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Choudhury A, Santra S, Ghosh D. Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment. J Chem Theory Comput 2024; 20:4951-4964. [PMID: 38864715 DOI: 10.1021/acs.jctc.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.
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Affiliation(s)
- Arpan Choudhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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2
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Huang H, Peng J, Zhang Y, Gu FL, Lan Z, Xu C. The development of the QM/MM interface and its application for the on-the-fly QM/MM nonadiabatic dynamics in JADE package: Theory, implementation, and applications. J Chem Phys 2024; 160:234101. [PMID: 38884395 DOI: 10.1063/5.0215036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024] Open
Abstract
Understanding the nonadiabatic dynamics of complex systems is a challenging task in computational photochemistry. Herein, we present an efficient and user-friendly quantum mechanics/molecular mechanics (QM/MM) interface to run on-the-fly nonadiabatic dynamics. Currently, this interface consists of an independent set of codes designed for general-purpose use. Herein, we demonstrate the ability and feasibility of the QM/MM interface by integrating it with our long-term developed JADE package. Tailored to handle nonadiabatic processes in various complex systems, especially condensed phases and protein environments, we delve into the theories, implementations, and applications of on-the-fly QM/MM nonadiabatic dynamics. The QM/MM approach is established within the framework of the additive QM/MM scheme, employing electrostatic embedding, link-atom inclusion, and charge-redistribution schemes to treat the QM/MM boundary. Trajectory surface-hopping dynamics are facilitated using the fewest switches algorithm, encompassing classical and quantum treatments for nuclear and electronic motions, respectively. Finally, we report simulations of nonadiabatic dynamics for two typical systems: azomethane in water and the retinal chromophore PSB3 in a protein environment. Our results not only illustrate the power of the QM/MM program but also reveal the important roles of environmental factors in nonadiabatic processes.
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Affiliation(s)
- Haiyi Huang
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
- MOE Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jiawei Peng
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Yulin Zhang
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Feng Long Gu
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Zhenggang Lan
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Chao Xu
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
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3
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Blanco-Gonzalez A, Manathunga M, Yang X, Olivucci M. Comparative quantum-classical dynamics of natural and synthetic molecular rotors show how vibrational synchronization modulates the photoisomerization quantum efficiency. Nat Commun 2024; 15:3499. [PMID: 38664371 PMCID: PMC11045841 DOI: 10.1038/s41467-024-47477-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
We use quantum-classical trajectories to investigate the origin of the different photoisomerization quantum efficiency observed in the dim-light visual pigment Rhodopsin and in the light-driven biomimetic molecular rotor para-methoxy N-methyl indanylidene-pyrrolinium (MeO-NAIP) in methanol. Our results reveal that effective light-energy conversion requires, in general, an auxiliary molecular vibration (called promoter) that does not correspond to the rotary motion but synchronizes with it at specific times. They also reveal that Nature has designed Rhodopsin to exploit two mechanisms working in a vibrationally coherent regime. The first uses a wag promoter to ensure that ca. 75% of the absorbed photons lead to unidirectional rotations. The second mechanism ensures that the same process is fast enough to avoid directional randomization. It is found that MeO-NAIP in methanol is incapable of exploiting the above mechanisms resulting into a 50% quantum efficiency loss. However, when the solvent is removed, MeO-NAIP rotation is predicted to synchronize with a ring-inversion promoter leading to a 30% increase in quantum efficiency and, therefore, biomimetic behavior.
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Affiliation(s)
- Alejandro Blanco-Gonzalez
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Madushanka Manathunga
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Xuchun Yang
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Massimo Olivucci
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100, Siena, Italy.
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4
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Toldo JM, Mattos RS, Pinheiro M, Mukherjee S, Barbatti M. Recommendations for Velocity Adjustment in Surface Hopping. J Chem Theory Comput 2024; 20:614-624. [PMID: 38207213 DOI: 10.1021/acs.jctc.3c01159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
This study investigates velocity adjustment directions after hopping in surface hopping dynamics. Using fulvene and a protonated Schiff base (PSB4) as case studies, we investigate the population decay and reaction yields of different sets of dynamics with the velocity adjusted in either the nonadiabatic coupling, gradient difference, or momentum directions. For the latter, in addition to the conventional algorithm, we investigated the performance of a reduced kinetic energy reservoir approach recently proposed. Our evaluation also considered velocity adjustment in the directions of approximate nonadiabatic coupling vectors. While results for fulvene are susceptible to the adjustment approach, PSB4 is not. We correlated this dependence to the topography near the conical intersections. When nonadiabatic coupling vectors are unavailable, the gradient difference direction is the best adjustment option. If the gradient difference is also unavailable, a semiempirical vector direction or the momentum direction with a reduced kinetic energy reservoir becomes an excellent option to prevent an artificial excess of back hoppings. The precise velocity adjustment direction is less crucial for describing the nonadiabatic dynamics than the kinetic energy reservoir's size.
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Affiliation(s)
- Josene M Toldo
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
| | - Rafael S Mattos
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
| | - Max Pinheiro
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
| | | | - Mario Barbatti
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
- Institut Universitaire de France, Paris 75231, France
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Gruhl T, Weinert T, Rodrigues MJ, Milne CJ, Ortolani G, Nass K, Nango E, Sen S, Johnson PJM, Cirelli C, Furrer A, Mous S, Skopintsev P, James D, Dworkowski F, Båth P, Kekilli D, Ozerov D, Tanaka R, Glover H, Bacellar C, Brünle S, Casadei CM, Diethelm AD, Gashi D, Gotthard G, Guixà-González R, Joti Y, Kabanova V, Knopp G, Lesca E, Ma P, Martiel I, Mühle J, Owada S, Pamula F, Sarabi D, Tejero O, Tsai CJ, Varma N, Wach A, Boutet S, Tono K, Nogly P, Deupi X, Iwata S, Neutze R, Standfuss J, Schertler G, Panneels V. Ultrafast structural changes direct the first molecular events of vision. Nature 2023; 615:939-944. [PMID: 36949205 PMCID: PMC10060157 DOI: 10.1038/s41586-023-05863-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 02/17/2023] [Indexed: 03/24/2023]
Abstract
Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)1. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation2, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature3 to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.
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Affiliation(s)
- Thomas Gruhl
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Matthew J Rodrigues
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Christopher J Milne
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- European XFEL, Schenefeld, Germany
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Karol Nass
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Eriko Nango
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Saumik Sen
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Philip J M Johnson
- Photon Science Division, Laboratory for Nonlinear Optics, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Claudio Cirelli
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Biologics Center, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Petr Skopintsev
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Daniel James
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Physics, Utah Valley University, Orem, UT, USA
| | - Florian Dworkowski
- Photon Science Division, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Demet Kekilli
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Division Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Rie Tanaka
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hannah Glover
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Camila Bacellar
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Azeglio D Diethelm
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dardan Gashi
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Guillaume Gotthard
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ramon Guixà-González
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Victoria Kabanova
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- Laboratory for Ultrafast X-ray Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gregor Knopp
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Elena Lesca
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Pikyee Ma
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Isabelle Martiel
- Photon Science Division, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Jonas Mühle
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Shigeki Owada
- RIKEN SPring-8 Center, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Filip Pamula
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Daniel Sarabi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Oliver Tejero
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Ching-Ju Tsai
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Niranjan Varma
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Anna Wach
- Institute of Nuclear Physics Polish Academy of Sciences, Kraców, Poland
- Operando X-ray Spectroscopy, Energy and Environment Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Dioscuri Center For Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Xavier Deupi
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - So Iwata
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jörg Standfuss
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
- Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Valerie Panneels
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
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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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7
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Kabir MP, Ouedraogo D, Orozco-Gonzalez Y, Gadda G, Gozem S. Alternative Strategy for Spectral Tuning of Flavin-Binding Fluorescent Proteins. J Phys Chem B 2023; 127:1301-1311. [PMID: 36740810 PMCID: PMC9940217 DOI: 10.1021/acs.jpcb.2c06475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
iLOV is an engineered flavin-binding fluorescent protein (FbFP) with applications for in vivo cellular imaging. To expand the range of applications of FbFPs for multicolor imaging and FRET-based biosensing, it is desirable to understand how to modify their absorption and emission wavelengths (i.e., through spectral tuning). There is particular interest in developing FbFPs that absorb and emit light at longer wavelengths, which has proven challenging thus far. Existing spectral tuning strategies that do not involve chemical modification of the flavin cofactor have focused on placing positively charged amino acids near flavin's C4a and N5 atoms. Guided by previously reported electrostatic spectral tunning maps (ESTMs) of the flavin cofactor and by quantum mechanical/molecular mechanical (QM/MM) calculations reported in this work, we suggest an alternative strategy: placing a negatively charged amino acid near flavin's N1 atom. We predict that a single-point mutant, iLOV-Q430E, has a slightly red-shifted absorption and fluorescence maximum wavelength relative to iLOV. To validate our theoretical prediction, we experimentally expressed and purified iLOV-Q430E and measured its spectral properties. We found that the Q430E mutation results in a slight change in absorption and a 4-8 nm red shift in the fluorescence relative to iLOV, in good agreement with the computational predictions. Molecular dynamics simulations showed that the carboxylate side chain of the glutamate in iLOV-Q430E points away from the flavin cofactor, which leads to a future expectation that further red shifting may be achieved by bringing the side chain closer to the cofactor.
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8
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Smedley GD, McElroy KE, Feller KD, Serb JM. Additive and epistatic effects influence spectral tuning in molluscan retinochrome opsin. J Exp Biol 2022; 225:275511. [DOI: 10.1242/jeb.242929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 04/26/2022] [Indexed: 11/20/2022]
Abstract
The relationship between genotype and phenotype is nontrivial due to often complex molecular pathways that make it difficult to unambiguously relate phenotypes to specific genotypes. Photopigments, an opsin apoprotein bound to a light-absorbing chromophore, present an opportunity to directly relate the amino acid sequence to an absorbance peak phenotype (λmax). We examined this relationship by conducting a series of site-directed mutagenesis experiments of retinochrome, a non-visual opsin, from two closely related species: the common bay scallop, Argopecten irradians, and the king scallop, Pecten maximus. Using protein folding models, we identified three amino acid sites of likely functional importance and expressed mutated retinochrome proteins in vitro. Our results show that the mutation of amino acids lining the opsin binding pocket are responsible for fine spectral tuning, or small changes in the λmax of these light sensitive proteins Mutations resulted in a blue or red shift as predicted, but with dissimilar magnitudes. Shifts ranged from a 16 nm blue shift to a 12 nm red shift from the wild-type λmax. These mutations do not show an additive effect, but rather suggests the presence of epistatic interactions. This work highlights the importance of binding pocket shape in the evolution of spectral tuning and builds on our ability to relate genotypic changes to phenotypes in an emerging model for opsin functional analysis.
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Affiliation(s)
- G. Dalton Smedley
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
| | - Kyle E. McElroy
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
| | - Kathryn D. Feller
- Department of Biological Sciences, Union College, Schenectady, New York, USA
| | - Jeanne M. Serb
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
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9
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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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10
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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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11
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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: 7] [Impact Index Per Article: 2.3] [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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12
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Figon F, Casas J. The integrative biology of pigment organelles, a quantum chemical approach. Integr Comp Biol 2021; 61:1490-1501. [PMID: 33940609 DOI: 10.1093/icb/icab045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Coloration is a complex phenotypic trait involving both physical and chemical processes at a multiscale level, from molecules to tissues. Pigments, whose main property is to absorb specific wavelengths of visible light, are usually deposited in specialized organelles or complex matrices comprising proteins, metals, ions and redox compounds, among others. By modulating electronic properties and stability, interactions between pigments and these molecular actors can lead to color tuning. Furthermore, pigments are not only important for visual effects but also provide other critical functions, such as detoxification and antiradical activity. Hence, integrative studies of pigment organelles are required to understand how pigments interact with their cellular environment. In this review, we show how quantum chemistry, a computational method that models the molecular and optical properties of pigments, has provided key insights into the mechanisms by which pigment properties, from color to reactivity, are modulated by their organellar environment. These results allow to rationalize and to predict the way pigments behave in supramolecular complexes, up to the complete modelling of pigment organelles. We also discuss the main limitations of quantum chemistry, emphasizing the need for carrying experimental work with identical vigor. We finally suggest that taking into account the ecology of pigments (i.e. how they interact with these various other cellular components and at higher organizational levels) will lead to a greater understanding of how and why animals are vividly and variably colored, two fundamental questions in organismal biology.
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Affiliation(s)
- Florent Figon
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, 37200 Tours, France
| | - Jérôme Casas
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, 37200 Tours, France
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13
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Fedorov AK, Gelfand MS. Towards practical applications in quantum computational biology. NATURE COMPUTATIONAL SCIENCE 2021; 1:114-119. [PMID: 38217223 DOI: 10.1038/s43588-021-00024-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/12/2021] [Indexed: 01/15/2024]
Abstract
Fascinating progress in understanding our world at the smallest scales moves us to the border of a new technological revolution governed by quantum physics. By taking advantage of quantum phenomena, quantum computing devices allow a speedup in solving diverse tasks. In this Perspective, we discuss the potential impact of quantum computing on computational biology. Bearing in mind the limitations of existing quantum computing devices, we attempt to indicate promising directions for further research in the emerging area of quantum computational biology.
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Affiliation(s)
- A K Fedorov
- Russian Quantum Center, Moscow, Russia.
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - M S Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Kharkevitch Institute for Information Transmission Problems, Moscow, Russia
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14
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Abstract
Microbial rhodopsins are distributed through many microorganisms. Heliorhodopsins are newly discovered but have an unclear function. They have seven transmembrane helices similar to type-I and type-II rhodopsins, but they are different in that the N-terminal region of heliorhodopsin is cytoplasmic. We chose 13 representative heliorhodopsins from various microorganisms, expressed and purified with an N-terminal His tag, and measured the absorption spectra. The 13 natural variants had an absorption maximum (λmax) in the range 530–556 nm similar to proteorhodopsin (λmax = 490–525 nm). We selected several candidate residues that influence rhodopsin color-tuning based on sequence alignment and constructed mutants via site-directed mutagenesis to confirm the spectral changes. We found two important residues located near retinal chromophore that influence λmax. We also predict the 3D structure via homology-modeling of Thermoplasmatales heliorhodopsin. The results indicate that the color-tuning mechanism of type-I rhodopsin can be applied to understand the color-tuning of heliorhodopsin.
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15
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Bauer B, Bravyi S, Motta M, Chan GKL. Quantum Algorithms for Quantum Chemistry and Quantum Materials Science. Chem Rev 2020; 120:12685-12717. [DOI: 10.1021/acs.chemrev.9b00829] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Bela Bauer
- Microsoft Quantum, Station Q, University of California
, Santa Barbara, California 93106, United States
| | - Sergey Bravyi
- IBM Quantum, IBM T. J. Watson Research Center
, Yorktown Heights, New York 10598, United States
| | - Mario Motta
- IBM Quantum, IBM Research Almaden
, San Jose, California 95120, United States
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology
, Pasadena, California 91125, United States
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16
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Marsili E, Olivucci M, Lauvergnat D, Agostini F. Quantum and Quantum-Classical Studies of the Photoisomerization of a Retinal Chromophore Model. J Chem Theory Comput 2020; 16:6032-6048. [PMID: 32931266 DOI: 10.1021/acs.jctc.0c00679] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report an in-depth analysis of the photo-induced isomerization of the 2-cis-penta-2,4-dieniminium cation: a minimal model of the 11-cis retinal protonated Schiff base chromophore of the dim-light photoreceptor rhodopsin. Based on recently developed three-dimensional potentials parametrized on ab initio multi-state multi-configurational second-order perturbation theory data, we perform quantum-dynamical studies. In addition, simulations based on various quantum-classical methods, among which Tully surface hopping and the coupled-trajectory approach derived from the exact factorization, allow us to validate their performance against vibronic wavepacket propagation and, therefore, a purely quantum treatment. Quantum-dynamics results uncover qualitative differences with respect to the two-dimensional Hahn-Stock potentials, widely used as model potentials for the isomerization of the same chromophore, due to the increased dimensionality and three-mode correlation. Quantum-classical simulations show, instead, that three-dimensional model potentials are capable of capturing a number of features revealed by atomistic simulations and experimental observations. In particular, a recently reported vibrational phase relationship between double-bond torsion and hydrogen-out-of-plane modes critical for rhodopsin isomerization efficiency is correctly reproduced.
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Affiliation(s)
- Emanuele Marsili
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France.,Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Massimo Olivucci
- Department of Biotechnology, 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
| | - David Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
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17
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Shigaev AS, Feldman TB, Nadtochenko VA, Ostrovsky MA, Lakhno VD. Quantum-classical model of the rhodopsin retinal chromophore cis–trans photoisomerization with modified inter-subsystem coupling. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Aquilante F, Autschbach J, Baiardi A, Battaglia S, Borin VA, Chibotaru LF, Conti I, De Vico L, Delcey M, Fdez Galván I, Ferré N, Freitag L, Garavelli M, Gong X, Knecht S, Larsson ED, Lindh R, Lundberg M, Malmqvist PÅ, Nenov A, Norell J, Odelius M, Olivucci M, Pedersen TB, Pedraza-González L, Phung QM, Pierloot K, Reiher M, Schapiro I, Segarra-Martí J, Segatta F, Seijo L, Sen S, Sergentu DC, Stein CJ, Ungur L, Vacher M, Valentini A, Veryazov V. Modern quantum chemistry with [Open]Molcas. J Chem Phys 2020; 152:214117. [PMID: 32505150 DOI: 10.1063/5.0004835] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
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Affiliation(s)
- Francesco Aquilante
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260-3000, USA
| | - Alberto Baiardi
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stefano Battaglia
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Veniamin A Borin
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Liviu F Chibotaru
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Irene Conti
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Mickaël Delcey
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Ignacio Fdez Galván
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Nicolas Ferré
- Aix-Marseille University, CNRS, Institut Chimie Radicalaire, Marseille, France
| | - Leon Freitag
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Xuejun Gong
- Department of Chemistry, University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Stefan Knecht
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Ernst D Larsson
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
| | - Roland Lindh
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Marcus Lundberg
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Per Åke Malmqvist
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Jesper Norell
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Michael Odelius
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Thomas B Pedersen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Laura Pedraza-González
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Quan M Phung
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Kristine Pierloot
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Javier Segarra-Martí
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, United Kingdom
| | - Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Luis Seijo
- Departamento de Química, Instituto Universitario de Ciencia de Materiales Nicolás Cabrera, and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Saumik Sen
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | | | - Christopher J Stein
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Liviu Ungur
- Department of Chemistry, University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Morgane Vacher
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 44300 Nantes, France
| | - Alessio Valentini
- Theoretical Physical Chemistry, Research Unit MolSys, Université de Liège, Allée du 6 Août, 11, 4000 Liège, Belgium
| | - Valera Veryazov
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
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19
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Saura P, Röpke M, Gamiz-Hernandez AP, Kaila VRI. Quantum Chemical and QM/MM Models in Biochemistry. Methods Mol Biol 2020; 2022:75-104. [PMID: 31396900 DOI: 10.1007/978-1-4939-9608-7_4] [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] [Indexed: 02/25/2023]
Abstract
Quantum chemical (QC) calculations provide a basis for deriving a microscopic understanding of enzymes and photobiological systems. Here we describe how QC models can be used to explore the electronic structure, dynamics, and energetics of biomolecules. We introduce the hybrid quantum mechanics/classical mechanics (QM/MM) approach, where a quantum mechanically described system of interest is embedded in a classically described force field representation of the biochemical surroundings. We also discuss the QM cluster model approach, as well as embedding theories, that provide complementary methodologies to model quantum mechanical effects in biomolecules. The chapter also provides some practical guides for building quantum biochemical models using the quinone reduction catalysis in respiratory complex I and a model reaction in solution as examples.
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Affiliation(s)
- Patricia Saura
- Department Chemie, Technische Universität München, Garching, Germany
| | - Michael Röpke
- Department Chemie, Technische Universität München, Garching, Germany
| | | | - Ville R I Kaila
- Department Chemie, Technische Universität München, Garching, Germany.
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20
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Pawlak M, Szidarovszky T, Halász GJ, Vibók Á. Robust field-dressed spectra of diatomics in an optical lattice. Phys Chem Chem Phys 2020; 22:3715-3723. [PMID: 32003765 DOI: 10.1039/c9cp06587c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The absorption spectra of the cold Na2 molecule dressed by a linearly polarized standing laser wave is investigated with a theoretical model incorporating translational, electronic, vibrational as well as rotational degrees of freedom. In such a situation a light-induced conical intersection (LICI) can be formed (J. Phys. B: At. Mol. Opt. Phys., 2008, 41, 221001). To measure the spectra a weak field is used whose propagation direction is perpendicular to the direction of the dressing field but has identical polarization direction. Although LICIs are present in our model, the simulations demonstrate a very robust absorption spectrum, which is insensitive to the intensity and the wavelength of the dressing field and which does not reflect clear signatures of light-induced nonadiabatic phenomena related to the strong mixing between the electronic, vibrational, rotational and translational motions. However, by widening artificially the very narrow translational energy level gaps, the fingerprint of the LICI appears to some extent in the spectrum.
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Affiliation(s)
- Mariusz Pawlak
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland.
| | - Tamás Szidarovszky
- Laboratory of Molecular Structure and Dynamics, Institute of Chemistry, ELTE Eötvös Loránd University and MTA-ELTE Complex Chemical Systems Research Group, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Gábor J Halász
- Department of Information Technology, University of Debrecen, H-4002 Debrecen, PO Box 400, Hungary
| | - Ágnes Vibók
- Department of Theoretical Physics, University of Debrecen, H-4002 Debrecen, PO Box 400, Hungary. and ELI-ALPS, ELI-HU Non-Profit Ltd, H-6720 Szeged, Dugonics tér 13, Hungary
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21
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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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22
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Misra R, Hirshfeld A, Sheves M. Molecular mechanism for thermal denaturation of thermophilic rhodopsin. Chem Sci 2019; 10:7365-7374. [PMID: 31489158 PMCID: PMC6713869 DOI: 10.1039/c9sc00855a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/18/2019] [Indexed: 12/29/2022] Open
Abstract
Understanding the factors affecting the stability and function of proteins at the molecular level is of fundamental importance. In spite of their use in bioelectronics and optogenetics, factors influencing thermal stability of microbial rhodopsins, a class of photoreceptor protein ubiquitous in nature are not yet well-understood. Here we report on the molecular mechanism for thermal denaturation of microbial retinal proteins, including, a highly thermostable protein, thermophilic rhodopsin (TR). External stimuli-dependent thermal denaturation of TR, the proton pumping rhodopsin of Thermus thermophilus bacterium, and other microbial rhodopsins are spectroscopically studied to decipher the common factors guiding their thermal stability. The thermal denaturation process of the studied proteins is light-catalyzed and the apo-protein is thermally less stable than the corresponding retinal-covalently bound opsin. In addition, changes in structure of the retinal chromophore affect the thermal stability of TR. Our results indicate that the hydrolysis of the retinal protonated Schiff base (PSB) is the rate-determining step for denaturation of the TR as well as other retinal proteins. Unusually high thermal stability of TR multilayers, in which PSB hydrolysis is restricted due to lack of bulk water, strongly supports this proposal. Our results also show that the protonation state of the PSB counter-ion does not affect the thermal stability of the studied proteins. Thermal photo-bleaching of an artificial TR pigment derived from non-isomerizable trans-locked retinal suggests, rather counterintuitively, that the photoinduced retinal trans-cis isomerization is not a pre-requisite for light catalyzed thermal denaturation of TR. Protein conformation alteration triggered by light-induced retinal excited state formation is likely to facilitate the PSB hydrolysis.
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Affiliation(s)
- Ramprasad Misra
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel .
| | - Amiram Hirshfeld
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel .
| | - Mordechai Sheves
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel .
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23
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Agathangelou D, Orozco-Gonzalez Y, Del Carmen Marín M, Roy PP, Brazard J, Kandori H, Jung KH, Léonard J, Buckup T, Ferré N, Olivucci M, Haacke S. Effect of point mutations on the ultrafast photo-isomerization of Anabaena sensory rhodopsin. Faraday Discuss 2019; 207:55-75. [PMID: 29388996 DOI: 10.1039/c7fd00200a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anabaena sensory rhodopsin (ASR) is a particular microbial retinal protein for which light-adaptation leads to the ability to bind both the all-trans, 15-anti (AT) and the 13-cis, 15-syn (13C) isomers of the protonated Schiff base of retinal (PSBR). In the context of obtaining insight into the mechanisms by which retinal proteins catalyse the PSBR photo-isomerization reaction, ASR is a model system allowing to study, within the same protein, the protein-PSBR interactions for two different PSBR conformers at the same time. A detailed analysis of the vibrational spectra of AT and 13C, and their photo-products in wild-type ASR obtained through femtosecond (pump-) four-wave-mixing is reported for the first time, and compared to bacterio- and channelrhodopsin. As part of an extensive study of ASR mutants with blue-shifted absorption spectra, we present here a detailed computational analysis of the origin of the mutation-induced blue-shift of the absorption spectra, and identify electrostatic interactions as dominating steric effects that would entail a red-shift. The excited state lifetimes and isomerization reaction times (IRT) for the three mutants V112N, W76F, and L83Q are studied experimentally by femtosecond broadband transient absorption spectroscopy. Interestingly, in all three mutants, isomerization is accelerated for AT with respect to wild-type ASR, and this the more, the shorter the wavelength of maximum absorption. On the contrary, the 13C photo-reaction is slightly slowed down, leading to an inversion of the ESLs of AT and 13C, with respect to wt-ASR, in the blue-most absorbing mutant L83Q. Possible mechanisms for these mutation effects, and their steric and electrostatic origins are discussed.
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Affiliation(s)
- D Agathangelou
- University of Strasbourg, CNRS, Inst. de Physique et Chimie des Matériaux de Strasbourg, 67034 Strasbourg, France.
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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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25
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Valentini A, Nucci M, Frutos LM, Marazzi M. Photosensitized Retinal Isomerization in Rhodopsin Mediated by a Triplet State. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Alessio Valentini
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Department of Biotechnology, Chemistry and PharmacyUniversity of Siena via A. Moro 2 53100 Siena Italy
- Theoretical Physical Chemistry, Research Unit MolSysUniversité de Liège Allée du 6 Aôut, 11 4000 Liège Belgium
| | - Martina Nucci
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
| | - Luis Manuel Frutos
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR)Universidad de Alcalá E-28871 Alcalá de Henares, Madrid Spain
| | - Marco Marazzi
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR)Universidad de Alcalá E-28871 Alcalá de Henares, Madrid Spain
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26
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Red-shifting mutation of light-driven sodium-pump rhodopsin. Nat Commun 2019; 10:1993. [PMID: 31040285 PMCID: PMC6491443 DOI: 10.1038/s41467-019-10000-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 04/12/2019] [Indexed: 11/08/2022] Open
Abstract
Microbial rhodopsins are photoreceptive membrane proteins that transport various ions using light energy. While they are widely used in optogenetics to optically control neuronal activity, rhodopsins that function with longer-wavelength light are highly demanded because of their low phototoxicity and high tissue penetration. Here, we achieve a 40-nm red-shift in the absorption wavelength of a sodium-pump rhodopsin (KR2) by altering dipole moment of residues around the retinal chromophore (KR2 P219T/S254A) without impairing its ion-transport activity. Structural differences in the chromophore of the red-shifted protein from that of the wildtype are observed by Fourier transform infrared spectroscopy. QM/MM models generated with an automated protocol show that the changes in the electrostatic interaction between protein and chromophore induced by the amino-acid replacements, lowered the energy gap between the ground and the first electronically excited state. Based on these insights, a natural sodium pump with red-shifted absorption is identified from Jannaschia seosinensis. Microbial rhodopsins are photoreceptive and widely used in optogenetics for which they should preferable function with longer-wavelength light. Here, authors achieve a 40-nm red-shift in the absorption wavelength of a sodium-pump rhodopsin (KR2) by altering the distribution of the retinal chromophore.
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27
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Orozco-Gonzalez Y, Kabir MP, Gozem S. Electrostatic Spectral Tuning Maps for Biological Chromophores. J Phys Chem B 2019; 123:4813-4824. [DOI: 10.1021/acs.jpcb.9b00489] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Mohammad Pabel Kabir
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
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28
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García-Iriepa C, Sampedro D, Mendicuti F, Léonard J, Frutos LM. Photoreactivity Control Mediated by Molecular Force Probes in Stilbene. J Phys Chem Lett 2019; 10:1063-1067. [PMID: 30707586 DOI: 10.1021/acs.jpclett.8b03802] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We report theoretical and experimental evidence showing that photochemical reactivity of a chromophore can be modified by applying mechanical forces via molecular force probes. This mechanical action permits us to modulate main photochemical properties, such as fluorescence yield, excited-state lifetime, or photoisomerization quantum yield. The effect of molecular force probes can be rationalized in terms of simple mechanochemical models, establishing a qualitative framework for understanding the mechanical control of photoreactivity in stilbenes.
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Affiliation(s)
- Cristina García-Iriepa
- Departamento de Química Analítica, Química Física e Ingeniería Química , Universidad de Alcalá , E-28871 Alcalá de Henares, Madrid , Spain
- Departamento de Química, Centro de Investigación en Síntesis Química (CISQ) , Universidad de La Rioja , E-26006 Logroño , Spain
| | - Diego Sampedro
- Departamento de Química, Centro de Investigación en Síntesis Química (CISQ) , Universidad de La Rioja , E-26006 Logroño , Spain
| | - Francisco Mendicuti
- Departamento de Química Analítica, Química Física e Ingeniería Química , Universidad de Alcalá , E-28871 Alcalá de Henares, Madrid , Spain
- Instituto de Investigación Química "Andrés M. del Río" , Universidad de Alcalá , 28805 Alcalá de Henares, Madrid , Spain
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg , Université de Strasbourg , CNRS, UMR 7504 and Labex NIE, 67034 Strasbourg , France
| | - Luis Manuel Frutos
- Departamento de Química Analítica, Química Física e Ingeniería Química , Universidad de Alcalá , E-28871 Alcalá de Henares, Madrid , Spain
- Instituto de Investigación Química "Andrés M. del Río" , Universidad de Alcalá , 28805 Alcalá de Henares, Madrid , Spain
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29
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Sala M, Egorova D. Quantum dynamics of multi-dimensional rhodopsin photoisomerization models: Approximate versus accurate treatment of the secondary modes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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30
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Grabarek D, Andruniów T. Initial excited-state relaxation of locked retinal protonated schiff base chromophore. An insight from coupled cluster and multireference perturbation theory calculations. J Comput Chem 2018; 39:1720-1727. [PMID: 29727036 DOI: 10.1002/jcc.25346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/06/2018] [Accepted: 04/12/2018] [Indexed: 11/07/2022]
Abstract
The initial S1 excited-state relaxation of retinal protonated Schiff base (RPSB) analog with central C11C12 double bond locked by eight-membered ring (locked-11.8) was investigated by means of multireference perturbation theory methods (XMCQDPT2, XMS-CASPT2, MS-CASPT2) as well as single-reference coupled-cluster CC2 method. The analysis of XMCQDPT2-based geometries reveals rather weak coupling between in-plane and out-of-plane structural evolution and minor energetical relaxation of three locked-11.8 conformers. Therefore, a strong coupling between bonds length inversion and backbone out-of-plane deformation resulting in a very steep S1 energy profile predicted by CASSCF/CASPT2 calculations is in clear contradiction with the reference XMCQDPT2 results. Even though CC2 method predicts good quality ground-state structures, the excited-state structures display more advanced torsional deformation leading to ca. 0.2 eV exaggerated energy relaxation and significantly red shifted (0.4-0.7 eV) emission maxima. According to our findings, the initial photoisomerization process in locked-11.8, and possibly in other RPSB analogs, studied fully (both geometries and energies) by multireference perturbation theory may be somewhat slower than predicted by CASSCF/CASPT2 or CC2 methods. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Dawid Grabarek
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
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31
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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32
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Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Northwestern University , Evanston, IL, USA
| | - Toru Shiozaki
- Department of Chemistry, Northwestern University , Evanston, IL, USA
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33
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Barata-Morgado R, Sánchez ML, Muñoz-Losa A, Martín ME, Olivares Del Valle FJ, Aguilar MA. How Methylation Modifies the Photophysics of the Native All- trans-Retinal Protonated Schiff Base: A CASPT2/MD Study in Gas Phase and in Methanol. J Phys Chem A 2018; 122:3096-3106. [PMID: 29489369 DOI: 10.1021/acs.jpca.8b00773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A comparison between the free-energy surfaces of the all- trans-retinal protonated Schiff base (RPSB) and its 10-methylated derivative in gas phase and methanol solution is performed at CASSCF//CASSCF and CASPT2//CASSCF levels. Solvent effects were included using the average solvent electrostatic potential from molecular dynamics method. This is a QM/MM (quantum mechanics/molecular mechanics) method that makes use of the mean field approximation. It is found that the methyl group bonded to C10 produces noticeable changes in the solution free-energy profile of the S1 excited state, mainly in the relative stability of the minimum energy conical intersections (MECIs) with respect to the Franck-Condon (FC) point. The conical intersections yielding the 9- cis and 11- cis isomers are stabilized while that yielding the 13- cis isomer is destabilized; in fact, it becomes inaccessible by excitation to S1. Furthermore, the planar S1 minimum is not present in the methylated compound. The solvent notably stabilizes the S2 excited state at the FC geometry. Therefore, if the S2 state has an effect on the photoisomerization dynamics, it must be because it permits the RPSB population to branch around the FC point. All these changes combine to speed up the photoisomerization in the 10-methylated compound with respect to the native compound.
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Affiliation(s)
- Rute Barata-Morgado
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
| | - M Luz Sánchez
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
| | - Aurora Muñoz-Losa
- Dpto. Didáctica de las Ciencias Experimentales y Matemáticas, Facultad de Formación del Profesorado , University of Extremadura , Avda. Universidad s/n , Cáceres 10003 , Spain
| | - M Elena Martín
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
| | - Francisco J Olivares Del Valle
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
| | - Manuel A Aguilar
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
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34
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Barca GMJ, Gilbert ATB, Gill PMW. Simple Models for Difficult Electronic Excitations. J Chem Theory Comput 2018; 14:1501-1509. [DOI: 10.1021/acs.jctc.7b00994] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giuseppe M. J. Barca
- Research School of Chemistry, Australian National University, Acton ACT 2601, Australia
| | - Andrew T. B. Gilbert
- Research School of Chemistry, Australian National University, Acton ACT 2601, Australia
| | - Peter M. W. Gill
- Research School of Chemistry, Australian National University, Acton ACT 2601, Australia
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35
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Guo Y, Wolff FE, Schapiro I, Elstner M, Marazzi M. Different hydrogen bonding environments of the retinal protonated Schiff base control the photoisomerization in channelrhodopsin-2. Phys Chem Chem Phys 2018; 20:27501-27509. [DOI: 10.1039/c8cp05210g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The first event of the channelrhodopsin-2 (ChR2) photocycle, i.e. trans-to-cis photoisomerization, is studied by means of quantum mechanics/molecular mechanics, taking into account the flexible retinal environment in the ground state.
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Affiliation(s)
- Yanan Guo
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Franziska E. Wolff
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research
- Institute of Chemistry
- Hebrew University of Jerusalem
- Jerusalem
- Israel
| | - Marcus Elstner
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Marco Marazzi
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
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36
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Farag MH, Jansen TLC, Knoester J. The origin of absorptive features in the two-dimensional electronic spectra of rhodopsin. Phys Chem Chem Phys 2018; 20:12746-12754. [DOI: 10.1039/c8cp00638e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A three-state three-mode model Hamiltonian reveals the origin of the absorptive features in the two-dimensional electronic spectra of rhodopsin.
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Affiliation(s)
- Marwa H. Farag
- University of Groningen
- Zernike Institute for Advanced Materials
- 9747 AG Groningen
- The Netherlands
| | - Thomas L. C. Jansen
- University of Groningen
- Zernike Institute for Advanced Materials
- 9747 AG Groningen
- The Netherlands
| | - Jasper Knoester
- University of Groningen
- Zernike Institute for Advanced Materials
- 9747 AG Groningen
- The Netherlands
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37
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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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38
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Szefczyk B, Grabarek D, Walczak E, Andruniów T. Excited-state minima and emission energies of retinal chromophore analogues: Performance of CASSCF and CC2 methods as compared with CASPT2. J Comput Chem 2017; 38:1799-1810. [PMID: 28512740 DOI: 10.1002/jcc.24821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/10/2017] [Accepted: 04/13/2017] [Indexed: 11/08/2022]
Abstract
This study provides gas-phase S1 excited-state geometries along with emission and adiabatic energies for methylated/demethylated and ring-locked analogues of protonated Schiff base retinal models comprising system of five conjugated double bonds (PSB5), using second order multiconfiguration perturbation theory (CASPT2). CASPT2 results serve as reference data to assess the performance of CC2 (second-order approximate coupled cluster singles and doubles) and a commonly used CASSCF/CASPT2 protocol, that is, complete active space self-consistent field (CASSCF) geometry optimization followed by CASPT2 energy calculation. We find that the CASSCF methodology fails to locate planar S1 minimum energy structures for four out of five investigated planar models in contrast to CC2 and CASPT2 methods. However, for those which were found: one planar and two twisted minima, there is an excellent agreement between CASSCF and CASPT2 results in terms of geometrical parameters, one-electron properties, as well as emission and adiabatic energies. CC2 performs well for in-plane S1 minima and their spectroscopic and electronic properties. However, this picture deteriorates for twisted minima. As expected, the CC2 description of the S2 electronic state, with strong multireference and significant double excitation character, is very poor, exhibiting errors in transition energies exceeding 1 eV. They may be substantially diminished by recalculating transition energies with CASPT2 method. Our work shows that CASSCF/CASPT2 and CC2 shortcomings may influence gas-phase retinal analogues' excited state description in a dramatic way. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Borys Szefczyk
- Advanced Materials Engineering and Modelling Group, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Dawid Grabarek
- Advanced Materials Engineering and Modelling Group, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Elżbieta Walczak
- Advanced Materials Engineering and Modelling Group, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
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39
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Kamiya M, Hayashi S. Photoactivation Intermediates of a G-Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation. J Phys Chem B 2017; 121:3842-3852. [PMID: 28240904 DOI: 10.1021/acs.jpcb.6b13050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopsin is a G-protein coupled receptor functioning as a photoreceptor for vision through photoactivation of a covalently bound ligand of a retinal protonated Schiff base chromophore. Despite the availability of structural information on the inactivated and activated forms of the receptor, the transition processes initiated by the photoabsorption have not been well understood. Here we theoretically examined the photoactivation processes by means of molecular dynamics (MD) simulations and ab initio quantum mechanical/molecular mechanical (QM/MM) free energy geometry optimizations which enabled accurate geometry determination of the ligand molecule in ample statistical conformational samples of the protein. Structures of the intermediate states of the activation process, blue-shifted intermediate and Lumi, as well as the dark state first generated by MD simulations and then refined by the QM/MM free energy geometry optimizations were characterized by large displacement of the β-ionone ring of retinal along with change in the hydrogen bond of the protonated Schiff base. The ab initio calculations of vibrational and electronic spectroscopic properties of those states well reproduced the experimental observations and successfully identified the molecular origins underlying the spectroscopic features. The structural evolution in the formation of the intermediates provides a molecular insight into the efficient activation processes of the receptor.
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Affiliation(s)
- Motoshi Kamiya
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
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40
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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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41
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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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42
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Lakhno VD, Shigaev AS, Feldman TB, Nadtochenko VA, Ostrovsky MA. Quantum-classical model of retinal photoisomerization reaction in visual pigment rhodopsin. DOKL BIOCHEM BIOPHYS 2017; 471:435-439. [PMID: 28058680 DOI: 10.1134/s1607672916060168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Indexed: 11/23/2022]
Abstract
A quantum-classical model of photoisomerization of the visual pigment rhodopsin chromophore is proposed. At certain (and more realistic) parameter value combinations, the model is shown to accurately reproduce a number of independent experimental data on the photoreaction dynamics: the quantum yield, the time to reach the point of conical intersection of potential energy surfaces, the termination time of the evolution of quantum subsystem, as well as the characteristic low frequencies of retinal molecular lattice fluctuations during photoisomerization. In addition, the model behavior is in good accordance with experimental data about coherence and local character of quantum transition.
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Affiliation(s)
- V D Lakhno
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences-branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russia
| | - A S Shigaev
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences-branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russia.
| | - T B Feldman
- Moscow State University, Moscow, 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
| | - V A Nadtochenko
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - M A Ostrovsky
- Moscow State University, Moscow, 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
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43
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Stenrup M, Pieri E, Ledentu V, Ferré N. pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin. Phys Chem Chem Phys 2017; 19:14073-14084. [DOI: 10.1039/c7cp00991g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A minimal electrostatic model is introduced which aims at reproducing and analyzing the visible-light absorption energy shift of a protein with pH.
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44
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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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45
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Hedegård ED, Reiher M. Polarizable Embedding Density Matrix Renormalization Group. J Chem Theory Comput 2016; 12:4242-53. [PMID: 27537835 DOI: 10.1021/acs.jctc.6b00476] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The polarizable embedding (PE) approach is a flexible embedding model where a preselected region out of a larger system is described quantum mechanically, while the interaction with the surrounding environment is modeled through an effective operator. This effective operator represents the environment by atom-centered multipoles and polarizabilities derived from quantum mechanical calculations on (fragments of) the environment. Thereby, the polarization of the environment is explicitly accounted for. Here, we present the coupling of the PE approach with the density matrix renormalization group (DMRG). This PE-DMRG method is particularly suitable for embedded subsystems that feature a dense manifold of frontier orbitals which requires large active spaces. Recovering such static electron-correlation effects in multiconfigurational electronic structure problems, while accounting for both electrostatics and polarization of a surrounding environment, allows us to describe strongly correlated electronic structures in complex molecular environments. We investigate various embedding potentials for the well-studied first excited state of water with active spaces that correspond to a full configuration-interaction treatment. Moreover, we study the environment effect on the first excited state of a retinylidene Schiff base within a channelrhodopsin protein. For this system, we also investigate the effect of dynamical correlation included through short-range density functional theory.
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Affiliation(s)
- Erik D Hedegård
- Laboratorium für Physikalische Chemie, ETH Zürich , Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich , Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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46
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Farag MH, Jansen TLC, Knoester J. Probing the Interstate Coupling near a Conical Intersection by Optical Spectroscopy. J Phys Chem Lett 2016; 7:3328-3334. [PMID: 27509384 DOI: 10.1021/acs.jpclett.6b01463] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Conical intersections are points where adiabatic potential energy surfaces cross. The interstate coupling between the potential energy surfaces plays a crucial role in many processes associated with conical intersections. Still no method exists to measure this coupling driving the chemical reactions between the potential energy surfaces involved. In this Letter, using a generic model for photoisomerization, we propose a novel experimental approach to estimate the coupling that mixes the electronic states near a conical intersection. The approach is based on analyzing the vibrational wavepacket of the reactant in the adiabatic ground and excited electronic states. The nuclear wavepacket dynamics are extracted from linear absorption and two-dimensional electronic spectroscopy. Comparing the frequencies of the coupling mode in the adiabatic ground and excited states from models with and without coupling between the potential energy surfaces suggests an experimental tool to determine the interstate coupling.
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Affiliation(s)
- Marwa H Farag
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jasper Knoester
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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47
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El-Tahawy MMT, Nenov A, Garavelli M. Photoelectrochromism in the Retinal Protonated Schiff Base Chromophore: Photoisomerization Speed and Selectivity under a Homogeneous Electric Field at Different Operational Regimes. J Chem Theory Comput 2016; 12:4460-75. [DOI: 10.1021/acs.jctc.6b00558] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mohsen M. T. El-Tahawy
- Dipartimento
di Chimica “G. Ciamician″, Universita’ degli Studi di Bologna, Via Selmi, 2 I - 40126 Bologna, Italy
- Chemistry
Department, Faculty of Science, Damanhour University, Damanhour 22511, Egypt
| | - Artur Nenov
- Dipartimento
di Chimica “G. Ciamician″, Universita’ degli Studi di Bologna, Via Selmi, 2 I - 40126 Bologna, Italy
| | - Marco Garavelli
- Dipartimento
di Chimica “G. Ciamician″, Universita’ degli Studi di Bologna, Via Selmi, 2 I - 40126 Bologna, Italy
- Université
de Lyon, Université Claude Bernard Lyon 1, ENS Lyon, Centre
Nationale de Recherche Scientifique, 46 allée d’Italie, 69007 Lyon Cedex 07, France
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48
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Zen A, Coccia E, Gozem S, Olivucci M, Guidoni L. Quantum Monte Carlo Treatment of the Charge Transfer and Diradical Electronic Character in a Retinal Chromophore Minimal Model. J Chem Theory Comput 2016; 11:992-1005. [PMID: 25821414 PMCID: PMC4357234 DOI: 10.1021/ct501122z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Indexed: 01/22/2023]
Abstract
![]()
The
penta-2,4-dieniminium cation (PSB3) displays similar ground
state and first excited state potential energy features as those of
the retinal protonated Schiff base (RPSB) chromophore in rhodopsin.
Recently, PSB3 has been used to benchmark several electronic structure
methods, including highly correlated multireference wave function
approaches, highlighting the necessity to accurately describe the
electronic correlation in order to obtain reliable properties even
along the ground state (thermal) isomerization paths. In this work,
we apply two quantum Monte Carlo approaches, the variational Monte
Carlo and the lattice regularized diffusion Monte Carlo, to study
the energetics and electronic properties of PSB3 along representative
minimum energy paths and scans related to its thermal cis–trans isomerization. Quantum Monte Carlo
is used in combination with the Jastrow antisymmetrized geminal power
ansatz, which guarantees an accurate and balanced description of the
static electronic correlation thanks to the multiconfigurational nature
of the antisymmetrized geminal power term, and of the dynamical correlation,
due to the presence of the Jastrow factor explicitly depending on
electron–electron distances. Along the two ground state isomerization
minimum energy paths of PSB3, CASSCF calculations yield wave functions
having either charge transfer or diradical character in proximity
of the two transition state configurations. Here, we observe that
at the quantum Monte Carlo level of theory, only the transition state
with charge transfer character can be located. The conical intersection,
which becomes highly sloped, is observed only if the path connecting
the two original CASSCF transition states is extended beyond the diradical
one, namely by increasing the bond-length-alternation (BLA). These
findings are in good agreement with the results obtained by MRCISD+Q
calculations, and they demonstrate the importance of having an accurate
description of the static and dynamical correlation when studying
isomerization and transition states of conjugated systems.
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49
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Maza JR, Jenkins S, Kirk SR. 11-cis retinal torsion: A QTAIM and stress tensor analysis of the S1 excited state. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.04.051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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50
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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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