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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Baxter J, Hutchison CD, Fadini A, Maghlaoui K, Cordon-Preciado V, Morgan RML, Agthe M, Horrell S, Tellkamp F, Mehrabi P, Pfeifer Y, Müller-Werkmeister HM, von Stetten D, Pearson AR, van Thor JJ. Power Density Titration of Reversible Photoisomerization of a Fluorescent Protein Chromophore in the Presence of Thermally Driven Barrier Crossing Shown by Quantitative Millisecond Serial Synchrotron X-ray Crystallography. J Am Chem Soc 2024; 146:16394-16403. [PMID: 38848551 PMCID: PMC11191680 DOI: 10.1021/jacs.3c12883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024]
Abstract
We present millisecond quantitative serial X-ray crystallography at 1.7 Å resolution demonstrating precise optical control of reversible population transfer from Trans-Cis and Cis-Trans photoisomerization of a reversibly switchable fluorescent protein, rsKiiro. Quantitative results from the analysis of electron density differences, extrapolated structure factors, and occupancy refinements are shown to correspond to optical measurements of photoinduced population transfer and have sensitivity to a few percent in concentration differences. Millisecond time-resolved concentration differences are precisely and reversibly controlled through intense continuous wave laser illuminations at 405 and 473 nm for the Trans-to-Cis and Cis-to-Trans reactions, respectively, while the X-ray crystallographic measurement and laser illumination of the metastable Trans chromophore conformation causes partial thermally driven reconversion across a 91.5 kJ/mol thermal barrier from which a temperature jump between 112 and 128 K is extracted.
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Affiliation(s)
- James
M. Baxter
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | | | - Alisia Fadini
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - Karim Maghlaoui
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | | | - R. Marc L. Morgan
- Center
for Structural Biology, Imperial College
London, London SW7 2AZ, U.K.
| | - Michael Agthe
- European
Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany
| | - Sam Horrell
- Department
of Physics, Center for Free-Electron Laser Science, Institute for
Nanostructure and Solid State Physics, University
of Hamburg, Hamburg 22607, Germany
| | - Friedjof Tellkamp
- Scientific
Support Unit Machine Physics, Max-Planck-Institute
for Structure and Dynamics of Matter, Hamburg 22761, Germany
| | - Pedram Mehrabi
- Max
Planck Institute for the Structure and Dynamics of Matter, CFEL, Hamburg 22607, Germany
| | - Yannik Pfeifer
- Institute
of Chemistry—Physical Chemistry, University of Potsdam, Potsdam 14469, Germany
| | | | - David von Stetten
- European
Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany
| | - Arwen R. Pearson
- Institute
for Nanostructure and Solid State Physics & The Hamburg Centre
for Ultrafast Imaging, HARBOR, Universität
Hamburg, Hamburg 22607, Germany
| | - Jasper J. van Thor
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
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3
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Boyko KM, Khrenova MG, Nikolaeva AY, Dorovatovskii PV, Vlaskina AV, Subach OM, Popov VO, Subach FV. Combined Structural and Computational Study of the mRubyFT Fluorescent Timer Locked in Its Blue Form. Int J Mol Sci 2023; 24:ijms24097906. [PMID: 37175610 PMCID: PMC10178504 DOI: 10.3390/ijms24097906] [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: 03/30/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
The mRubyFT is a monomeric genetically encoded fluorescent timer based on the mRuby2 fluorescent protein, which is characterized by the complete maturation of the blue form with the subsequent conversion to the red one. It has higher brightness in mammalian cells and higher photostability compared with other fluorescent timers. A high-resolution structure is a known characteristic of the mRubyFT with the red form chromophore, but structural details of its blue form remain obscure. In order to obtain insight into this, we obtained an S148I variant of the mRubyFT (mRubyFTS148I) with the blocked over time blue form of the chromophore. X-ray data at a 1.8 Å resolution allowed us to propose a chromophore conformation and its interactions with the neighboring residues. The imidazolidinone moiety of the chromophore is completely matured, being a conjugated π-system. The methine bridge is not oxidized in the blue form bringing flexibility to the phenolic moiety that manifests itself in poor electron density. Integration of these data with the results of molecular dynamic simulation disclosed that the OH group of the phenolic moiety forms a hydrogen bond with the side chain of the T163 residue. A detailed comparison of mRubyFTS148I with other available structures of the blue form of fluorescent proteins, Blue102 and mTagBFP, revealed a number of characteristic differences. Molecular dynamic simulations with the combined quantum mechanic/molecular mechanic potentials demonstrated that the blue form exists in two protonation states, anion and zwitterion, both sharing enolate tautomeric forms of the C=C-O- fragment. These two forms have similar excitation energies, as evaluated by calculations. Finally, excited state molecular dynamic simulations showed that excitation of the chromophore in both protonation states leads to the same anionic fluorescent state. The data obtained shed light on the structural features and spectral properties of the blue form of the mRubyFT timer.
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Affiliation(s)
- Konstantin M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt. 33, bld. 2, 119071 Moscow, Russia
| | - Maria G Khrenova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt. 33, bld. 2, 119071 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119992 Moscow, Russia
| | - Alena Y Nikolaeva
- National Research Centre "Kurchatov Institute", Kurchatov Complex NBICS-Technologies, Akad. Kurchatova sqr., 1, 123182 Moscow, Russia
| | - Pavel V Dorovatovskii
- National Research Centre "Kurchatov Institute", Kurchatov Complex NBICS-Technologies, Akad. Kurchatova sqr., 1, 123182 Moscow, Russia
| | - Anna V Vlaskina
- National Research Centre "Kurchatov Institute", Kurchatov Complex NBICS-Technologies, Akad. Kurchatova sqr., 1, 123182 Moscow, Russia
| | - Oksana M Subach
- National Research Centre "Kurchatov Institute", Kurchatov Complex NBICS-Technologies, Akad. Kurchatova sqr., 1, 123182 Moscow, Russia
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt. 33, bld. 2, 119071 Moscow, Russia
- National Research Centre "Kurchatov Institute", Kurchatov Complex NBICS-Technologies, Akad. Kurchatova sqr., 1, 123182 Moscow, Russia
| | - Fedor V Subach
- National Research Centre "Kurchatov Institute", Kurchatov Complex NBICS-Technologies, Akad. Kurchatova sqr., 1, 123182 Moscow, Russia
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4
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Bozhanova NG, Baranov MS, Sarkisyan KS, Gritcenko R, Mineev KS, Golodukhina SV, Baleeva NS, Lukyanov KA, Mishin AS. Yellow and Orange Fluorescent Proteins with Tryptophan-based Chromophores. ACS Chem Biol 2017; 12:1867-1873. [PMID: 28525263 DOI: 10.1021/acschembio.7b00337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid development of new microscopy techniques exposed the need for genetically encoded fluorescent tags with special properties. Recent works demonstrated the potential of fluorescent proteins with tryptophan-based chromophores. We applied rational design and random mutagenesis to the monomeric red fluorescent protein FusionRed and found two groups of mutants carrying a tryptophan-based chromophore: with yellow (535 nm) or orange (565 nm) emission. On the basis of the properties of proteins, a model synthetic chromophore, and a computational modeling, we concluded that the presence of a ketone-containing chromophore in different isomeric forms can explain the observed yellow and orange phenotypes.
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Affiliation(s)
- Nina G Bozhanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Pirogov Russian National Research Medical University , Ostrovitianov 1, 117997 Moscow, Russia
| | - Karen S Sarkisyan
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Roman Gritcenko
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University , 22100 Lund, Sweden
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology , Institutsky per., 9, 141701 Dolgoprudny, Russia
| | - Svetlana V Golodukhina
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Pirogov Russian National Research Medical University , Ostrovitianov 1, 117997 Moscow, Russia
| | - Konstantin A Lukyanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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5
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Grigorenko BL, Krylov AI, Nemukhin AV. Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein. J Am Chem Soc 2017; 139:10239-10249. [DOI: 10.1021/jacs.7b00676] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Bella L. Grigorenko
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna I. Krylov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Alexander V. Nemukhin
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
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6
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Pauly MD, Procario MC, Lauring AS. A novel twelve class fluctuation test reveals higher than expected mutation rates for influenza A viruses. eLife 2017; 6. [PMID: 28598328 PMCID: PMC5511008 DOI: 10.7554/elife.26437] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 06/09/2017] [Indexed: 12/21/2022] Open
Abstract
Influenza virus’ low replicative fidelity contributes to its capacity for rapid evolution. Clonal sequencing and fluctuation tests have suggested that the influenza virus mutation rate is 2.7 × 10–6 - 3.0 × 10–5 substitutions per nucleotide per strand copied (s/n/r). However, sequencing assays are biased toward mutations with minimal fitness impacts and fluctuation tests typically investigate only a subset of all possible single nucleotide mutations. We developed a fluctuation test based on reversion to fluorescence in a set of virally encoded mutant green fluorescent proteins, which allowed us to measure the rates of selectively neutral mutations representative of the twelve different mutation types. We measured an overall mutation rate of 1.8 × 10–4 s/n/r for PR8 (H1N1) and 2.5 × 10–4 s/n/r for Hong Kong 2014 (H3N2) and a transitional bias of 2.7–3.6. Our data suggest that each replicated genome will have an average of 2–3 mutations and highlight the importance of mutational load in influenza virus evolution. DOI:http://dx.doi.org/10.7554/eLife.26437.001
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Affiliation(s)
- Matthew D Pauly
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States
| | - Megan C Procario
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States
| | - Adam S Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
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7
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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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8
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Ma Y, Zhang H, Sun Q, Smith SC. New Insights on the Mechanism of Cyclization in Chromophore Maturation of Wild-Type Green Fluorescence Protein: A Computational Study. J Phys Chem B 2016; 120:5386-94. [DOI: 10.1021/acs.jpcb.6b04406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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, Hohhot 010051, P. R. China
| | - Hao Zhang
- College
of Life Science and Engineering, Northwest University for Nationalities, Lanzhou 730030, P. R. China
| | - 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, NSW2052, Sydney, Australia
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9
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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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10
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Cui X, He R, Yang Q, Shen W, Li M. Theoretical study on the chemical mechanism of enoyl-CoA hydratase and the form of inhibitor binding. J Mol Model 2014; 20:2411. [PMID: 25174944 DOI: 10.1007/s00894-014-2411-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 07/30/2014] [Indexed: 10/24/2022]
Abstract
Enoyl-CoA hydratase (ECH) catalyzes the second step in the vital β-oxidation pathway of fatty acid metabolism. This enzyme catalyzes the syn-addition of a water molecule across the double bond of 4-(N,N-dimethylamino) cinnamoyl-CoA (DAC-CoA). In this work, the reaction mechanisms of ECH were investigated using the density functional theory (DFT) methods. The different protonation states in which the important residues Glu164 and Glu144 are either neutral or ionized were considered. Four models of the active site were designed based on the X-ray crystal structure of the enzyme. The calculations gave strong support to the proposed mechanism and confirmed that both Glu164 and Glu144 are in a deprotonated state in the reaction mechanism of ECH. In addition, we constructed a model of the active site with the inhibitor acetoacetyl-CoA based on the crystal structure. Caomparison of the calculated energy barriers showed that binding of the keto-enol form of the inhibitor is more reasonable than that of the di-keto form in the inhibition process. Moreover, acetoacetyl-CoA was found to exhibit a keto-enol tautomerism when it acts as an inhibitor in the reaction. The present theoretical results indicated that both residues Glu164 and Glu144 are unprotonated in ECH with the substrate bound, while only Glu164 is unprotonated when the inhibitor binds ECH.
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Affiliation(s)
- Xiaobin Cui
- School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 40071, China
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11
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Zhang H, Ma Y, Liu K, Yu JG. Theoretical studies on the reaction mechanism of PP1 and the effects of different oxidation states of the Mn–Mn center on the mechanism. J Biol Inorg Chem 2013; 18:451-9. [DOI: 10.1007/s00775-013-0989-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 02/13/2013] [Indexed: 01/18/2023]
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12
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A theoretical investigation of the mechanism of formation of a simplified analog of the green fluorescent protein (GFP) from a peptide model. Struct Chem 2012. [DOI: 10.1007/s11224-012-0134-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Sun Q, Li Z, Lan Z, Pfisterer C, Doerr M, Fischer S, Smith SC, Thiel W. Isomerization mechanism of the HcRed fluorescent protein chromophore. Phys Chem Chem Phys 2012; 14:11413-24. [PMID: 22801745 DOI: 10.1039/c2cp41217a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To understand how the protein achieves fluorescence, the isomerization mechanism of the HcRed chromophore is studied both under vacuum and in the solvated red fluorescent protein. Quantum mechanical (QM) and quantum mechanical/molecular mechanical (QM/MM) methods are applied both for the ground and the first excited state. The photoinduced processes in the chromophore mainly involve torsions around the imidazolinone-bridge bond (τ) and the phenoxy-bridge bond (φ). Under vacuum, the isomerization of the cis-trans chromophore essentially proceeds by τ twisting, while the radiationless decay requires φ torsion. By contrast, the isomerization of the cis-trans chromophore in HcRed occurs via simultaneous τ and φ twisting. The protein environment significantly reduces the barrier of this hula twist motion compared with vacuum. The excited-state isomerization barrier via the φ rotation of the cis-coplanar conformer in HcRed is computed to be significantly higher than that of the trans-non-coplanar conformer. This is consistent with the experimental observation that the cis-coplanar-conformation of the chromophore is related to the fluorescent properties of HcRed, while the trans-non-planar conformation is weakly fluorescent or non-fluorescent. Our study shows how the protein modifies the isomerization mechanism, notably by interactions involving the nearby residue Ile197, which keeps the chromophore coplanar and blocks the twisting motion that leads to photoinduced radiationless decay.
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Affiliation(s)
- Qiao Sun
- Centre for Computational Molecular Science, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Qld 4072, Brisbane, Australia.
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14
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First principle study of proton transfer in the green fluorescent protein (GFP): Ab initio PES in a cluster model. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.02.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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Ma Y, Sun Q, Li Z, Yu JG, Smith SC. Theoretical studies of chromophore maturation in the wild-type green fluorescent protein: ONIOM(DFT:MM) investigation of the mechanism of cyclization. J Phys Chem B 2012; 116:1426-36. [PMID: 22212013 DOI: 10.1021/jp208749v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The availability of a gene encoding green fluorescence immediately stimulates interest in the puzzle of autocatalytic formation of the green fluorescent protein (GFP) chromophore. Numerous experimental and theoretical studies have indicated that cyclization is the first and most important step in the maturation process of the GFP. In our previous paper based on cluster models [J. Phys. Chem. B2010, 114, 9698-9705], two possible mechanisms have been investigated with the conclusion that the backbone condensation initiated by deprotonation of the Gly67 amide nitrogen is easier than deprotonation of the Tyr66 α-carbon. However, the impact of the protein environment on the reaction mechanism remains to be explored. In this paper, we investigated the two possible mechanisms with inclusion of protein environmental effects by using molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Our calculations reveal no hydrogen bonding network that would facilitate deprotonation of the amide nitrogen of Gly67, although it is the lower energy pathway in the cluster model system. Contrastingly, there is a hydrogen bonding network between Tyr66 α-carbon and Glu222, which is in good agreement with X-ray data. The ONIOM studies show that proton transfer from Tyr66 α-carbon to Glu222 is a long-distance charge transfer process. The charge distribution of the MM region has a significant perturbation to the wave function for the QM region, with the QM energy for the proton transfer product being increased under the influence of the electrostatic protein environment. The barrier for the rate-limiting step in cyclization is quite high, about 40.0 kcal/mol in the case of ONIOM-EE.
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Affiliation(s)
- Yingying Ma
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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16
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Cui FC, Pan XL, Liu W, Liu JY. Elucidation of the methyl transfer mechanism catalyzed by chalcone O-methyltransferase: A density functional study. J Comput Chem 2011; 32:3068-74. [DOI: 10.1002/jcc.21890] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 05/17/2011] [Accepted: 06/22/2011] [Indexed: 11/07/2022]
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