilization therefore represents an important and widespread mechanism of sensory plasticity. This review provides an up-to-date account of the A1/A2 chromophore exchange system.
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Affiliation(s)
- Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, United States.
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11
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Nikolaev DM, Shtyrov AA, Mereshchenko AS, Panov MS, Tveryanovich YS, Ryazantsev MN. An assessment of water placement algorithms in quantum mechanics/molecular mechanics modeling: the case of rhodopsins' first spectral absorption band maxima. Phys Chem Chem Phys 2020; 22:18114-18123. [PMID: 32761024 DOI: 10.1039/d0cp02638g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) models are a widely used tool to obtain detailed insight into the properties and functioning of proteins. The outcome of QM/MM studies heavily depends on the quality of the applied QM/MM model. Prediction and right placement of internal water molecules in protein cavities is one of the critical parts of any QM/MM model construction. Herein, we performed a systematic study of four protein hydration algorithms. We tested these algorithms for their ability to predict X-ray-resolved water molecules for a set of membrane photosensitive rhodopsin proteins, as well as the influence of the applied water placement algorithms on the QM/MM calculated absorption maxima (λmax) of these proteins. We used 49 rhodopsins and their intermediates with available X-ray structures as the test set. We found that a proper choice of hydration algorithms and setups is needed to predict functionally important water molecules in the chromophore-binding cavity of rhodopsins, such as the water cluster in the N-H region of bacteriorhodopsin or two water molecules in the binding pocket of bovine visual rhodopsin. The QM/MM calculated λmax of rhodopsins is also quite sensitive to the applied protein hydration protocols. The best methodology allows obtaining an 18.0 nm average value for the absolute deviation of the calculated λmax from the experimental λmax. Although the major effect of water molecules on λmax originates from the water molecules located in the binding pocket, the water molecules outside the binding pocket also affect the calculated λmax mainly by causing a reorganization of the protein structure. The results reported in this study can be used for the evaluation and further development of hydration methodologies, in general, and rhodopsin QM/MM models, in particular.
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Affiliation(s)
- Dmitrii M Nikolaev
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia.
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12
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Nakliang P, Lazim R, Chang H, Choi S. Multiscale Molecular Modeling in G Protein-Coupled Receptor (GPCR)-Ligand Studies. Biomolecules 2020; 10:E631. [PMID: 32325877 PMCID: PMC7226129 DOI: 10.3390/biom10040631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/13/2020] [Accepted: 04/17/2020] [Indexed: 12/17/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are major drug targets due to their ability to facilitate signal transduction across cell membranes, a process that is vital for many physiological functions to occur. The development of computational technology provides modern tools that permit accurate studies of the structures and properties of large chemical systems, such as enzymes and GPCRs, at the molecular level. The advent of multiscale molecular modeling permits the implementation of multiple levels of theories on a system of interest, for instance, assigning chemically relevant regions to high quantum mechanics (QM) level of theory while treating the rest of the system using classical force field (molecular mechanics (MM) potential). Multiscale QM/MM molecular modeling have far-reaching applications in the rational design of GPCR drugs/ligands by affording precise ligand binding configurations through the consideration of conformational plasticity. This enables the identification of key binding site residues that could be targeted to manipulate GPCR function. This review will focus on recent applications of multiscale QM/MM molecular simulations in GPCR studies that could boost the efficiency of future structure-based drug design (SBDD) strategies.
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Affiliation(s)
| | | | | | - Sun Choi
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea; (P.N.); (R.L.); (H.C.)
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13
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Competing excited-state deactivation processes in bacteriophytochromes. ADVANCES IN QUANTUM CHEMISTRY 2020. [DOI: 10.1016/bs.aiq.2020.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Prentice JCA, Charlton RJ, Mostofi AA, Haynes PD. Combining Embedded Mean-Field Theory with Linear-Scaling Density-Functional Theory. J Chem Theory Comput 2019; 16:354-365. [DOI: 10.1021/acs.jctc.9b00956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Joseph C. A. Prentice
- Department of Materials, Department of Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Robert J. Charlton
- Department of Materials, Department of Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Arash A. Mostofi
- Department of Materials, Department of Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Peter D. Haynes
- Department of Materials, Department of Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
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15
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Ryazantsev MN, Nikolaev DM, Struts AV, Brown MF. Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins. J Membr Biol 2019; 252:425-449. [PMID: 31570961 DOI: 10.1007/s00232-019-00095-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/10/2019] [Indexed: 12/20/2022]
Abstract
Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.
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Affiliation(s)
- Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, Saint Petersburg, Russia, 198504
| | - Dmitrii M Nikolaev
- Saint-Petersburg Academic University - Nanotechnology Research and Education Centre RAS, Saint Petersburg, Russia, 194021
| | - Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Laboratory of Biomolecular NMR, Saint Petersburg State University, Saint Petersburg, Russia, 199034
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Physics, University of Arizona, Tucson, AZ, 85721, USA.
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16
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Abstract
For nearly a century adaptive landscapes have provided overviews of the evolutionary process and yet they remain metaphors. We redefine adaptive landscapes in terms of biological processes rather than descriptive phenomenology. We focus on the underlying mechanisms that generate emergent properties such as epistasis, dominance, trade-offs and adaptive peaks. We illustrate the utility of landscapes in predicting the course of adaptation and the distribution of fitness effects. We abandon aged arguments concerning landscape ruggedness in favor of empirically determining landscape architecture. In so doing, we transform the landscape metaphor into a scientific framework within which causal hypotheses can be tested.
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Affiliation(s)
- Xiao Yi
- BioTechnology Institute, University of Minnesota, St. Paul, MN
| | - Antony M Dean
- BioTechnology Institute, University of Minnesota, St. Paul, MN.,Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
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17
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Pieri E, Ledentu V, Sahlin M, Dehez F, Olivucci M, Ferré N. CpHMD-Then-QM/MM Identification of the Amino Acids Responsible for the Anabaena Sensory Rhodopsin pH-Dependent Electronic Absorption Spectrum. J Chem Theory Comput 2019; 15:4535-4546. [PMID: 31264415 DOI: 10.1021/acs.jctc.9b00221] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anabaena Sensory Rhodopsin (ASR), a microbial photoactive protein featuring the retinal chromophore in two different conformations, exhibits a pH-dependent electronic absorption spectrum. Using the recently developed CpHMD-then-QM/MM multiscale protocol applied to ASR embedded in a membrane model, the pH-induced changes in its maximum absorption wavelength have been reproduced and analyzed. While the acidic tiny red-shift is essentially correlated with the deprotonation of an aspartic acid located on the ASR extracellular side, the larger blue-shift experimentally reported at pH values larger than 5 involves a cluster of titrating residues sitting on the cytoplasmic side. The ASR pH-dependent spectrum is the consequence of the competitive stabilization of retinal ground and excited states by the protein electrostatic potential.
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Affiliation(s)
- Elisa Pieri
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
| | | | - Michael Sahlin
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
| | - François Dehez
- Laboratoire de Physique et Chimie Théorique , UMR 7019, Faculté des Sciences et Technique , Campus Aiguillettes , 54506 Vandoeuvre-les-Nancy , France
| | - Massimo Olivucci
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States.,Dipartimento di Biotecnologie, Chimica e Farmacia , Università degli Studi di Siena , via A. Moro 2 , 53100 Siena , Italy
| | - Nicolas Ferré
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
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18
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Pedraza-González L, De Vico L, del Carmen Marín M, Fanelli F, Olivucci M. a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement. J Chem Theory Comput 2019; 15:3134-3152. [PMID: 30916955 PMCID: PMC7141608 DOI: 10.1021/acs.jctc.9b00061] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Automatic Rhodopsin Modeling (ARM) protocol has recently been proposed as a tool for the fast and parallel generation of basic hybrid quantum mechanics/molecular mechanics (QM/MM) models of wild type and mutant rhodopsins. However, in its present version, input preparation requires a few hours long user's manipulation of the template protein structure, which also impairs the reproducibility of the generated models. This limitation, which makes model building semiautomatic rather than fully automatic, comprises four tasks: definition of the retinal chromophore cavity, assignment of protonation states of the ionizable residues, neutralization of the protein with external counterions, and finally congruous generation of single or multiple mutations. In this work, we show that the automation of the original ARM protocol can be extended to a level suitable for performing the above tasks without user's manipulation and with an input preparation time of minutes. The new protocol, called a-ARM, delivers fully reproducible (i.e., user independent) rhodopsin QM/MM models as well as an improved model quality. More specifically, we show that the trend in vertical excitation energies observed for a set of 25 wild type and 14 mutant rhodopsins is predicted by the new protocol better than when using the original. Such an agreement is reflected by an estimated (relative to the probed set) trend deviation of 0.7 ± 0.5 kcal mol-1 (0.03 ± 0.02 eV) and mean absolute error of 1.0 kcal mol-1 (0.04 eV).
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Affiliation(s)
- Laura Pedraza-González
- Department of Biotechnologies, Chemistry and Pharmacy, Università degli Studi di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Luca De Vico
- Department of Biotechnologies, Chemistry and Pharmacy, Università degli Studi di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - María del Carmen Marín
- Department of Biotechnologies, Chemistry and Pharmacy, Università degli Studi di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Francesca Fanelli
- Department of Life Sciences, Center for Neuroscience and Neurotechnology, Università degli Studi di Modena e Reggio Emilia, I-41125 Modena, Italy
| | - Massimo Olivucci
- Department of Biotechnologies, Chemistry and Pharmacy, Università degli Studi di Siena, via A. Moro 2, I-53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
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19
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Marín MDC, De Vico L, Dong SS, Gagliardi L, Truhlar DG, Olivucci M. Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins. J Chem Theory Comput 2019; 15:1915-1923. [PMID: 30721054 PMCID: PMC7096677 DOI: 10.1021/acs.jctc.8b01069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A methodology for the automatic production of quantum mechanical/molecular mechanical (QM/MM) models of retinal-binding rhodopsin proteins and subsequent prediction of their spectroscopic properties has been proposed recently by some of the authors. The technology employed for the evaluation of the excitation energies is called Automatic Rhodopsin Modeling (ARM), and it involves the use of the complete active space self-consistent field (CASSCF) method followed by a multiconfiguration second-order perturbation theory (in particular, CASPT2) calculation of external correlation energies. Although it was shown that ARM is capable of successfully reproducing and predicting spectroscopic property trends in chromophore-embedding protein sets, practical applications of such technology are limited by the high computational costs of the multiconfiguration perturbation theory calculations. In the present work we benchmark the more affordable multiconfiguration pair-density functional theory (MC-PDFT) method whose accuracy has been recently validated for retinal chromophores in the gas phase, indicating that MC-PDFT could potentially be used to analyze large (e.g., few hundreds) sets of rhodopsin proteins. Here, we test this theory for a set of rhodopsin QM/MM models whose experimental absorption maxima (λ a max) have been measured. The results indicate that MC-PDFT may be employed to calculate λ a max values for this important class of photoresponsive proteins.
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Affiliation(s)
- María Del Carmen Marín
- Department of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy
- Chemistry Department , Bowling Green State University , Bowling Green , 43403 Ohio , United States
| | - Luca De Vico
- Department of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy
| | - Sijia S Dong
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States
| | - Massimo Olivucci
- Department of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy
- Chemistry Department , Bowling Green State University , Bowling Green , 43403 Ohio , United States
- USIAS Institut d'Études Avanceés , Université de Strasbourg , 67083 Strasbourg , France
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20
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Modi V, Donnini S, Groenhof G, Morozov D. Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome. J Phys Chem B 2019; 123:2325-2334. [PMID: 30762368 PMCID: PMC6727380 DOI: 10.1021/acs.jpcb.9b01117] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
The
tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome
from Deinococcus radiodurans (DrBphP)
is usually assumed to be fully protonated, but this assumption has
not been systematically validated by experiments or extensive computations.
Here, we use force field molecular dynamics simulations and quantum
mechanics/molecular mechanics calculations with density functional
theory and XMCQDPT2 methods to investigate the effect of the five
most probable protonation forms of BV on structural stability, binding
pocket interactions, and absorption spectra in the two photochromic
states of DrBphP. While agreement with X-ray structural data and measured
UV/vis spectra suggest that in both states the protonated form of
the chromophore dominates, we also find that a minor population with
a deprotonated D-ring could contribute to the red-shifted tail in
the absorption spectra.
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21
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Yanai K, Ishimura K, Nakayama A, Hasegawa JY. First-Order Interacting Space Approach to Excited-State Molecular Interaction: Solvatochromic Shift of p-Coumaric Acid and Retinal Schiff Base. J Chem Theory Comput 2018; 14:3643-3655. [DOI: 10.1021/acs.jctc.7b01089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kazuma Yanai
- Institute for Catalysis, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
| | - Kazuya Ishimura
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Akira Nakayama
- Institute for Catalysis, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
| | - Jun-ya Hasegawa
- Institute for Catalysis, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
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22
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Zuehlsdorff TJ, Haynes PD, Payne MC, Hine NDM. Predicting solvatochromic shifts and colours of a solvated organic dye: The example of nile red. J Chem Phys 2018; 146:124504. [PMID: 28388154 DOI: 10.1063/1.4979196] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The solvatochromic shift, as well as the change in colour of the simple organic dye nile red, is studied in two polar and two non-polar solvents in the context of large-scale time-dependent density-functional theory (TDDFT) calculations treating large parts of the solvent environment from first principles. We show that an explicit solvent representation is vital to resolve absorption peak shifts between nile red in n-hexane and toluene, as well as acetone and ethanol. The origin of the failure of implicit solvent models for these solvents is identified as being due to the strong solute-solvent interactions in form of π-stacking and hydrogen bonding in the case of toluene and ethanol. We furthermore demonstrate that the failures of the computationally inexpensive Perdew-Burke-Ernzerhof (PBE) functional in describing some features of the excited state potential energy surface of the S1 state of nile red can be corrected for in a straightforward fashion, relying only on a small number of calculations making use of more sophisticated range-separated hybrid functionals. The resulting solvatochromic shifts and predicted colours are in excellent agreement with experiment, showing the computational approach outlined in this work to yield very robust predictions of optical properties of dyes in solution.
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Affiliation(s)
- T J Zuehlsdorff
- School of Natural Sciences, University of California Merced, 5200 N. Lake Road, Merced, California 95343, USA
| | - P D Haynes
- Department of Physics, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - M C Payne
- Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - N D M Hine
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
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23
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Collette F, Renger T, Müh F, Schmidt am Busch M. Red/Green Color Tuning of Visual Rhodopsins: Electrostatic Theory Provides a Quantitative Explanation. J Phys Chem B 2018; 122:4828-4837. [DOI: 10.1021/acs.jpcb.8b02702] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florimond Collette
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Frank Müh
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Marcel Schmidt am Busch
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
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24
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Abstract
Channelrhodopsin-2 (ChR2) is a light-sensitive ion channel widely used in optogenetics. Photoactivation triggers a trans-to-cis isomerization of a covalently bound retinal. Ensuing conformational changes open a cation-selective channel. We explore the structural dynamics in the early photocycle leading to channel opening by classical (MM) and quantum mechanical (QM) molecular simulations. With QM/MM simulations, we generated a protein-adapted force field for the retinal chromophore, which we validated against absorption spectra. In a 4-µs MM simulation of a dark-adapted ChR2 dimer, water entered the vestibules of the closed channel. Retinal all-trans to 13-cis isomerization, simulated with metadynamics, triggered a major restructuring of the charge cluster forming the channel gate. On a microsecond time scale, water penetrated the gate to form a membrane-spanning preopen pore between helices H1, H2, H3, and H7. This influx of water into an ion-impermeable preopen pore is consistent with time-resolved infrared spectroscopy and electrophysiology experiments. In the retinal 13-cis state, D253 emerged as the proton acceptor of the Schiff base. Upon proton transfer from the Schiff base to D253, modeled by QM/MM simulations, we obtained an early-M/P2390-like intermediate. Rapid rotation of the unprotonated Schiff base toward the cytosolic side effectively prevents its reprotonation from the extracellular side. From MM and QM simulations, we gained detailed insight into the mechanism of ChR2 photoactivation and early events in pore formation. By rearranging the network of charges and hydrogen bonds forming the gate, water emerges as a key player in light-driven ChR2 channel opening.
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Affiliation(s)
- Albert Ardevol
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany;
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany;
- Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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25
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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26
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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27
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Demoulin B, Altavilla SF, Rivalta I, Garavelli M. Fine Tuning of Retinal Photoinduced Decay in Solution. J Phys Chem Lett 2017; 8:4407-4412. [PMID: 28853582 DOI: 10.1021/acs.jpclett.7b01780] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single methylation at position C10 of the all-trans retinal protonated Schiff base switches its excited-state decay in methanol from a slower picosecond into an ultrafast, protein-like subpicosecond process. QM/MM modeling in conjunction with on-the-fly excited-state dynamics provides fundamental understanding of the fine-tuning mechanics that "catalyzes" the photoinduced decay of solvated retinals. Methylation alters the interplay between the ionic S1 and covalent S2 states, reducing the excited-state lifetime by favoring the formation of a S1 transient fluorescent state with fully inverted bond lengths that accounts for the recorded transient spectroscopy and from which a space-saving conical intersection seam is quickly (<1 ps) reached. Minimal and apparently innocent chemical modifications thus affect the characteristic intramolecular charge-transfer of the S1 state as well as the interaction with the covalent S2 excited state, eventually providing the high tunability of retinal photophysics and photochemistry and delivering a new concept for the rational design of retinal-based photoactive molecular devices.
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Affiliation(s)
- Baptiste Demoulin
- Univ Lyon, ENS de Lyon , CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Salvatore Flavio Altavilla
- Univ Lyon, ENS de Lyon , CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , V. F. Selmi 2, 40126 Bologna, Italy
| | - Ivan Rivalta
- Univ Lyon, ENS de Lyon , CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Marco Garavelli
- Univ Lyon, ENS de Lyon , CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , V. F. Selmi 2, 40126 Bologna, Italy
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28
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Xie P, Zhou P, Alsaedi A, Zhang Y. pH-dependent absorption spectra of rhodopsin mutant E113Q: On the role of counterions and protein. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 174:25-31. [PMID: 27865136 DOI: 10.1016/j.saa.2016.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/08/2016] [Accepted: 11/12/2016] [Indexed: 06/06/2023]
Abstract
The absorption spectra of bovine rhodopsin mutant E113Q in solutions were investigated at the molecular level by using a hybrid quantum mechanics/molecular mechanics (QM/MM) method. The calculations suggest the mechanism of the absorption variations of E113Q at different pH values. The results indicate that the polarizations of the counterions in the vicinity of Schiff base under protonation and unprotonation states of the mutant E113Q would be a crucial factor to change the energy gap of the retinal to tune the absorption spectra. Glu-181 residue, which is close to the chromophore, cannot serve as the counterion of the protonated Schiff base of E113Q in dark state. Moreover, the results of the absorption maximum in mutant E113Q with the various anions (Cl-, Br-, I- and NO3-) manifested that the mutant E113Q could have the potential for use as a template of anion biosensors at visible wavelength.
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Affiliation(s)
- Peng Xie
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Ahmed Alsaedi
- Nonlinear Analysis and Applied Mathematics (NAAM) Research Group, Department of Mathematics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Yan Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China.
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29
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Varsano D, Caprasecca S, Coccia E. Theoretical description of protein field effects on electronic excitations of biological chromophores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:013002. [PMID: 27830666 DOI: 10.1088/0953-8984/29/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.
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Affiliation(s)
- Daniele Varsano
- S3 Center, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
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30
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Nikolaev DM, Emelyanov A, Boitsov VM, Panov MS, Ryazantsev MN. A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling. F1000Res 2017; 6:33. [PMID: 28435665 PMCID: PMC5381632 DOI: 10.12688/f1000research.10541.3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/23/2017] [Indexed: 12/25/2022] Open
Abstract
It was demonstrated in recent studies that some rhodopsins can be used in optogenetics as fluorescent indicators of membrane voltage. One of the promising candidates for these applications is archaerhodopsin-3. While it has already shown encouraging results, there is still a large room for improvement. One of possible directions is increasing the intensity of the protein's fluorescent signal. Rational design of mutants with an improved signal is an important task, which requires both experimental and theoretical studies. Herein, we used a homology-based computational approach to predict the three-dimensional structure of archaerhodopsin-3, and a Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid approach with high-level multireference ab initio methodology (SORCI+Q/AMBER) to model optical properties of this protein. We demonstrated that this methodology allows for reliable prediction of structure and spectral properties of archaerhodopsin-3. The results of this study can be utilized for computational molecular design of efficient fluorescent indicators of membrane voltage for modern optogenetics on the basis of archaerhodopsin-3.
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Affiliation(s)
- Dmitrii M Nikolaev
- Saint-Petersburg National Research Academic University of the Russian Academy of Science, St. Petersburg, Russian Federation
| | - Anton Emelyanov
- Saint-Petersburg National Research Academic University of the Russian Academy of Science, St. Petersburg, Russian Federation
| | - Vitaly M Boitsov
- Saint-Petersburg National Research Academic University of the Russian Academy of Science, St. Petersburg, Russian Federation
| | - Maxim S Panov
- Saint-Petersburg State University, St. Petersburg, Russian Federation
| | - Mikhail N Ryazantsev
- Saint-Petersburg State University, St. Petersburg, Russian Federation.,Saint-Petersburg Scientific Center of the Russian Academy of Sciences, St. Petersburg, Russian Federation
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31
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Pan QQ, Li SB, Duan YC, Wu Y, Zhang J, Geng Y, Zhao L, Su ZM. Exploring what prompts ITIC to become a superior acceptor in organic solar cell by combining molecular dynamics simulation with quantum chemistry calculation. Phys Chem Chem Phys 2017; 19:31227-31235. [DOI: 10.1039/c7cp05938h] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A comparison on charge transfer process in OSC between non-fullerene electron acceptor ITIC and PC71BM was taken by microscopic analysis based on the molecular dynamics and quantum chemistry method.
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Affiliation(s)
- Qing-Qing Pan
- Institute of Functional Material Chemistry
- Faculty of Chemistry
- Northeast Normal University
- Chang Chun 130024
- P. R. China
| | - Shuang-Bao Li
- Institute of Functional Material Chemistry
- Faculty of Chemistry
- Northeast Normal University
- Chang Chun 130024
- P. R. China
| | - Ying-Chen Duan
- Institute of Functional Material Chemistry
- Faculty of Chemistry
- Northeast Normal University
- Chang Chun 130024
- P. R. China
| | - Yong Wu
- School of Pharmaceutical Sciences
- Changchun University of Chinese Medicine
- Changchun
- P. R. China
| | - Ji Zhang
- College of Chemistry and Life Science
- Changchun University of Technology
- ChangChun
- P. R. China
| | - Yun Geng
- Institute of Functional Material Chemistry
- Faculty of Chemistry
- Northeast Normal University
- Chang Chun 130024
- P. R. China
| | - Liang Zhao
- Institute of Functional Material Chemistry
- Faculty of Chemistry
- Northeast Normal University
- Chang Chun 130024
- P. R. China
| | - Zhong-Min Su
- Institute of Functional Material Chemistry
- Faculty of Chemistry
- Northeast Normal University
- Chang Chun 130024
- P. R. China
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32
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Xie P, Zhang Y. Why choose 9-cis retinal for therapy of congenital stationary night blindness caused by G90D rhodopsin? Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2039-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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33
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Melaccio F, del Carmen Marín M, Valentini A, Montisci F, Rinaldi S, Cherubini M, Yang X, Kato Y, Stenrup M, Orozco-Gonzalez Y, Ferré N, Luk HL, Kandori H, Olivucci M. Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology. J Chem Theory Comput 2016; 12:6020-6034. [DOI: 10.1021/acs.jctc.6b00367] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Federico Melaccio
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - María del Carmen Marín
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Alessio Valentini
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Fabio Montisci
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Silvia Rinaldi
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Marco Cherubini
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Xuchun Yang
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Yoshitaka Kato
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Japan
| | - Michael Stenrup
- Aix-Marseille Université, CNRS, ICR, 13284 Marseille, France
| | - Yoelvis Orozco-Gonzalez
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Institut
de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 Université de Strasbourg-CNRS, F-67034 Strasbourg, France
- USIAS
Institut d’Études Avancées, Université de Strasbourg, 5 allée du Général Rouvillois, F-67083 Strasbourg, France
| | - Nicolas Ferré
- Aix-Marseille Université, CNRS, ICR, 13284 Marseille, France
| | - Hoi Ling Luk
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Hideki Kandori
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Japan
| | - Massimo Olivucci
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Institut
de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 Université de Strasbourg-CNRS, F-67034 Strasbourg, France
- USIAS
Institut d’Études Avancées, Université de Strasbourg, 5 allée du Général Rouvillois, F-67083 Strasbourg, France
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34
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Suomivuori CM, Lang L, Sundholm D, Gamiz-Hernandez AP, Kaila VRI. Tuning the Protein-Induced Absorption Shifts of Retinal in Engineered Rhodopsin Mimics. Chemistry 2016; 22:8254-61. [DOI: 10.1002/chem.201505126] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/23/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Carl-Mikael Suomivuori
- Department of Chemistry; University of Helsinki; A.I. Virtanens plats 1, P.O. Box 55 FI-00014 Helsinki Finland
- Department Chemie; Technische Universität München (TUM); Lichtenbergstrasse 4 85747 Garching Germany
| | - Lucas Lang
- Department Chemie; Technische Universität München (TUM); Lichtenbergstrasse 4 85747 Garching Germany
| | - Dage Sundholm
- Department of Chemistry; University of Helsinki; A.I. Virtanens plats 1, P.O. Box 55 FI-00014 Helsinki Finland
| | - Ana P. Gamiz-Hernandez
- Department Chemie; Technische Universität München (TUM); Lichtenbergstrasse 4 85747 Garching Germany
| | - Ville R. I. Kaila
- Department Chemie; Technische Universität München (TUM); Lichtenbergstrasse 4 85747 Garching Germany
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35
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Yang Y, Xu Z, Zhang Z, Yang Z, Liu Y, Wang J, Cai T, Li S, Chen K, Shi J, Zhu W. Like-Charge Guanidinium Pairing between Ligand and Receptor: An Unusual Interaction for Drug Discovery and Design? J Phys Chem B 2015; 119:11988-97. [DOI: 10.1021/acs.jpcb.5b04130] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yang Yang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhijian Xu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- State
Key Laboratory of Medicinal Chemical Biology, Nankai University, 94
Weijin Road, Nankai District, Tianjin300071, China
| | - Zhengyan Zhang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- College
of Chemistry, Chemical Engineering and Materials Science of Soochow
University, Soochow University, Suzhou, Jiangsu 215123, China
| | - Zhuo Yang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yingtao Liu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jinan Wang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tingting Cai
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shujin Li
- College
of Chemistry, Chemical Engineering and Materials Science of Soochow
University, Soochow University, Suzhou, Jiangsu 215123, China
| | - Kaixian Chen
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiye Shi
- Informatics
Department, UCB Pharma, 216 Bath Road, Slough SL1 4EN, United Kingdom
| | - Weiliang Zhu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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36
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 299] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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37
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 738] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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38
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Farrokhpour H, Pakatchian V, Hajipour A, Abyar F, Najafi Chermahini A, Fakhari F. Protein–ligand interaction study of signal transducer smoothened protein with different drugs: molecular docking and QM/MM calculations. RSC Adv 2015. [DOI: 10.1039/c5ra08609d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A part of signal transducer smoothened (SMO) protein including antitumor agent LY2940680. The site of this antitumor was considered for the docking of 716 ligands.
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Affiliation(s)
| | | | | | - Fatemeh Abyar
- Chemistry Department
- Isfahan University of Technology
- Isfahan
- Iran
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39
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Varsano D, Coccia E, Pulci O, Conte AM, Guidoni L. Ground state structures and electronic excitations of biological chromophores at Quantum Monte Carlo/Many Body Green’s Function Theory level. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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40
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Caprasecca S, Jurinovich S, Viani L, Curutchet C, Mennucci B. Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation. J Chem Theory Comput 2014; 10:1588-98. [DOI: 10.1021/ct500021d] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefano Caprasecca
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Risorgimento
35, 56126 Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Risorgimento
35, 56126 Pisa, Italy
| | - Lucas Viani
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Risorgimento
35, 56126 Pisa, Italy
| | - Carles Curutchet
- Departament
de Fisicoquímica Facultat de Farmàcia, Universitat de Barcelona Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Risorgimento
35, 56126 Pisa, Italy
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41
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Campomanes P, Neri M, Horta BAC, Röhrig UF, Vanni S, Tavernelli I, Rothlisberger U. Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle. J Am Chem Soc 2014; 136:3842-51. [DOI: 10.1021/ja411303v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Pablo Campomanes
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Marilisa Neri
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Bruno A. C. Horta
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Ute F. Röhrig
- Molecular Modeling
Group, Swiss Institute of
Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Stefano Vanni
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
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42
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McKeone R, Wikstrom M, Kiel C, Rakoczy PE. Assessing the correlation between mutant rhodopsin stability and the severity of retinitis pigmentosa. Mol Vis 2014; 20:183-99. [PMID: 24520188 PMCID: PMC3919671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 02/05/2014] [Indexed: 10/27/2022] Open
Abstract
PURPOSE Following a previous study that demonstrated a correlation between rhodopsin stability and the severity of retinitis pigmentosa (RP), we investigated whether predictions of severity can be improved with a regional analysis of this correlation. The association between changes to the stability of the protein and the relative amount of rhodopsin reaching the plasma membrane was assessed. METHODS Crystallography-based estimations of mutant rhodopsin stability were compared with descriptions in the scientific literature of the visual function of mutation carriers to determine the extent of associations between rhodopsin stability and clinical phenotype. To test the findings of this analysis, three residues of a green fluorescent protein (GFP) tagged rhodopsin plasmid were targeted with site-directed random mutagenesis to generate mutant variants with a range of stability changes. These plasmids were transfected into HEK-293 cells, and then flow cytometry was used to measure rhodopsin on the cells' plasma membrane. The GFP signal was used to measure the ratio between this membrane-bound rhodopsin and total cellular rhodopsin. FoldX stability predictions were then compared with the surface staining data and clinical data from the database to characterize the relationship between rhodopsin stability, the severity of RP, and the expression of rhodopsin at the cell surface. RESULTS There was a strong linear correlation between the scale of the destabilization of mutant variants and the severity of retinal disease. A correlation was also seen in vitro between stability and the amount of rhodopsin at the plasma membrane. Rhodopsin is drastically reduced on the surface of cells transfected with variants that differ in their inherent stability from the wild-type by more than 2 kcal/mol. Below this threshold, surface levels are closer to those of the wild-type. CONCLUSIONS There is a correlation between the stability of rhodopsin mutations and disease severity and levels of membrane-bound rhodopsin. Measuring membrane-bound rhodopsin with flow cytometry could improve prognoses for poorly characterized mutations and could provide a platform for measuring the effectiveness of treatments.
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Affiliation(s)
- Richard McKeone
- Department of Molecular Ophthalmology, Lions Eye Institute, Perth, Western Australia,Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Western Australia
| | - Matthew Wikstrom
- Centre for Experimental Immunology, Lions Eye Institute, Perth, Western Australia,Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Western Australia
| | - Christina Kiel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - P. Elizabeth Rakoczy
- Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Western Australia
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43
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Comparison of the isomerization mechanisms of human melanopsin and invertebrate and vertebrate rhodopsins. Proc Natl Acad Sci U S A 2014; 111:1714-9. [PMID: 24449866 DOI: 10.1073/pnas.1309508111] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Comparative modeling and ab initio multiconfigurational quantum chemistry are combined to investigate the reactivity of the human nonvisual photoreceptor melanopsin. It is found that both the thermal and photochemical isomerization of the melanopsin 11-cis retinal chromophore occur via a space-saving mechanism involving the unidirectional, counterclockwise twisting of the =C11H-C12H= moiety with respect to its Lys340-linked frame as proposed by Warshel for visual pigments [Warshel A (1976) Nature 260(5553):679-683]. A comparison with the mechanisms documented for vertebrate (bovine) and invertebrate (squid) visual photoreceptors shows that such a mechanism is not affected by the diversity of the three chromophore cavities. Despite such invariance, trajectory computations indicate that although all receptors display less than 100 fs excited state dynamics, human melanopsin decays from the excited state ∼40 fs earlier than bovine rhodopsin. Some diversity is also found in the energy barriers controlling thermal isomerization. Human melanopsin features the highest computed barrier which appears to be ∼2.5 kcal mol(-1) higher than that of bovine rhodopsin. When assuming the validity of both the reaction speed/quantum yield correlation discussed by Warshel, Mathies and coworkers [Weiss RM, Warshel A (1979) J Am Chem Soc 101:6131-6133; Schoenlein RW, Peteanu LA, Mathies RA, Shank CV (1991) Science 254(5030):412-415] and of a relationship between thermal isomerization rate and thermal activation of the photocycle, melanopsin turns out to be a highly sensitive pigment consistent with the low number of melanopsin-containing cells found in the retina and with the extraretina location of melanopsin in nonmammalian vertebrates.
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44
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Gozem S, Melaccio F, Luk HL, Rinaldi S, Olivucci M. Learning from photobiology how to design molecular devices using a computer. Chem Soc Rev 2014; 43:4019-36. [DOI: 10.1039/c4cs00037d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Learning how to model photo-responsive proteins may open the way to the design of lightpowered biomimetic molecular devices.
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Affiliation(s)
- S. Gozem
- Department of Chemistry
- Bowling Green State University
- Bowling Green, USA
| | - F. Melaccio
- Dipartimento di Chimica
- Università di Siena
- Siena, Italy
| | - H. L. Luk
- Department of Chemistry
- Bowling Green State University
- Bowling Green, USA
| | - S. Rinaldi
- Dipartimento di Chimica
- Università di Siena
- Siena, Italy
| | - M. Olivucci
- Department of Chemistry
- Bowling Green State University
- Bowling Green, USA
- Dipartimento di Chimica
- Università di Siena
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45
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Rivalta I, Nenov A, Garavelli M. Modelling retinal chromophores photoisomerization: from minimal models in vacuo to ultimate bidimensional spectroscopy in rhodopsins. Phys Chem Chem Phys 2014; 16:16865-79. [DOI: 10.1039/c3cp55211j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modelling of retinal photoisomerization in different environments is reviewed and ultimate ultrafast electronic spectroscopy is proposed for obtaining new insights.
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Affiliation(s)
- Ivan Rivalta
- Université de Lyon
- CNRS
- 69364 Lyon, Cedex 07, France
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
| | - Artur Nenov
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna, Italy
| | - Marco Garavelli
- Université de Lyon
- CNRS
- 69364 Lyon, Cedex 07, France
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
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46
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Zhou P, Liu J, Han K, He G. The photoisomerization of 11-cis-retinal protonated schiff base in gas phase: Insight from spin-flip density functional theory. J Comput Chem 2013; 35:109-20. [DOI: 10.1002/jcc.23463] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/12/2013] [Accepted: 09/24/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
| | - Jianyong Liu
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
| | - Guozhong He
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
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47
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Doemer M, Maurer P, Campomanes P, Tavernelli I, Rothlisberger U. Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin. J Chem Theory Comput 2013; 10:412-22. [PMID: 26579920 DOI: 10.1021/ct400697n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the retinal protonated Schiff base in dark state bovine rhodopsin. We were able to develop a highly accurate force field that is able to capture subtle structural changes within the chromophore that have a pronounced influence on the optical properties. The optical absorption spectrum calculated from configurations extracted from a MD trajectory using the new force field is in excellent agreement with QM/MM and experimental references.
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Affiliation(s)
- Manuel Doemer
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Patrick Maurer
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Pablo Campomanes
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Ivano Tavernelli
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Ursula Rothlisberger
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
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48
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Huix-Rotllant M, Filatov M, Gozem S, Schapiro I, Olivucci M, Ferré N. Assessment of Density Functional Theory for Describing the Correlation Effects on the Ground and Excited State Potential Energy Surfaces of a Retinal Chromophore Model. J Chem Theory Comput 2013; 9:3917-32. [PMID: 26592387 DOI: 10.1021/ct4003465] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In the quest for a cost-effective level of theory able to describe a large portion of the ground and excited potential energy surfaces of large chromophores, promising approaches are rooted in various approximations to the exact density functional theory (DFT). In the present work, we investigate how generalized Kohn-Sham DFT (GKS-DFT), time-dependent DFT (TDDFT), and spin-restricted ensemble-DFT (REKS) methods perform along three important paths characterizing a model retinal chromophore (the penta-2,4-dieniminium cation) in a region of near-degeneracy (close to a conical intersection) with respect to reference high-level multiconfigurational wave function methods. If GKS-DFT correctly describes the closed-shell charge transfer state, only TDDFT and REKS approaches give access to the open-shell diradical, one which sometimes corresponds to the electronic ground state. It is demonstrated that the main drawback of the usual DFT-based methods lies in the absence of interactions between the charge transfer and the diradicaloid configurations. Hence, we test a new computational scheme based on the State-averaged REKS (SA-REKS) approach, which explicitly includes these interactions into account. The State-Interaction SA-REKS (SI-SA-REKS) method significantly improves on the REKS and the SA-REKS results for the target system. The similarities and differences between DFT and wave function-based approaches are analyzed according to (1) the active space dimensions of the wave function-based methods and (2) the relative electronegativities of the allyl and protonated Schiff base moieties.
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Affiliation(s)
- Miquel Huix-Rotllant
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire , 13397 Marseille Cedex 20, France
| | - Michael Filatov
- Institut für Physicalische und Theoretische Chemie, Universität Bonn , Beringstr. 4, 53115 Bonn, Germany
| | - Samer Gozem
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43402, United States
| | - Igor Schapiro
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43402, United States.,Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34 - 36, Mülheim an der Ruhr, Germany
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43402, United States.,Dipartimento di Chimica, Università di Siena , Siena, Italy
| | - Nicolas Ferré
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire , 13397 Marseille Cedex 20, France
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49
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Kellie JL, Wetmore SD. Selecting DFT methods for use in optimizations of enzyme active sites: applications to ONIOM treatments of DNA glycosylases. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
When using a hybrid methodology to treat an enzymatic reaction, many factors contribute to selecting the method for the high-level region, which can be complicated by the presence of dispersion-driven interactions such as π–π stacking. In addition, the proper treatment of the reaction center often requires a large number of heavy atoms to be included in the high-level region, precluding the use of ab initio methods such as MP2 as well as large basis sets, in the optimization step. In the present work, popular DFT methods were tested to identify an appropriate functional for treating the high-level region in ONIOM optimizations of reactions catalyzed by nonmetalloenzymes. Eight different DFT methods (B3LYP, B97-2, MPW1K, MPWB1K, BB1K, B1B95, M06-2X, and ωB97X-D) in combination with four double-ζ quality Pople basis sets were tested for their ability to optimize noncovalent interactions (hydrogen bonding and π–π) and characterize reactions (proton transfer, SN2 hydrolysis, and unimolecular cleavage). Although the primary focus of this study is accurate structure determination, energetics were also examined at both the optimization level of theory, and with triple-ζ quality basis set and select (M06-2X or ωB97X-D) methods. If dispersion-driven interactions exist within the active site, then MPWB1K/6-31G(d,p) or M06-2X/6-31+G(d,p) are recommended for the optimization step with subsequent triple-ζ quality single-point energies. However, since dispersion-corrected functionals (M06-2X and ωB97X-D) generally require diffuse functions to yield appropriate geometries, the possible size of the high-level region is greatly limited with these methods. In contrast, if the model is large enough to recover steric constraints on π–π interactions, then B3LYP with a small basis set performs comparatively well for the optimization step and is significantly less computationally expensive. Interestingly, the functionals that afford the best geometries often do not yield the best energetics, which emphasizes the importance of structural benchmark studies.
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Affiliation(s)
- Jennifer L. Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
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50
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Valsson O, Campomanes P, Tavernelli I, Rothlisberger U, Filippi C. Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls. J Chem Theory Comput 2013; 9:2441-54. [PMID: 26583734 DOI: 10.1021/ct3010408] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bovine rhodopsin is the most extensively studied retinal protein and is considered the prototype of this important class of photosensitive biosystems involved in the process of vision. Many theoretical investigations have attempted to elucidate the role of the protein matrix in modulating the absorption of retinal chromophore in rhodopsin, but, while generally agreeing in predicting the correct location of the absorption maximum, they often reached contradicting conclusions on how the environment tunes the spectrum. To address this controversial issue, we combine here a thorough structural and dynamical characterization of rhodopsin with a careful validation of its excited-state properties via the use of a wide range of state-of-the-art quantum chemical approaches including various flavors of time-dependent density functional theory (TDDFT), different multireference perturbative schemes (CASPT2 and NEVPT2), and quantum Monte Carlo (QMC) methods. Through extensive quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, we obtain a comprehensive structural description of the chromophore-protein system and sample a wide range of thermally accessible configurations. We show that, in order to obtain reliable excitation properties, it is crucial to employ a sufficient number of representative configurations of the system. In fact, the common use of a single, ad hoc structure can easily lead to an incorrect model and an agreement with experimental absorption spectra due to cancelation of errors. Finally, we show that, to properly account for polarization effects on the chromophore and to quench the large blue-shift induced by the counterion on the excitation energies, it is necessary to adopt an enhanced description of the protein environment as given by a large quantum region including as many as 250 atoms.
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Affiliation(s)
- Omar Valsson
- MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Pablo Campomanes
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Claudia Filippi
- MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands
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