1
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Pieri E, Walker AR, Zhu M, Martínez TJ. Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins. J Am Chem Soc 2024; 146:17646-17658. [PMID: 38885641 DOI: 10.1021/jacs.4c00458] [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: 06/20/2024]
Abstract
Red fluorescent protein (RFP) variants are highly sought after for in vivo imaging since longer wavelengths improve depth and contrast in fluorescence imaging. However, the lower energy emission wavelength usually correlates with a lower fluorescent quantum yield compared to their green emitting counterparts. To guide the rational design of bright variants, we have theoretically assessed two variants (mScarlet and mRouge) which are reported to have very different brightness. Using an α-CASSCF QM/MM framework (chromophore and all protein residues within 6 Å of it in the QM region, for a total of more than 450 QM atoms), we identify key points on the ground and first excited state potential energy surfaces. The brighter variant mScarlet has a rigid scaffold, and the chromophore stays largely planar on the ground state. The dimmer variant mRouge shows more flexibility and can accommodate a pretwisted chromophore conformation which provides easier access to conical intersections. The main difference between the variants lies in the intersection seam regions, which appear largely inaccessible in mScarlet but partially accessible in mRouge. This observation is mainly related with changes in the cavity charge distribution, the hydrogen-bonding network involving the chromophore and a key ARG/THR mutation (which changes both charge and steric hindrance).
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Affiliation(s)
- Elisa Pieri
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Alice R Walker
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Mingning Zhu
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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2
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Zhu YH, Liu XX, Fang Q, Liu XY, Fang WH, Cui G. Multiple Photoisomerization Pathways of the Green Fluorescent Protein Chromophore in a Reversibly Photoswitchable Fluorescent Protein: Insights from Quantum Mechanics/Molecular Mechanics Simulations. J Phys Chem Lett 2023; 14:2588-2598. [PMID: 36881005 DOI: 10.1021/acs.jpclett.3c00165] [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: 06/18/2023]
Abstract
Herein, we have employed a combined CASPT2//CASSCF approach within the quantum mechanics/molecular mechanics (QM/MM) framework to explore the early time photoisomerization of rsEGFP2 starting from its two OFF trans states, i.e., Trans1 and Trans2. The results show similar vertical excitation energies to the S1 state in their Franck-Condon regions. Considering the clockwise and counterclockwise rotations of the C11-C9 bond, four pairs of the S1 excited-state minima and low-lying S1/S0 conical intersections were optimized, based on which we determined four S1 photoisomerization paths that are essentially barrierless to the relevant S1/S0 conical intersections leading to efficient excited-state deactivation to the S0 state. Most importantly, our work first identified multiple photoisomerization and excited-state decay paths, which must be seriously considered in the future. This work not only sheds significant light on the primary trans-cis photoisomerization of rsEGFP2 but also aids in the understanding of the microscopic mechanism of GFP-like RSFPs and the design of novel GFP-like fluorescent proteins.
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Affiliation(s)
- Yun-Hua Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xin-Xin Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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3
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Legault S, Fraser-Halberg DP, McAnelly RL, Eason MG, Thompson MC, Chica RA. Generation of bright monomeric red fluorescent proteins via computational design of enhanced chromophore packing. Chem Sci 2022; 13:1408-1418. [PMID: 35222925 PMCID: PMC8809391 DOI: 10.1039/d1sc05088e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/07/2022] [Indexed: 12/11/2022] Open
Abstract
Red fluorescent proteins (RFPs) have found widespread application in chemical and biological research due to their longer emission wavelengths. Here, we use computational protein design to increase the quantum yield and thereby brightness of a dim monomeric RFP (mRojoA, quantum yield = 0.02) by optimizing chromophore packing with aliphatic residues, which we hypothesized would reduce torsional motions causing non-radiative decay. Experimental characterization of the top 10 designed sequences yielded mSandy1 (λ em = 609 nm, quantum yield = 0.26), a variant with equivalent brightness to mCherry, a widely used RFP. We next used directed evolution to further increase brightness, resulting in mSandy2 (λ em = 606 nm, quantum yield = 0.35), the brightest Discosoma sp. derived monomeric RFP with an emission maximum above 600 nm reported to date. Crystallographic analysis of mSandy2 showed that the chromophore p-hydroxybenzylidene moiety is sandwiched between the side chains of Leu63 and Ile197, a structural motif that has not previously been observed in RFPs, and confirms that aliphatic packing leads to chromophore rigidification. Our results demonstrate that computational protein design can be used to generate bright monomeric RFPs, which can serve as templates for the evolution of novel far-red fluorescent proteins.
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Affiliation(s)
- Sandrine Legault
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Derek P Fraser-Halberg
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Ralph L McAnelly
- Department of Chemistry and Biochemistry, University of California, Merced Merced California 95343 USA
| | - Matthew G Eason
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Merced Merced California 95343 USA
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
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4
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Rossano‐Tapia M, Brown A. Quantum mechanical/molecular mechanical studies of photophysical properties of fluorescent proteins. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Alex Brown
- Department of Chemistry University of Alberta Edmonton Alberta Canada
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5
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Drobizhev M, Molina RS, Callis PR, Scott JN, Lambert GG, Salih A, Shaner NC, Hughes TE. Local Electric Field Controls Fluorescence Quantum Yield of Red and Far-Red Fluorescent Proteins. Front Mol Biosci 2021; 8:633217. [PMID: 33763453 PMCID: PMC7983054 DOI: 10.3389/fmolb.2021.633217] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
Genetically encoded probes with red-shifted absorption and fluorescence are highly desirable for imaging applications because they can report from deeper tissue layers with lower background and because they provide additional colors for multicolor imaging. Unfortunately, red and especially far-red fluorescent proteins have very low quantum yields, which undermines their other advantages. Elucidating the mechanism of nonradiative relaxation in red fluorescent proteins (RFPs) could help developing ones with higher quantum yields. Here we consider two possible mechanisms of fast nonradiative relaxation of electronic excitation in RFPs. The first, known as the energy gap law, predicts a steep exponential drop of fluorescence quantum yield with a systematic red shift of fluorescence frequency. In this case the relaxation of excitation occurs in the chromophore without any significant changes of its geometry. The second mechanism is related to a twisted intramolecular charge transfer in the excited state, followed by an ultrafast internal conversion. The chromophore twisting can strongly depend on the local electric field because the field can affect the activation energy. We present a spectroscopic method of evaluating local electric fields experienced by the chromophore in the protein environment. The method is based on linear and two-photon absorption spectroscopy, as well as on quantum-mechanically calculated parameters of the isolated chromophore. Using this method, which is substantiated by our molecular dynamics simulations, we obtain the components of electric field in the chromophore plane for seven different RFPs with the same chromophore structure. We find that in five of these RFPs, the nonradiative relaxation rate increases with the strength of the field along the chromophore axis directed from the center of imidazolinone ring to the center of phenolate ring. Furthermore, this rate depends on the corresponding electrostatic energy change (calculated from the known fields and charge displacements), in quantitative agreement with the Marcus theory of charge transfer. This result supports the dominant role of the twisted intramolecular charge transfer mechanism over the energy gap law for most of the studied RFPs. It provides important guidelines of how to shift the absorption wavelength of an RFP to the red, while keeping its brightness reasonably high.
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Affiliation(s)
- Mikhail Drobizhev
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, United States
| | - Rosana S Molina
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, United States
| | - Patrik R Callis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Gerard G Lambert
- Department of Neurosciences, UC San Diego, San Diego, CA, United States
| | - Anya Salih
- Antares & Fluoresci Research, Dangar Island, NSW, Australia
| | - Nathan C Shaner
- Department of Neurosciences, UC San Diego, San Diego, CA, United States
| | - Thomas E Hughes
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, United States
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6
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Geng L, Yu X, Wang Y, Li Y, Shen F, Ren J. Ultrasound-induced emission color and transmittance changes of organogel based on "trans-to-cis" isomerization. ULTRASONICS SONOCHEMISTRY 2019; 58:104659. [PMID: 31450314 DOI: 10.1016/j.ultsonch.2019.104659] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/11/2019] [Accepted: 06/24/2019] [Indexed: 06/10/2023]
Abstract
Herein, instant and precise control of fluorescent emission color and transmittance could be carried out by ultrasound-promoted gel-to-gel transition of naphthalimide derivatives containing CN unit. It is proved that ultrasound triggered an irreversible and efficient configuration transformation of N1 from "trans to cis" form in gel state, which is stabilized by intermolecular hydrogen bonding interaction and not observed in the solution state.
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Affiliation(s)
- Lijun Geng
- College of Science and Hebei Research Center of Pharmaceutical and Chemical Engineering, Hebei University of Science and Technology, Yuhua Road 70, Shijiazhuang 050080, PR China
| | - Xudong Yu
- College of Science and Hebei Research Center of Pharmaceutical and Chemical Engineering, Hebei University of Science and Technology, Yuhua Road 70, Shijiazhuang 050080, PR China.
| | - Yanqiu Wang
- College of Science and Hebei Research Center of Pharmaceutical and Chemical Engineering, Hebei University of Science and Technology, Yuhua Road 70, Shijiazhuang 050080, PR China
| | - Yajuan Li
- College of Science and Hebei Research Center of Pharmaceutical and Chemical Engineering, Hebei University of Science and Technology, Yuhua Road 70, Shijiazhuang 050080, PR China
| | - Fengjuan Shen
- College of Science and Hebei Research Center of Pharmaceutical and Chemical Engineering, Hebei University of Science and Technology, Yuhua Road 70, Shijiazhuang 050080, PR China
| | - Jujie Ren
- College of Science and Hebei Research Center of Pharmaceutical and Chemical Engineering, Hebei University of Science and Technology, Yuhua Road 70, Shijiazhuang 050080, PR China
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7
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Moron V, Marazzi M, Wanko M. Far Red Fluorescent Proteins: Where Is the Limit of the Acylimine Chromophore? J Chem Theory Comput 2019; 15:4228-4240. [PMID: 31146524 DOI: 10.1021/acs.jctc.9b00070] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The search for new near-infrared probes for fluorescence imaging applications is a rapidly growing field of research. Monomeric fluorescent proteins that autocatalyze their chromophore are the most versatile markers for in vivo applications, but the development of bright far-red fluorescent proteins (RFPs) has proven difficult. In this contribution, we search for the theoretical limit of the red shift and how it can be reached without sacrificing the fluorescence quantum yield. Through extensive excited-state pathway calculations, molecular dynamics sampling, and statistical modeling using QM/MM schemes, we provide a new understanding of the chromophore's photophysics including the role of its acylimine extension, which is the main difference from other families of fluorescent proteins. The excited-state dynamics of the mPlum RFP and its mutants provide an ideal basis due to mPlum's flexible binding pocket and extended dynamic Stokes shift. We found a large number of structural species with red-shifted emission that differ in rotamer states and H-bonds between key amino acid residues in the binding pocket. By analyzing their spectral and structural features, we derive guidelines for future rational genetic design strategies.
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Affiliation(s)
- Victor Moron
- Nano-Bio Spectroscopy Group and ETSF, Dpto. Fisica de Materiales , Universidad del País Vasco, CFM CSIC-UPV/EHU-MPC and DIPC , Av. Tolosa 72 , 20018 San Sebastián , Spain
| | - Marco Marazzi
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry, KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering , Universidad de Alcalá, Ctra , Madrid-Barcelona Km. 33,600 , E-28805 Alcalá de Henares, Madrid , Spain
- "Andrés M. del Rı́o" (IQAR) , Universidad de Alcalá , E-28871 Alcalá de Henares, Madrid , Spain
| | - Marius Wanko
- Nano-Bio Spectroscopy Group and ETSF, Dpto. Fisica de Materiales , Universidad del País Vasco, CFM CSIC-UPV/EHU-MPC and DIPC , Av. Tolosa 72 , 20018 San Sebastián , Spain
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8
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Wolff FE, Höfener S, Elstner M, Wesołowski TA. Origin of the Solvatochromism in Organic Fluorophores with Flexible Side Chains: A Case Study of Flugi-2. J Phys Chem A 2019; 123:4581-4587. [DOI: 10.1021/acs.jpca.9b02474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Tomasz A. Wesołowski
- Département de Chimie Physique, Université de Genève, 30 quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
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9
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Kemmler L, Ibrahim M, Dobbek H, Zouni A, Bondar AN. Dynamic water bridging and proton transfer at a surface carboxylate cluster of photosystem II. Phys Chem Chem Phys 2019; 21:25449-25466. [DOI: 10.1039/c9cp03926k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A hydrogen-bond cluster at a negatively-charged protein interface with a bound protein and long-lived waters might be a proton storage site.
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Affiliation(s)
- Lukas Kemmler
- Freie Universität Berlin
- Department of Physics
- Theoretical Molecular Biophysics Group
- D-14195 Berlin
- Germany
| | - Mohamed Ibrahim
- Humboldt Universtät zu Berlin
- Institute for Biology, Structural Biology and Biochemistry
- Berlin
- Germany
| | - Holger Dobbek
- Humboldt Universtät zu Berlin
- Institute for Biology, Structural Biology and Biochemistry
- Berlin
- Germany
| | - Athina Zouni
- Humboldt Universtät zu Berlin
- Institute for Biology, Biophysics of Photosynthesis
- Berlin
- Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin
- Department of Physics
- Theoretical Molecular Biophysics Group
- D-14195 Berlin
- Germany
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10
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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11
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Ma Y, Sun Q, Smith SC. The mechanism of oxidation in chromophore maturation of wild-type green fluorescent protein: a theoretical study. Phys Chem Chem Phys 2017; 19:12942-12952. [DOI: 10.1039/c6cp07983k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DFT calculations suggested that the thermodynamically unfavourable cyclized product was trapped by oxidation.
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Affiliation(s)
- Yingying Ma
- Institue of Mining Technology
- Inner Mongolia University of Technology
- Hohhot 010051
- P. R. China
- Inner Mongolia Key Laboratory of Theoretical and Computational Chemistry Simulation
| | - Qiao Sun
- School of Radiation Medicine and Radiation Protection
- Soochow University
- Suzhou 215123
- P. R. China
| | - Sean C. Smith
- Integrated Materials Design Centre
- School of Chemical Engineering
- The University of New South Wales
- Sydney
- Australia
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12
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Tuna D, Lu Y, Koslowski A, Thiel W. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks of Electronically Excited States. J Chem Theory Comput 2016; 12:4400-22. [DOI: 10.1021/acs.jctc.6b00403] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - You Lu
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
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13
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Ma Y, Yu JG, Sun Q, Li Z, Smith SC. The mechanism of dehydration in chromophore maturation of wild-type green fluorescent protein: A theoretical study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.04.061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Kang B, Baek KY, Lee JY. Electric Field Effect on trans-p-Hydroxybenzylideneimidazolidinone: A DFT Study and Implication to Green Fluorescent Protein. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Baotao Kang
- Department of Chemistry; Sungkyunkwan University; Suwon 440746 Korea
| | - Kyung Yup Baek
- Department of Chemistry; Sungkyunkwan University; Suwon 440746 Korea
| | - Jin Yong Lee
- Department of Chemistry; Sungkyunkwan University; Suwon 440746 Korea
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15
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An overview of nonadiabatic dynamics simulations methods, with focus on the direct approach versus the fitting of potential energy surfaces. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1526-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Catalytic strategy used by the myosin motor to hydrolyze ATP. Proc Natl Acad Sci U S A 2014; 111:E2947-56. [PMID: 25006262 DOI: 10.1073/pnas.1401862111] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Myosin is a molecular motor responsible for biological motions such as muscle contraction and intracellular cargo transport, for which it hydrolyzes adenosine 5'-triphosphate (ATP). Early steps of the mechanism by which myosin catalyzes ATP hydrolysis have been investigated, but still missing are the structure of the final ADP·inorganic phosphate (Pi) product and the complete pathway leading to it. Here, a comprehensive description of the catalytic strategy of myosin is formulated, based on combined quantum-classical molecular mechanics calculations. A full exploration of catalytic pathways was performed and a final product structure was found that is consistent with all experiments. Molecular movies of the relevant pathways show the different reorganizations of the H-bond network that lead to the final product, whose γ-phosphate is not in the previously reported HPγO4(2-) state, but in the H2PγO4(-) state. The simulations reveal that the catalytic strategy of myosin employs a three-pronged tactic: (i) Stabilization of the γ-phosphate of ATP in a dissociated metaphosphate (PγO3(-)) state. (ii) Polarization of the attacking water molecule, to abstract a proton from that water. (iii) Formation of multiple proton wires in the active site, for efficient transfer of the abstracted proton to various product precursors. The specific role played in this strategy by each of the three loops enclosing ATP is identified unambiguously. It explains how the precise timing of the ATPase activation during the force generating cycle is achieved in myosin. The catalytic strategy described here for myosin is likely to be very similar in most nucleotide hydrolyzing enzymes.
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17
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Raghunanan L, Yue J, Narine SS. Synthesis and Characterization of Novel Diol, Diacid and Di-isocyanate from Oleic Acid. J AM OIL CHEM SOC 2013. [DOI: 10.1007/s11746-013-2376-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Mironov VA, Khrenova MG, Grigorenko BL, Savitsky AP, Nemukhin AV. Thermal isomerization of the chromoprotein asFP595 and its kindling mutant A143G: QM/MM molecular dynamics simulations. J Phys Chem B 2013; 117:13507-14. [PMID: 24079704 DOI: 10.1021/jp407406k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chromoprotein asFP595 and its A143G variant called kindling fluorescent protein (KFP) are among the chronologically first species for which trans-cis chromophore isomerization has been proposed as a driving force of photoswitching. In spite of long-lasting efforts to characterize the route between protein conformations referring to the trans and cis forms of the chromophore, the molecular mechanism of this transformation is still under debate. We report the results of computational studies of the trans-cis isomerization of the anionic and neutral chromophore inside the protein matrices in the ground electronic state for both variants, asFP595 and KFP. Corresponding free energy profiles (potentials of mean force) were evaluated by using molecular dynamics simulations with the quantum mechanical-molecular mechanical (QM/MM) forces. The computed free energy barrier for the cis-trans ground state (thermal) isomerization reaction is about 2 kcal/mol higher in KFP than that in asFP595. These results provide interpretation of experimental studies on thermal relaxation from the light-induced activation of fluorescence of these proteins and correctly show that the A143G mutation in asFP595 noticeably increases the lifetime of the fluorescence species.
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Affiliation(s)
- Vladimir A Mironov
- Department of Chemistry, M.V. Lomonosov Moscow State University , Leninskie Gory, 1/3, Moscow, 119991, Russian Federation
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19
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Goerigk L, Reimers JR. Efficient Methods for the Quantum Chemical Treatment of Protein Structures: The Effects of London-Dispersion and Basis-Set Incompleteness on Peptide and Water-Cluster Geometries. J Chem Theory Comput 2013; 9:3240-51. [DOI: 10.1021/ct400321m] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lars Goerigk
- School of Chemistry, The University of Sydney, New South Wales 2006, Australia
| | - Jeffrey R. Reimers
- School of Chemistry, The University of Sydney, New South Wales 2006, Australia
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