1
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Beaujean P, Champagne B, Grimme S, de Wergifosse M. All-Atom Quantum Mechanical Calculation of the Second-Harmonic Generation of Fluorescent Proteins. J Phys Chem Lett 2021; 12:9684-9690. [PMID: 34590850 DOI: 10.1021/acs.jpclett.1c02911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fluorescent proteins (FPs) are biotags of choice for second-harmonic imaging microscopy (SHIM). Because of their large size, computing their second-harmonic generation (SHG) response represents a great challenge for quantum chemistry. In this contribution, we propose a new all-atom quantum mechanics methodology to compute SHG of large systems. This is now possible because of two recent implementations: the tight-binding GFN2-xTB method to optimize geometries and a related version of the simplified time-dependent density functional theory (sTD-DFT-xTB) to evaluate quadratic response functions. In addition, a new dual-threshold configuration selection scheme is introduced to reduce the computational costs while retaining overall similar accuracy. This methodology was tested to evaluate the SHG of the proteins iLOV and bacteriorhodopsin (bR). In the case of bR, quantitative agreement with respect to experiment was reached for the out-of-resonance low-energy part of the βHRS frequency dispersion. This work paves the way toward an accurate prediction of the SHG of large structures-a requirement for the design of new and improved SHIM biotags.
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Affiliation(s)
- Pierre Beaujean
- Laboratory of Theoretical Chemistry, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Benoît Champagne
- Laboratory of Theoretical Chemistry, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Berings. 4, D-53115 Bonn, Germany
| | - Marc de Wergifosse
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Berings. 4, D-53115 Bonn, Germany
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2
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Metal-ion promiscuity of microbial enzyme DapE at its second metal-binding site. J Biol Inorg Chem 2021; 26:569-582. [PMID: 34241683 DOI: 10.1007/s00775-021-01875-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/28/2021] [Indexed: 10/20/2022]
Abstract
Metalloenzymes are ubiquitous in nature catalyzing a number of crucial biochemical processes in animal and plant kingdoms. For better adaptation to the relative abundance of different metal ions in different cellular fluids, many of these enzymes exhibit metal promiscuity. The microbial enzyme DapE, an essential enzyme for bacterial growth and survival and a potentially safe target for antibiotics, continues to show enzyme activity when the two zinc ions in its active site are replaced by other transition metal ions. The effect of metal-ion substitution at the second metal-binding site of DapE on its substrate affinity and catalytic efficiency is investigated by QM/MM treatment of the enzyme-substrate complex, by modelling the enzyme with Mn(II), Co(II), Ni(II), or Cu(II) ion in place of Zn(II) at its second metal-binding site, while retaining Zn(II) ion at the first metal-binding site. On the basis of substrate binding energy and activation energy barrier for the chemical catalysis, it is found that Zn-Mn DapE shows poor binding affinity as well as inefficient chemical catalysis. Although Zn-Cu and Zn-Ni DapEs show activation energy barriers comparable to that of wild-type Zn-Zn DapE, their weaker substrate affinity renders these mixed-metal enzymes less efficient. On the other hand, Zn-Co DapE is found to outperform the naturally occurring Zn-Zn DapE, both in terms of substrate affinity and chemical catalysis. The observed metal promiscuity may have played an important role in the survival of bacteria even in those cellular media where Zn ions are in limited supply. Metal nonspecificity in the catalysis of DapE enzyme allows bacteria to thrive in different cellular media.
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3
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Dajnowicz S, Langan PS, Weiss KL, Ivanov IN, Kovalevsky A. Room-temperature photo-induced martensitic transformation in a protein crystal. IUCRJ 2019; 6:619-629. [PMID: 31316806 PMCID: PMC6608640 DOI: 10.1107/s2052252519005761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/26/2019] [Indexed: 06/10/2023]
Abstract
Martensitic transformations are the first-order crystal-to-crystal phase transitions that occur mostly in materials such as steel, alloys and ceramics, thus having many technological applications. These phase transitions are rarely observed in molecular crystals and have not been detected in protein crystals. Reversibly switchable fluorescent proteins are widely used in biotechnology, including super-resolution molecular imaging, and hold promise as candidate biomaterials for future high-tech applications. Here, we report on a reversibly switchable fluorescent protein, Tetdron, whose crystals undergo a photo-induced martensitic transformation at room temperature. Room-temperature X-ray crystallography demonstrates that at equilibrium Tetdron chromophores are all in the trans configuration, with an ∼1:1 mixture of their protonated and deprotonated forms. Irradiation of a Tetdron crystal with 400 nm light induces a martensitic transformation, which results in Tetdron tetramerization at room temperature revealed by X-ray photocrystallography. Crystal and solution spectroscopic measurements provide evidence that the photo-induced martensitic phase transition is coupled with the chromophore deprotonation, but no trans-cis isomerization is detected in the structure of an irradiated crystal. It is hypothesized that protein dynamics assists in the light-induced proton transfer from the chromophore to the bulk solvent and in the ensuing martensitic phase transition. The unique properties of Tetdron may be useful in developing novel biomaterials for optogenetics, data storage and nanotechnology.
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Affiliation(s)
- Steven Dajnowicz
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Patricia S. Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Ilia N. Ivanov
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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4
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Takaba K, Tai Y, Eki H, Dao HA, Hanazono Y, Hasegawa K, Miki K, Takeda K. Subatomic resolution X-ray structures of green fluorescent protein. IUCRJ 2019; 6:387-400. [PMID: 31098020 PMCID: PMC6503917 DOI: 10.1107/s205225251900246x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/17/2019] [Indexed: 05/06/2023]
Abstract
Green fluorescent protein (GFP) is a light-emitting protein that does not require a prosthetic group for its fluorescent activity. As such, GFP has become indispensable as a molecular tool in molecular biology. Nonetheless, there has been no subatomic elucidation of the GFP structure owing to the structural polymorphism around the chromophore. Here, subatomic resolution X-ray structures of GFP without the structural polymorphism are reported. The positions of H atoms, hydrogen-bonding network patterns and accurate geometric parameters were determined for the two protonated forms. Compared with previously determined crystal structures and theoretically optimized structures, the anionic chromophores of the structures represent the authentic resonance state of GFP. In addition, charge-density analysis based on atoms-in-molecules theory and noncovalent interaction analysis highlight weak but substantial interactions between the chromophore and the protein environment. Considered with the derived chemical indicators, the lone pair-π interactions between the chromophore and Thr62 should play a sufficient role in maintaining the electronic state of the chromophore. These results not only reveal the fine structural features that are critical to understanding the properties of GFP, but also highlight the limitations of current quantum-chemical calculations.
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Affiliation(s)
- Kiyofumi Takaba
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yang Tai
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Haruhiko Eki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hoang-Anh Dao
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuya Hanazono
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuya Hasegawa
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- Correspondence e-mail:
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5
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Nemukhin AV, Grigorenko BL, Khrenova MG, Krylov AI. Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes. J Phys Chem B 2019; 123:6133-6149. [DOI: 10.1021/acs.jpcb.9b00591] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Alexander V. Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Bella L. Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria G. Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Federal Research Center of Biotechnology, Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russian
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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6
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de Wergifosse M, Botek E, De Meulenaere E, Clays K, Champagne B. ONIOM Investigation of the Second-Order Nonlinear Optical Responses of Fluorescent Proteins. J Phys Chem B 2018; 122:4993-5005. [DOI: 10.1021/acs.jpcb.8b01430] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Marc de Wergifosse
- Laboratory of Theoretical Chemistry, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Edith Botek
- Laboratory of Theoretical Chemistry, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Evelien De Meulenaere
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
- Laboratory for Molecular Electronics and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | - Koen Clays
- Laboratory for Molecular Electronics and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | - Benoît Champagne
- Laboratory of Theoretical Chemistry, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
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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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Skúpa K, Urban J. Modifications of the chromophore of Spinach aptamer based on QM:MM calculations. J Mol Model 2017; 23:46. [PMID: 28154983 DOI: 10.1007/s00894-017-3232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/13/2017] [Indexed: 10/20/2022]
Abstract
Spinach aptamer was developed as an RNA analog of the green fluorescent protein. The aptamer interacts with its ligand and modifies its electronic spectrum so that it fluoresces brightly at the wavelength of 501 nm. Song et al. investigated modifications of the ligand in their experimental study and found a molecule emitting at 523 nm upon creating a complex with the Spinach aptamer. The crystal structure of the aptamer in complex with its original ligand has been published, which enabled us to study the system computationally. In this article, we suggest several new modifications of the ligand that shift the emission maximum of the complex to even longer wavelengths. Our results are based on combined quantum mechanical/molecular mechanical calculations with DFT method used for geometry optimization and TD-DFT for calculations of absorption and emission energies.
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Affiliation(s)
- Katarína Skúpa
- Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia.
| | - Ján Urban
- Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
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9
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Dutta D, Mishra S. Loss of Catalytic Activity in the E134D, H67A, and H349A Mutants of DapE: Mechanistic Analysis with QM/MM Investigation. J Phys Chem B 2016; 120:11654-11664. [DOI: 10.1021/acs.jpcb.6b07446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Debodyuti Dutta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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10
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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: 174] [Impact Index Per Article: 21.8] [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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11
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Tachikawa H. Reaction Dynamics Following Ionization of Ammonia Dimer Adsorbed on Ice Surface. J Phys Chem A 2016; 120:7301-10. [DOI: 10.1021/acs.jpca.6b04699] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroto Tachikawa
- Division
of Applied Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, JAPAN
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12
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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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13
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Berardozzi R, Adam V, Martins A, Bourgeois D. Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins. J Am Chem Soc 2016; 138:558-65. [PMID: 26675944 DOI: 10.1021/jacs.5b09923] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoactivated localization microscopy (PALM) is a powerful technique to investigate cellular nanostructures quantitatively and dynamically. However, the use of PALM for molecular counting or single-particle tracking remains limited by the propensity of photoconvertible fluorescent protein markers (PCFPs) to repeatedly enter dark states. By designing the single mutants mEos2-A69T and Dendra2-T69A, we completely swapped the blinking behaviors of mEos2 and Dendra2, two popular PCFPs. We combined X-ray crystallography and single-molecule microscopy to show that blinking in mEos2 and Dendra2 is largely controlled by the orientation of arginine 66, a highly conserved residue in Anthozoan PCFPs. The Arg66 side-chain conformation affects the bleaching and the on-to-off transition quantum yields, as well as the fraction of molecules entering long-lived dark states, resulting in widely different apparent blinking behaviors that largely modulate the efficiency of current blinking correction procedures. The present work provides mechanistic insight into the complex photophysics of Anthozoan PCFPs and will facilitate future engineering of bright and low-blinking variants suitable for PALM.
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Affiliation(s)
- Romain Berardozzi
- Institut de Biologie Structurale, Université Grenoble Alpes , CEA, CNRS, 38044 Grenoble, France
| | - Virgile Adam
- Institut de Biologie Structurale, Université Grenoble Alpes , CEA, CNRS, 38044 Grenoble, France
| | - Alexandre Martins
- Institut de Biologie Structurale, Université Grenoble Alpes , CEA, CNRS, 38044 Grenoble, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, Université Grenoble Alpes , CEA, CNRS, 38044 Grenoble, France
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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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Grigorenko BL, Nemukhin AV, Polyakov IV, Khrenova MG, Krylov AI. A Light-Induced Reaction with Oxygen Leads to Chromophore Decomposition and Irreversible Photobleaching in GFP-Type Proteins. J Phys Chem B 2015; 119:5444-52. [PMID: 25867185 DOI: 10.1021/acs.jpcb.5b02271] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Photobleaching and photostability of proteins of the green fluorescent protein (GFP) family are crucially important for practical applications of these widely used biomarkers. On the basis of simulations, we propose a mechanism for irreversible bleaching in GFP-type proteins under intense light illumination. The key feature of the mechanism is a photoinduced reaction of the chromophore with molecular oxygen (O2) inside the protein barrel leading to the chromophore's decomposition. Using quantum mechanics/molecular mechanics (QM/MM) modeling we show that a model system comprising the protein-bound Chro(-) and O2 can be excited to an electronic state of the intermolecular charge-transfer (CT) character (Chro(•)···O2(-•)). Once in the CT state, the system undergoes a series of chemical reactions with low activation barriers resulting in the cleavage of the bridging bond between the phenolic and imidazolinone rings and disintegration of the chromophore.
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Affiliation(s)
- Bella L Grigorenko
- †Department of Chemistry, 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
- †Department of Chemistry, 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
- †Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation
| | - Maria G Khrenova
- †Department of Chemistry, 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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16
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 738] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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17
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Chen J, Wang J, Zhang Q, Chen K, Zhu W. A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation. J Biomol Struct Dyn 2015; 33:2606-18. [PMID: 25562613 DOI: 10.1080/07391102.2014.1003146] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hydrogen bonding and polar interactions play a key role in identification of protein-inhibitor binding specificity. Quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulations combined with DFT and semi-empirical Hamiltonian (AM1d, RM1, PM3, and PM6) methods were performed to study the hydrogen bonding and polar interactions of two inhibitors BEN and BEN1 with trypsin. The results show that the accuracy of treating the hydrogen bonding and polar interactions using QM/MM MD simulation of PM6 can reach the one obtained by the DFT QM/MM MD simulation. Quantum mechanics/molecular mechanics generalized Born surface area (QM/MM-GBSA) method was applied to calculate binding affinities of inhibitors to trypsin and the results suggest that the accuracy of binding affinity prediction can be significantly affected by the accurate treatment of the hydrogen bonding and polar interactions. In addition, the calculated results also reveal the binding specificity of trypsin: (1) the amidinium groups of two inhibitors generate favorable salt bridge interaction with Asp189 and form hydrogen bonding interactions with Ser190 and Gly214, (2) the phenyl of inhibitors can produce favorable van der Waals interactions with the residues His58, Cys191, Gln192, Trp211, Gly212, and Cys215. This systematic and comparative study can provide guidance for the choice of QM/MM MD methods and the designs of new potent inhibitors targeting trypsin.
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Affiliation(s)
- Jianzhong Chen
- a School of Science , Shandong Jiaotong University , Jinan , 250014 , China
| | - Jinan Wang
- b Discovery and Design Center , CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai , 201203 , China
| | - Qinggang Zhang
- c College of Physics and Electronics , Shandong Normal University , Jinan , 250014 , China
| | - Kaixian Chen
- b Discovery and Design Center , CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai , 201203 , China
| | - Weiliang Zhu
- b Discovery and Design Center , CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai , 201203 , China
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18
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Perera L, Beard WA, Pedersen LG, Wilson SH. Applications of quantum mechanical/molecular mechanical methods to the chemical insertion step of DNA and RNA polymerization. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 97:83-113. [PMID: 25458356 PMCID: PMC5573153 DOI: 10.1016/bs.apcsb.2014.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We review theoretical attempts to model the chemical insertion reactions of nucleoside triphosphates catalyzed by the nucleic acid polymerases using combined quantum mechanical/molecular mechanical methodology. Due to an existing excellent database of high-resolution X-ray crystal structures, the DNA polymerase β system serves as a useful template for discussion and comparison. The convergence of structures of high-quality complexes and continued developments of theoretical techniques suggest a bright future for understanding the global features of nucleic acid polymerization.
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Affiliation(s)
- Lalith Perera
- Laboratory of Structural Biology, National Institution of Environmental Health Sciences, Research Triangle Park, North Carolina, USA.
| | - William A Beard
- Laboratory of Structural Biology, National Institution of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Lee G Pedersen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Samuel H Wilson
- Laboratory of Structural Biology, National Institution of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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19
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Adam V, Berardozzi R, Byrdin M, Bourgeois D. Phototransformable fluorescent proteins: Future challenges. Curr Opin Chem Biol 2014; 20:92-102. [DOI: 10.1016/j.cbpa.2014.05.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/19/2014] [Accepted: 05/22/2014] [Indexed: 01/28/2023]
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20
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Vegh R, Bravaya KB, Bloch DA, Bommarius A, Tolbert L, Verkhovsky M, Krylov AI, Solntsev KM. Chromophore photoreduction in red fluorescent proteins is responsible for bleaching and phototoxicity. J Phys Chem B 2014; 118:4527-34. [PMID: 24712386 PMCID: PMC4010289 DOI: 10.1021/jp500919a] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 04/05/2014] [Indexed: 12/11/2022]
Abstract
Red fluorescent proteins (RFPs) are indispensable tools for deep-tissue imaging, fluorescence resonance energy transfer applications, and super-resolution microscopy. Using time-resolved optical spectroscopy this study investigated photoinduced dynamics of three RFPs, KillerRed, mRFP, and DsRed. In all three RFPs, a new transient absorption intermediate was observed, which decays on a microsecond-millisecond time scale. This intermediate is characterized by red-shifted absorption at 1.68-1.72 eV (λmax = 720-740 nm). On the basis of electronic structure calculations, experimental evidence, and published literature, the chemical nature of the intermediate is assigned to an unusual open-shell dianionic chromophore (dianion-radical) formed via photoreduction. A doubly charged state that is not stable in the isolated (gas phase) chromophore is stabilized by the electrostatic field of the protein. Mechanistic implications for photobleaching, blinking, and phototoxicity are discussed.
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Affiliation(s)
- Russell
B. Vegh
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0400, United States
- Parker
H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0363, United States
| | - Ksenia B. Bravaya
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Dmitry A. Bloch
- Institute
of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Andreas
S. Bommarius
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0400, United States
- Parker
H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0363, United States
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0100, United States
| | - Laren
M. Tolbert
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0400, United States
| | | | - Anna I. Krylov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Kyril M. Solntsev
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0400, United States
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21
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Dutta D, Mishra S. The structural and energetic aspects of substrate binding and the mechanism of action of the DapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) investigated using a hybrid QM/MM method. Phys Chem Chem Phys 2014; 16:26348-58. [DOI: 10.1039/c4cp03986f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Substrate binding and the mechanism of action of the DapE-encodedN-succinyl-l,l-diaminopimelic acid desuccinylase (DapE).
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Affiliation(s)
- Debodyuti Dutta
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur, India
| | - Sabyashachi Mishra
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur, India
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22
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Duan C, Adam V, Byrdin M, Ridard J, Kieffer-Jaquinod S, Morlot C, Arcizet D, Demachy I, Bourgeois D. Structural Evidence for a Two-Regime Photobleaching Mechanism in a Reversibly Switchable Fluorescent Protein. J Am Chem Soc 2013; 135:15841-50. [DOI: 10.1021/ja406860e] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chenxi Duan
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
- Laboratoire
de Physiologie Cellulaire et Végétale, IRTSV, CNRS/CEA/INRA/Université Grenoble Alpes, Grenoble, 38054, France
| | - Virgile Adam
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
- Laboratoire
de Physiologie Cellulaire et Végétale, IRTSV, CNRS/CEA/INRA/Université Grenoble Alpes, Grenoble, 38054, France
| | - Martin Byrdin
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
- Laboratoire
de Physiologie Cellulaire et Végétale, IRTSV, CNRS/CEA/INRA/Université Grenoble Alpes, Grenoble, 38054, France
| | - Jacqueline Ridard
- Laboratoire
de Chimie Physique, UMR 8000, CNRS, Université Paris Sud 11, 91405 Orsay, France
| | | | - Cécile Morlot
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
| | - Delphine Arcizet
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
- Laboratoire
de Physiologie Cellulaire et Végétale, IRTSV, CNRS/CEA/INRA/Université Grenoble Alpes, Grenoble, 38054, France
| | - Isabelle Demachy
- Laboratoire
de Chimie Physique, UMR 8000, CNRS, Université Paris Sud 11, 91405 Orsay, France
| | - Dominique Bourgeois
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
- Laboratoire
de Physiologie Cellulaire et Végétale, IRTSV, CNRS/CEA/INRA/Université Grenoble Alpes, Grenoble, 38054, France
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23
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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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24
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Zhang Y, Yan S, Yao L. A Mechanistic Study of Trichoderma reesei Cel7B Catalyzed Glycosidic Bond Cleavage. J Phys Chem B 2013; 117:8714-22. [DOI: 10.1021/jp403999s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yu Zhang
- Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Shihai Yan
- Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Lishan Yao
- Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
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