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Nakanishi T, Hori Y, Shigeta Y, Sato H, Kiyanagi R, Munakata K, Ohhara T, Okazawa A, Shimada R, Sakamoto A, Sato O. Development of an Iron(II) Complex Exhibiting Thermal- and Photoinduced Double Proton-Transfer-Coupled Spin Transition in a Short Hydrogen Bond. J Am Chem Soc 2023; 145:19177-19181. [PMID: 37623927 DOI: 10.1021/jacs.3c06323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Multiple proton transfer (PT) controllable by external stimuli plays a crucial role in fundamental chemistry, biological activity, and material science. However, in crystalline systems, controlling multiple PT, which results in a distinct protonation state, remains challenging. In this study, we developed a novel tridentate ligand and iron(II) complex with a short hydrogen bond (HB) that exhibits a PT-coupled spin transition (PCST). Single-crystal X-ray and neutron diffraction measurements revealed that the positions of the two protons in the complex can be controlled by temperature and photoirradiation based on the thermal- and photoinduced PCST. The obtained results suggest that designing molecules that form short HBs is a promising approach for developing multiple PT systems in crystals.
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Affiliation(s)
- Takumi Nakanishi
- Institute for Materials Chemistry and Engineering & IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yuta Hori
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Hiroyasu Sato
- Rigaku Corporation, 3-9-12 Matsubaracho, Akishima, Tokyo 196-8666, Japan
| | - Ryoji Kiyanagi
- J-PARC center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Koji Munakata
- J-PARC center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Takashi Ohhara
- J-PARC center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Atsushi Okazawa
- Department of Electrical Engineering and Bioscience, Waseda University, Okubo 3-4-1, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Rintaro Shimada
- Graduate School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Akira Sakamoto
- Graduate School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Osamu Sato
- Institute for Materials Chemistry and Engineering & IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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2
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Yang WY, Yan CC, Wang XD, Liao LS. Recent progress on the excited-state multiple proton transfer process in organic molecules. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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3
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Excited State Structural Evolution of a GFP Single-Site Mutant Tracked by Tunable Femtosecond-Stimulated Raman Spectroscopy. Molecules 2018; 23:molecules23092226. [PMID: 30200474 PMCID: PMC6225354 DOI: 10.3390/molecules23092226] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 12/31/2022] Open
Abstract
Tracking vibrational motions during a photochemical or photophysical process has gained momentum, due to its sensitivity to the progression of reaction and change of environment. In this work, we implemented an advanced ultrafast vibrational technique, femtosecond-stimulated Raman spectroscopy (FSRS), to monitor the excited state structural evolution of an engineered green fluorescent protein (GFP) single-site mutant S205V. This mutation alters the original excited state proton transfer (ESPT) chain. By strategically tuning the Raman pump to different wavelengths (i.e., 801, 539, and 504 nm) to achieve pre-resonance with transient excited state electronic bands, the characteristic Raman modes of the excited protonated (A*) chromophore species and intermediate deprotonated (I*) species can be selectively monitored. The inhomogeneous distribution/population of A* species go through ESPT with a similar ~300 ps time constant, confirming that bridging a water molecule to protein residue T203 in the ESPT chain is the rate-limiting step. Some A* species undergo vibrational cooling through high-frequency motions on the ~190 ps time scale. At early times, a portion of the largely protonated A* species could also undergo vibrational cooling or return to the ground state with a ~80 ps time constant. On the photoproduct side, a ~1330 cm−1 delocalized motion is observed, with dispersive line shapes in both the Stokes and anti-Stokes FSRS with a pre-resonance Raman pump, which indicates strong vibronic coupling, as the mode could facilitate the I* species to reach a relatively stable state (e.g., the main fluorescent state) after conversion from A*. Our findings disentangle the contributions of various vibrational motions active during the ESPT reaction, and offer new structural dynamics insights into the fluorescence mechanisms of engineered GFPs and other analogous autofluorescent proteins.
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4
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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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Wineman-Fisher V, Simkovich R, Huppert D, Trujillo K, Remington SJ, Miller Y. Mutagenic induction of an ultra-fast water-chain proton wire. Phys Chem Chem Phys 2018; 18:23089-95. [PMID: 27492977 DOI: 10.1039/c6cp05071a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Replacement of the hydroxyl group of a hydrophilic sidechain by an H atom in the proton wire of GFP induces formation of a water-chain proton wire. Surprisingly, this "non-native" water chain functions as a proton wire with response times within 10 ps of the wild type protein. This remarkable rate retention is understood as a natural consequence of the well-known Grotthuss mechanism of proton transfer in water.
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Affiliation(s)
- Vered Wineman-Fisher
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva 84105, Israel. and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beér-Sheva 84105, Israel
| | - Ron Simkovich
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dan Huppert
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Kristina Trujillo
- Department of Physics and Institute of Molecular Biology, University of Oregon, Eugene, USA
| | - S James Remington
- Department of Physics and Institute of Molecular Biology, University of Oregon, Eugene, USA
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva 84105, Israel. and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beér-Sheva 84105, Israel
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6
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Conyard J, Heisler IA, Chan Y, Bulman Page PC, Meech SR, Blancafort L. A new twist in the photophysics of the GFP chromophore: a volume-conserving molecular torsion couple. Chem Sci 2018; 9:1803-1812. [PMID: 29675225 PMCID: PMC5892128 DOI: 10.1039/c7sc04091a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/30/2017] [Indexed: 01/19/2023] Open
Abstract
Dynamics of a nonplanar GFP chromophore are studied experimentally and theoretically. Coupled torsional motion is responsible for the ultrafast decay.
The simple structure of the chromophore of the green fluorescent protein (GFP), a phenol and an imidazolone ring linked by a methyne bridge, supports an exceptionally diverse range of excited state phenomena. Here we describe experimentally and theoretically the photochemistry of a novel sterically crowded nonplanar derivative of the GFP chromophore. It undergoes an excited state isomerization reaction accompanied by an exceptionally fast (sub 100 fs) excited state decay. The decay dynamics are essentially independent of solvent polarity and viscosity. Excited state structural dynamics are probed by high level quantum chemical calculations revealing that the fast decay is due to a conical intersection characterized by a twist of the rings and pyramidalization of the methyne bridge carbon. The intersection can be accessed without a barrier from the pre-twisted Franck–Condon structure, and the lack of viscosity dependence is due to the fact that the rings twist in the same direction, giving rise to a volume-conserving decay coordinate. Moreover, the rotation of the phenyl, methyl and imidazolone groups is coupled in the sterically crowded structure, with the methyl group translating the rotation of one ring to the next. As a consequence, the excited state dynamics can be viewed as a torsional couple, where the absorbed photon energy leads to conversion of the out-of-plane orientation from one ring to the other in a volume conserving fashion. A similar modification of the range of methyne dyes may provide a new family of devices for molecular machines, specifically torsional couples.
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Affiliation(s)
- Jamie Conyard
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Ismael A Heisler
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Yohan Chan
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Philip C Bulman Page
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Stephen R Meech
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi , Departament de Química , Facultat de Ciències , Universitat de Girona , C/ M. A. Capmany 69 , 17003 Girona , Spain .
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7
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Guo WW, Fang YG, Fang Q, Cui GL. Mechanistic Insights into the Photophysics of Ortho-hydroxyl GFP Core Chromophores. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1709179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Wei-wei Guo
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ye-guang Fang
- 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
| | - Gang-long Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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8
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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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9
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Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev 2016; 117:758-795. [PMID: 27754659 DOI: 10.1021/acs.chemrev.6b00238] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.
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Affiliation(s)
- Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
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10
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Li X, Chung LW, Li G. Multiscale Simulations on Spectral Tuning and the Photoisomerization Mechanism in Fluorescent RNA Spinach. J Chem Theory Comput 2016; 12:5453-5464. [PMID: 27685000 DOI: 10.1021/acs.jctc.6b00578] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Fluorescent RNA aptamer Spinach can bind and activate a green fluorescent protein (GFP)-like chromophore (an anionic DFHBDI chromophore) displaying green fluorescence. Spectroscopic properties, spectral tuning, and the photoisomerization mechanism in the Spinach-DFHBDI complex have been investigated by high-level QM and hybrid ONIOM(QM:AMBER) methods (QM method: (TD)DFT, SF-BHHLYP, SAC-CI, LT-DF-LCC2, CASSCF, or MS-CASPT2), as well as classical molecular dynamics (MD) simulations. First, our benchmark calculations have shown that TD-DFT and spin-flip (SF) TD-DFT (SF-BHHLYP) failed to give a satisfactory description of absorption and emission of the anionic DFHBDI chromophore. Comparatively, SAC-CI, LT-DF-LCC2, and MS-CASPT2 can give more reliable transition energies and are mainly used to further study the spectra of the anionic DFHBDI chromophore in Spinach. The RNA environmental effects on the spectral tuning and the photoisomerization mechanism have been elucidated. Our simulations show that interactions of the anionic cis-DFHBDI chromophore with two G-quadruplexes as well as a UAU base triple suppress photoisomerization of DFHBDI. In addition, strong hydrogen bonds between the anionic cis-DFHBDI chromophore and nearby nucleotides facilitate its binding to Spinach and further inhibit the cis-trans photoisomerization of DFHBDI. Solvent molecules, ions, and loss of key hydrogen bonds with nearby nucleotides could induce dissociation of the anionic trans-DFHBDI chromophore from the binding site. These results provide new insights into fluorescent RNA Spinach and may help rational design of other fluorescent RNAs.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Lung Wa Chung
- Department of Chemistry, South University of Science and Technology of China , Shenzhen 518055, China
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
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11
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Chen F, Zeng Q, Zhuang W, Liang W. Characterizing the Structures, Spectra, and Energy Landscapes Involved in the Excited-State Proton Transfer Process of Red Fluorescent Protein LSSmKate1. J Phys Chem B 2016; 120:9833-42. [PMID: 27581731 DOI: 10.1021/acs.jpcb.6b04708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
By applying molecular dynamics (MD) simulations and quantum chemical calculations, we have characterized the states and processes involved in the excited-state proton transfer (ESPT) of LSSmKate1. MD simulations identify two stable structures in the electronic ground state of LSSmKate1, one with a protonated chromophore and the other with a deprotonated chromophore, thus leading to two separate low-energy absorption maxima with a large energy spacing, as observed in the calculated and experimentally measured absorption spectra. Proton transfer is induced by electronic excitation. When LSSmKate1 is excited, the electrons in the chromophore are transferred from the phenol ring to the N-acylimine moiety; the acidity of a phenolic hydroxyl group is thus enhanced. The calculated potential energy curves (PECs) exhibit energetic feasibility in the generation of the fluorescent species in LSSmKate1, and the exact agreement between the calculated and experimentally measured values of the large Stokes shift further provides solid theoretical evidence for the ESPT process taking place in photoexcited LSSmKate1. The molecular environments play a significant role in the geometries and absorption/emission energies of the chromophores. Overall, TD-ωB97X-D/molecular mechanics (MM) provides a better description of the optical properties of LSSmKate1 than TD-B3LYP/MM, although it always overestimates the excitation energies.
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Affiliation(s)
- Fasheng Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Qiao Zeng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences , Fuzhou, Fujian 350002, China
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
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12
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Nadal-Ferret M, Gelabert R, Moreno M, Lluch JM. Transient low-barrier hydrogen bond in the photoactive state of green fluorescent protein. Phys Chem Chem Phys 2016; 17:30876-88. [PMID: 25953497 DOI: 10.1039/c5cp01067e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we have analyzed the feasibility of spontaneous proton transfer in GFP at the Franck-Condon region directly after photoexcitation. Computation of a sizeable portion of the potential energy surface at the Franck-Condon region of A the structure shows the process of proton transfer to be unfavorable by 3 kcal mol(-1) in S1 if no further structural relaxation is permitted. The ground vibrational state is found to lie above the potential energy barrier of the proton transfer in both S0 and S1. Expectation values of the geometry reveal that the proton shared between the chromophore and W22, and the proton shared between Ser205 and Glu222 are very close to the center of the respective hydrogen bonds, giving support to the claim that the first transient intermediate detected after photoexcitation (I0*) has characteristics similar to those of a low-barrier hydrogen bond [Di Donato et al., Phys. Chem. Chem. Phys., 2012, 13, 16295]. A quantum dynamical calculation of the evolution in the excited state shows an even larger probability of finding those two protons close to the center compared to in the ground state, but no formation of the proton-transferred product is observed. A QM/MM photoactive state geometry optimization, initiated using a configuration obtained by taking the A minimum and moving the protons to the product side, yields a minimum energy structure with the protons transferred and in which the His148 residue is substantially closer to the now anionic chromophore. These results indicate that: (1) proton transfer is not possible if structural relaxation of the surroundings of the chromophore is prevented; (2) protons H1 and H3 especially are found very close to the point halfway between the donor and acceptor after photoexcitation when the zero-point energy is considered; (3) a geometrical parameter exists (the His148-Cro distance) under which the structure with the protons transferred is not a minimum, and that, if included, should lead to the fluorescing I* structure. The existence of an oscillating stationary state between the reactants and products of the triple proton transfer reaction can explain the dual emission reported for the I0* intermediate of wtGFP.
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Affiliation(s)
- Marc Nadal-Ferret
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Ricard Gelabert
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Miquel Moreno
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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13
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Liu XY, Chang XP, Xia SH, Cui G, Thiel W. Excited-State Proton-Transfer-Induced Trapping Enhances the Fluorescence Emission of a Locked GFP Chromophore. J Chem Theory Comput 2016; 12:753-64. [PMID: 26744782 PMCID: PMC4750082 DOI: 10.1021/acs.jctc.5b00894] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The chemical locking of the central
single bond in core chromophores
of green fluorescent proteins (GFPs) influences their excited-state
behavior in a distinct manner. Experimentally, it significantly enhances
the fluorescence quantum yield of GFP chromophores with an ortho-hydroxyl
group, while it has almost no effect on the photophysics of GFP chromophores
with a para-hydroxyl group. To unravel the underlying physical reasons
for this different behavior, we report static electronic structure
calculations and nonadiabatic dynamics simulations on excited-state
intramolecular proton transfer, cis–trans isomerization, and
excited-state deactivation in a locked ortho-substituted GFP model
chromophore (o-LHBI). On the basis of our previous and present results,
we find that the S1 keto species is responsible for the
fluorescence emission of the unlocked o-HBI and the locked o-LHBI
species. Chemical locking does not change the parts of the S1 and S0 potential energy surfaces relevant to enol–keto
tautomerization; hence, in both chromophores, there is an ultrafast
excited-state intramolecular proton transfer that takes only 35 fs
on average. However, the locking effectively hinders the S1 keto species from approaching the keto S1/S0 conical intersections so that most of trajectories are trapped in
the S1 keto region for the entire 2 ps simulation time.
Therefore, the fluorescence quantum yield of o-LHBI is enhanced compared
with that of unlocked o-HBI, in which the S1 excited-state
decay is efficient and ultrafast. In the case of the para-substituted
GFP model chromophores p-HBI and p-LHBI, chemical locking hardly affects
their efficient excited-state deactivation via cis–trans isomerization;
thus, the fluorescence quantum yields in these chromophores remain
very low. The insights gained from the present work may help to guide
the design of new GFP chromophores with improved fluorescence emission
and brightness.
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Affiliation(s)
- Xiang-Yang Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, China and
| | - Xue-Ping Chang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, China and
| | - Shu-Hua Xia
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, China and
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, China and
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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14
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Park JW, Rhee YM. Emission shaping in fluorescent proteins: role of electrostatics and π-stacking. Phys Chem Chem Phys 2016; 18:3944-55. [DOI: 10.1039/c5cp07535a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We obtained the fluorescence spectrum of the GFP with trajectory simulations, and revealed the role of the protein sidechains in emission shifts.
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Affiliation(s)
- Jae Woo Park
- Center for Self-assembly and Complexity
- Institute for Basic Science (IBS)
- Pohang 37673
- Korea
- Department of Chemistry
| | - Young Min Rhee
- Center for Self-assembly and Complexity
- Institute for Basic Science (IBS)
- Pohang 37673
- Korea
- Department of Chemistry
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15
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Armengol P, Gelabert R, Moreno M, Lluch JM. Theoretical Computer-Aided Mutagenic Study on the Triple Green Fluorescent Protein Mutant S65T/H148D/Y145F. Chemphyschem 2015; 16:2134-9. [PMID: 25916771 DOI: 10.1002/cphc.201500158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 03/27/2015] [Indexed: 11/07/2022]
Abstract
Green fluorescent protein (GFP) mutant S65T/H148D has been proposed to host a photocycle that involves an excited-state proton transfer between the chromophore (Cro) and the Asp148 residue and takes place in less than 50 fs without a measurable kinetic isotope effect. It has been suggested that the interaction between the unsuspected Tyr145 residue and the chromophore is needed for the ultrafast sub-50 fs rise in fluorescence. To verify this, we have performed a computer-aided mutagenic study to introduce the additional mutation Y145F, which eliminates this interaction. By means of QM/MM molecular dynamics simulations and time-dependent density functional theory studies, we have assessed the importance of the Cro-Tyr145 interaction and the solvation of Asp148 and shown that in the triple mutant S65T/H148D/Y145F a significant loss in the ultrafast rise of the Stokes-shifted fluorescence should be expected.
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Affiliation(s)
- Pau Armengol
- Department de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)
| | - Ricard Gelabert
- Department de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona (Spain).
| | - Miquel Moreno
- Department de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)
| | - José M Lluch
- Department de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona (Spain).,Institut de Bioquímica i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)
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16
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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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17
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Laptenok SP, Lukacs A, Gil A, Brust R, Sazanovich IV, Greetham GM, Tonge PJ, Meech SR. Complete Proton Transfer Cycle in GFP and Its T203V and S205V Mutants. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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18
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Laptenok SP, Lukacs A, Gil A, Brust R, Sazanovich IV, Greetham GM, Tonge PJ, Meech SR. Complete Proton Transfer Cycle in GFP and Its T203V and S205V Mutants. Angew Chem Int Ed Engl 2015; 54:9303-7. [PMID: 26087935 PMCID: PMC4576823 DOI: 10.1002/anie.201503672] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Indexed: 11/17/2022]
Abstract
Proton transfer is critical in many important biochemical reactions. The unique three-step excited-state proton transfer in avGFP allows observations of protein proton transport in real-time. In this work we exploit femtosecond to microsecond transient IR spectroscopy to record, in D2O, the complete proton transfer photocycle of avGFP, and two mutants (T203V and S205V) which modify the structure of the proton wire. Striking differences and similarities are observed among the three mutants yielding novel information on proton transfer mechanism, rates, isotope effects, H-bond strength and proton wire stability. These data provide a detailed picture of the dynamics of long-range proton transfer in a protein against which calculations may be compared.
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Affiliation(s)
- Sergey P Laptenok
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ (UK)
| | - Andras Lukacs
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ (UK).,Department of Biophysics, Medical School, Szigeti str. 12, 7624 Pécs (Hungary)
| | - Agnieszka Gil
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400 (USA)
| | - Richard Brust
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400 (USA).,The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 (USA)
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX (UK)
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX (UK)
| | - Peter J Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400 (USA).
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ (UK).
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19
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Armengol P, Gelabert R, Moreno M, Lluch JM. New insights into the structure–spectrum relationship in S65T/H148D and E222Q/H148D green fluorescent protein mutants: a theoretical assessment. Org Biomol Chem 2014; 12:9845-52. [DOI: 10.1039/c4ob01462f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Wineman-Fisher V, Simkovitch R, Shomer S, Gepshtein R, Huppert D, Saif M, Kallio K, Remington SJ, Miller Y. Insight into the structure and the mechanism of the slow proton transfer in the GFP double mutant T203V/S205A. Phys Chem Chem Phys 2014; 16:11196-208. [PMID: 24776960 DOI: 10.1039/c4cp00311j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutations near the fluorescing chromophore of the green fluorescent protein (GFP) have direct effects on the absorption and emission spectra. Some mutants have significant band shifts and most of the mutants exhibit a loss of fluorescence intensity. In this study we continue our investigation of the factors controlling the excited state proton transfer (PT) process of GFP, in particular to study the effects of modifications to the key side chain Ser205 in wt-GFP, proposed to participate in the proton wire. To this aim we combined mutagenesis, X-ray crystallography, steady-state spectroscopy, time-resolved emission spectroscopy and all-atom explicit molecular dynamics (MD) simulations to study the double mutant T203V/S205A. Our results show that while in the previously described GFP double mutant T203V/S205V the PT process does not occur, in the T203V/S205A mutant the PT process does occur, but with a 350 times slower rate than in wild-type GFP (wt-GFP). Furthermore, the kinetic isotope effect in the GFP double mutant T203V/S205A is twice smaller than in the wt-GFP and in the GFP single mutant S205V, which forms a novel PT pathway. On the other hand, the crystal structure of GFP T203V/S205A does not reveal a viable proton transfer pathway. To explain PT in GFP T203V/S205A, we argue on the basis of the MD simulations for an alternative, novel proton-wire pathway which involves the phenol group of the chromophore and water molecules infrequently entering from the bulk. This alternative pathway may explain the dramatically slow PT in the GFP double mutant T203V/S205A compared to wt-GFP.
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Affiliation(s)
- Vered Wineman-Fisher
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva 84105, Israel.
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21
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Kang B, Liu H, Jang DJ, Lee JY. Electric field effect on the ground state proton transfer in the H-bonded HBDI complex: an implication of the green fluorescent protein. RSC Adv 2014. [DOI: 10.1039/c4ra00974f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this paper, first-principles calculations were performed regarding the electric field effect on the ground state proton transfer (GSPT) in the H-bonded p-hydroxybenzylideneimidazolidinone (HBDI) network that represents the active site of the green fluorescent protein (GFP).
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Affiliation(s)
- Baotao Kang
- Department of Chemistry
- Sungkyunkwan University
- Suwon, Korea
| | - Hongguang Liu
- Department of Chemistry
- Sungkyunkwan University
- Suwon, Korea
| | - Du-Jeon Jang
- Department of Chemistry
- Seoul National University
- Seoul 151-742, Korea
| | - Jin Yong Lee
- Department of Chemistry
- Sungkyunkwan University
- Suwon, Korea
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22
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Bolze CS, Helbling RE, Owen RL, Pearson AR, Pompidor G, Dworkowski F, Fuchs MR, Furrer J, Golczak M, Palczewski K, Cascella M, Stocker A. Human cellular retinaldehyde-binding protein has secondary thermal 9-cis-retinal isomerase activity. J Am Chem Soc 2013; 136:137-46. [PMID: 24328211 DOI: 10.1021/ja411366w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cellular retinaldehyde-binding protein (CRALBP) chaperones 11-cis-retinal to convert opsin receptor molecules into photosensitive retinoid pigments of the eye. We report a thermal secondary isomerase activity of CRALBP when bound to 9-cis-retinal. UV/vis and (1)H NMR spectroscopy were used to characterize the product as 9,13-dicis-retinal. The X-ray structure of the CRALBP mutant R234W:9-cis-retinal complex at 1.9 Å resolution revealed a niche in the binding pocket for 9-cis-aldehyde different from that reported for 11-cis-retinal. Combined computational, kinetic, and structural data lead us to propose an isomerization mechanism catalyzed by a network of buried waters. Our findings highlight a specific role of water molecules in both CRALBP-assisted specificity toward 9-cis-retinal and its thermal isomerase activity yielding 9,13-dicis-retinal. Kinetic data from two point mutants of CRALBP support an essential role of Glu202 as the initial proton donor in this isomerization reaction.
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Affiliation(s)
- Christin S Bolze
- Department of Chemistry and Biochemistry, and ‡Graduate School for Cellular and Biomedical Sciences, University of Bern , Freiestrasse 3, 3012 Bern, Switzerland
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23
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Simkovitch R, Huppert A, Huppert D, Remington SJ, Miller Y. Proton Transfer in Wild-Type GFP and S205V Mutant Is Reduced by Conformational Changes of Residues in the Proton Wire. J Phys Chem B 2013; 117:11921-31. [DOI: 10.1021/jp405698g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ron Simkovitch
- Raymond
and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Amit Huppert
- Gertner Research Center, Tel-Hashomer 52621, Israel
| | - Dan Huppert
- Raymond
and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - S. James Remington
- Department
of Physics and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, United States
| | - Yifat Miller
- Department
of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be’er
Sheva 84105, Israel
- Ilse
Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be’er-Sheva 84105, Israel
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24
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Grigorenko BL, Nemukhin AV, Polyakov IV, Morozov DI, Krylov AI. First-Principles Characterization of the Energy Landscape and Optical Spectra of Green Fluorescent Protein along the A→I→B Proton Transfer Route. J Am Chem Soc 2013; 135:11541-9. [DOI: 10.1021/ja402472y] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Bella L. Grigorenko
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie Gory
1/3, Moscow, 119991, Russian Federation
- N.M. Emanuel Institute of Biochemical
Physics, Russian Academy of Sciences, Kosygina
4, Moscow, 119334, Russian Federation
| | - Alexander V. Nemukhin
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie Gory
1/3, Moscow, 119991, Russian Federation
- N.M. Emanuel Institute of Biochemical
Physics, Russian Academy of Sciences, Kosygina
4, Moscow, 119334, Russian Federation
| | - Igor V. Polyakov
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie Gory
1/3, Moscow, 119991, Russian Federation
| | - Dmitry I. Morozov
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie Gory
1/3, Moscow, 119991, Russian Federation
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California
90089-0482, United States
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25
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Kang B, Karthikeyan S, Jang DJ, Kim H, Lee JY. Concerted Asynchronous Proton Transfer in H-Bonding Relay Model: An Implication of Green Fluorescent Protein. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.7.1961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Nadal-Ferret M, Gelabert R, Moreno M, Lluch JM. How Does the Environment Affect the Absorption Spectrum of the Fluorescent Protein mKeima? J Chem Theory Comput 2013; 9:1731-42. [DOI: 10.1021/ct301003t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Marc Nadal-Ferret
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Ricard Gelabert
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Miquel Moreno
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - José M. Lluch
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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27
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Ding L, Chung LW, Morokuma K. Reaction mechanism of photoinduced decarboxylation of the photoactivatable green fluorescent protein: an ONIOM(QM:MM) study. J Phys Chem B 2013; 117:1075-84. [PMID: 23272644 DOI: 10.1021/jp3112952] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photoactivatable (PA) fluorescent proteins are a new class of fluorescent proteins in which the intensity of fluorescence is dramatically enhanced through photoinduced decarboxylation process. In the present study, the reaction mechanism of the photoinduced decarboxylation in PA-GFP was investigated by the ONIOM(QM:MM) method. The decarboxylation process starts from the first excited state (IntraCT state) and then proceeds along an InterCT state after the first crossing (or an approximate transition state). Relative to an equilibrium structure in S(0), a barrier of ~94 kcal/mol to reach this approximate transition state is the rate-determining step for the entire decarboxylation process. The InterCT state becomes the open-shell ground state in the product, after the subsequent crossing with a closed-shell state that holds an extra electron on the dissociated CO(2). The present study elucidated for the first time the mechanism of the photoinduced decarboxylation of PA-GFP and supports the widely accepted Kolbe pathway, which could be a common mechanism for the irreversible photoinduced decarboxylation in different fluorescent proteins.
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Affiliation(s)
- Lina Ding
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan
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28
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A time-dependent DFT/molecular dynamics study of the proton-wire responsible for the red fluorescence in the LSSmKate2 protein. Theor Chem Acc 2013. [DOI: 10.1007/s00214-012-1327-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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29
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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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30
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Weinberg DR, Gagliardi CJ, Hull JF, Murphy CF, Kent CA, Westlake BC, Paul A, Ess DH, McCafferty DG, Meyer TJ. Proton-Coupled Electron Transfer. Chem Rev 2012; 112:4016-93. [DOI: 10.1021/cr200177j] [Citation(s) in RCA: 1125] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David R. Weinberg
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
- Department of Physical and Environmental
Sciences, Colorado Mesa University, 1100 North Avenue, Grand Junction,
Colorado 81501-3122, United States
| | - Christopher J. Gagliardi
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Jonathan F. Hull
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Christine Fecenko Murphy
- Department
of Chemistry, B219
Levine Science Research Center, Box 90354, Duke University, Durham,
North Carolina 27708-0354, United States
| | - Caleb A. Kent
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Brittany C. Westlake
- The American Chemical Society,
1155 Sixteenth Street NW, Washington, District of Columbia 20036,
United States
| | - Amit Paul
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Daniel H. Ess
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Dewey Granville McCafferty
- Department
of Chemistry, B219
Levine Science Research Center, Box 90354, Duke University, Durham,
North Carolina 27708-0354, United States
| | - Thomas J. Meyer
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
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31
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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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32
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Quantum chemical comparison of vertical, adiabatic, and 0-0 excitation energies: The PYP and GFP chromophores. J Comput Chem 2012; 33:1892-901. [DOI: 10.1002/jcc.23027] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/07/2012] [Accepted: 05/08/2012] [Indexed: 12/11/2022]
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33
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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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34
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Nadal-Ferret M, Gelabert R, Moreno M, Lluch JM. A method to compute probability current in generic coordinates. J Chem Phys 2011; 134:074115. [DOI: 10.1063/1.3555764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Ma Y, Sun Q, Zhang H, Peng L, Yu JG, Smith SC. The mechanism of cyclization in chromophore maturation of green fluorescent protein: a theoretical study. J Phys Chem B 2010; 114:9698-705. [PMID: 20593847 DOI: 10.1021/jp1039817] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An intriguing aspect of the green fluorescent protein (GFP) is the autocatalytic post-translational modification that results in the formation of its chromophore. Numerous experimental and theoretical studies indicate that cyclization is the first and the most important step in the maturation process. In this work, two proposed mechanisms for the cyclization were investigated by using the hybrid density functional theory method B3LYP. Cluster models corresponding to the two mechanisms proposed by Wachter et al. [J. Biol. Chem. 2005, 280, 26248-26255] are constructed on the basis of the X-ray crystal structure (PDB entry 2AWJ) and corresponding reaction path potential energy profiles for the two cyclization mechanisms are presented. Our results suggest that the backbone condensation initiated by deprotonation of the Gly67 amide nitrogen is easier than deprotonation of the Tyr66 alpha-carbon. Moreover, Arg96 fulfills the role of stabilizing the enolate moiety, and Glu222 plays the role of a general base. The formation of the cyclized product is found to be 16.0 and 18.6 kcal/mol endothermic with respect to the two models, which is in agreement with experimental observation.
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Affiliation(s)
- Yingying Ma
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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36
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Kowalski K, Krishnamoorthy S, Villa O, Hammond JR, Govind N. Active-space completely-renormalized equation-of-motion coupled-cluster formalism: Excited-state studies of green fluorescent protein, free-base porphyrin, and oligoporphyrin dimer. J Chem Phys 2010; 132:154103. [DOI: 10.1063/1.3385315] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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37
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Formation of Schiff-base for photoreaction mechanism of red shift of GFP spectra. Biophys Chem 2010; 147:140-5. [DOI: 10.1016/j.bpc.2010.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/16/2010] [Accepted: 01/20/2010] [Indexed: 11/19/2022]
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38
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Sun Q, Doerr M, Li Z, Smith SC, Thiel W. QM/MM studies of structural and energetic properties of the far-red fluorescent protein HcRed. Phys Chem Chem Phys 2010; 12:2450-8. [PMID: 20449359 DOI: 10.1039/b918523b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The far-red fluorescent protein HcRed was investigated using molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Three models of HcRed (anionic chromophore) were considered, differing in the protonation states of nearby Glu residues (A: Glu214 and Glu146 both protonated; B: Glu214 protonated and Glu146 deprotonated; C: Glu214 and Glu146 both deprotonated). SCC-DFTB/MM MD simulations of model B yield good agreement with the available crystallographic data at ambient pH. Bond lengths in the QM region are well reproduced, with a root mean square (rms) deviation between experimental and average MD data of 0.079 A; the chromophore is almost co-planar, which is consistent with experimental observation; and the five hydrogen bonds involving the chromophore are conserved. QM/MM geometry optimizations were performed on representative snapshot structures from the MD simulations for each model. They confirm the structural features observed in the MD simulations. According to the DFT(B3LYP)/MM results, the cis-conformation of the chromophore is more stable than the trans-form by 9.1-12.9 kcal mol(-1) in model B, and by 12.4-19.9 kcal mol(-1) in model C, consistent with the experimental preference for the cis-isomer. However, in model A when both Glu214 and Glu146 are protonated, the stability is inverted with the trans-form being favored. The different protonation states of the titratable active-site residues Glu214 and Glu146 thus critically influence the manner in which the relative stability and degree of planarity of the cis- and trans-conformers vary with pH. Coupled with the known correlation of chromophore conformation with fluorescence efficiency, this work provides a detailed structural basis for the observed phenomenon that red fluorescent proteins such as HcRed, mKate and Rtms5 show bright fluorescence at high pH.
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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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Abstract
The activity within a living cell is based on a complex network of interactions among biomolecules, exchanging information and energy through biochemical processes. These events occur on different scales, from the nano- to the macroscale, spanning about 10 orders of magnitude in the space domain and 15 orders of magnitude in the time domain. Consequently, many different modeling techniques, each proper for a particular time or space scale, are commonly used. In addition, a single process often spans more than a single time or space scale. Thus, the necessity arises for combining the modeling techniques in multiscale approaches. In this Account, I first review the different modeling methods for bio-systems, from quantum mechanics to the coarse-grained and continuum-like descriptions, passing through the atomistic force field simulations. Special attention is devoted to their combination in different possible multiscale approaches and to the questions and problems related to their coherent matching in the space and time domains. These aspects are often considered secondary, but in fact, they have primary relevance when the aim is the coherent and complete description of bioprocesses. Subsequently, applications are illustrated by means of two paradigmatic examples: (i) the green fluorescent protein (GFP) family and (ii) the proteins involved in the human immunodeficiency virus (HIV) replication cycle. The GFPs are currently one of the most frequently used markers for monitoring protein trafficking within living cells; nanobiotechnology and cell biology strongly rely on their use in fluorescence microscopy techniques. A detailed knowledge of the actions of the virus-specific enzymes of HIV (specifically HIV protease and integrase) is necessary to study novel therapeutic strategies against this disease. Thus, the insight accumulated over years of intense study is an excellent framework for this Account. The foremost relevance of these two biomolecular systems was recently confirmed by the assignment of two of the Nobel prizes in 2008: in chemistry for the discovery of GFP and in medicine for the discovery of HIV. Accordingly, these proteins were studied with essentially all of the available modeling techniques, making them ideal examples for studying the details of multiscale approaches in protein modeling.
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Affiliation(s)
- Valentina Tozzini
- NEST CNR-INFM, and Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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Isaev AN. Quantum-chemical calculations of a long proton wire. Application of a harmonic model to analysis of the structure of an ionic defect in a water chain with an excess proton. J Phys Chem A 2010; 114:2201-12. [PMID: 20085360 DOI: 10.1021/jp908259p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum-chemical calculations of molecular complexes (NH(3))(3)Zn(2+)...(H(2)O)(n)...NH(3) (C(n), n = 11, 16, 21, and 30) simulating a proton wire donor-water chain-acceptor were carried out. Earlier found periodicity in the length of the O-H bonds in water chain is explained within the framework of a one-component harmonic model. In complexes C(n), the geometry and electronic structure of ionic defect in water chain with an excess proton were studied. Calculations carried out at ab initio (B3LYP/6-31+G**) and semiempirical (PM3) levels of theory predict different patterns of distribution of the O-H bonds lengths and positive charge on the H-bond hydrogen atoms in the region of ionic defect. The obtained data show how a length of water chain and position of a protonated water link in the chain influence the ionic defect structure. To describe the observed structures of ionic defect, the harmonic model was used and the role of parameters of the H-bonded chain was investigated. The performed analysis explains different mechanisms (concerted and stepwise) of proton transfer along the H-bonded chain derived from ab initio and semiempirical calculation schemes.
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Affiliation(s)
- Alexander N Isaev
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky pr. 47, 119991 Moscow, Russia.
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Sun Q, Wang S, Zhang H, Li Z, Pifisterer C, Fischer S, Nanbu S, Smith SC. Structural and Relaxation Effects in Proton Wire Energetics: Model Studies of the Green Fluorescent Protein Photocycle. Aust J Chem 2010. [DOI: 10.1071/ch09509] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We present the results of a systematic series of constrained minimum energy pathway calculations on ground state potential energy surfaces, for a cluster model of the proton chain transfer that mediates the photocycle of the green fluorescent protein, as well as for a model including the solvated protein environment. The calculations vary in terms of the types of modes that are assumed to be capable of relaxing in concert with the movement of the protons and the results demonstrate that the nature and extent of dynamical relaxation has a substantive impact on the activation energy for the proton transfer. We discuss the implications of this in terms of currently available dynamical models and chemical rate theories that might be brought to bear on the kinetics of this important example of proton chain transfer in a biological system.
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Grigorenko BL, Polyakov IV, Savitskii AP, Nemukhina AV. Structural forms of green fluorescent protein by quantum mechanics/molecular mechanics calculations. Russ Chem Bull 2010. [DOI: 10.1007/s11172-010-0045-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Li X, Chung LW, Mizuno H, Miyawaki A, Morokuma K. A Theoretical Study on the Nature of On- and Off-States of Reversibly Photoswitching Fluorescent Protein Dronpa: Absorption, Emission, Protonation, and Raman. J Phys Chem B 2009; 114:1114-26. [DOI: 10.1021/jp909947c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Lung Wa Chung
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Hideaki Mizuno
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Atsushi Miyawaki
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
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Filippi C, Zaccheddu M, Buda F. Absorption Spectrum of the Green Fluorescent Protein Chromophore: A Difficult Case for ab Initio Methods? J Chem Theory Comput 2009; 5:2074-87. [DOI: 10.1021/ct900227j] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Claudia Filippi
- Instituut-Lorentz, Universiteit Leiden, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands, Faculty of Science and Technology and MESA+ Research Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, and Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Maurizio Zaccheddu
- Instituut-Lorentz, Universiteit Leiden, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands, Faculty of Science and Technology and MESA+ Research Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, and Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Francesco Buda
- Instituut-Lorentz, Universiteit Leiden, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands, Faculty of Science and Technology and MESA+ Research Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, and Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Zhang H, Wang S, Sun Q, Smith SC. Kinetic isotope effect for ground state proton transfer in the green fluorescent protein: a quantum-kinetic model. Phys Chem Chem Phys 2009; 11:8422-4. [DOI: 10.1039/b912507h] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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van Thor JJ. Photoreactions and dynamics of the green fluorescent protein. Chem Soc Rev 2009; 38:2935-50. [DOI: 10.1039/b820275n] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Ortiz-Sánchez JM, Gelabert R, Moreno M, Lluch JM. Study of the Photochemical Properties and Conical Intersections of [2,2′-Bipyridyl]-3-amine-3′-ol. Chemphyschem 2008; 9:2068-76. [DOI: 10.1002/cphc.200800322] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Vendrell O, Gelabert R, Moreno M, Lluch JM. Exploring the Effects of Intramolecular Vibrational Energy Redistribution on the Operation of the Proton Wire in Green Fluorescent Protein. J Phys Chem B 2008; 112:13443-52. [DOI: 10.1021/jp805049c] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oriol Vendrell
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| | - Ricard Gelabert
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| | - Miquel Moreno
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| | - José M. Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
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