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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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2
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Grabarek D, Andruniów T. Assessment of Functionals for TDDFT Calculations of One- and Two-Photon Absorption Properties of Neutral and Anionic Fluorescent Proteins Chromophores. J Chem Theory Comput 2018; 15:490-508. [PMID: 30485096 DOI: 10.1021/acs.jctc.8b00769] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Performance of DFT functionals with different percentages of exact Hartree-Fock exchange energy (EX) is assessed for recovery of the CC2 reference one- (OPA) and two-photon absorption (TPA) spectra of fluorescent proteins chromophores in vacuo. The investigated DFT functionals, together with their EX contributions are BLYP (0%), B3LYP (20%), B1LYP (25%), BHandHLYP (50%), and CAM-B3LYP (19% at short range and 65% at long range). Our test set consists of anionic and neutral chromophores as naturally occurring in the fluorescent proteins. For the first time, we compare TDDFT and CC2 methods for higher excited states than the S1 state, exhibiting relatively large TPA intensity. Our TDDFT results for neutral chromophores reveal an increase in excitation energies as well as TPA and OPA intensities errors, compared to CC2-derived results, as the DFT functional contains less exact exchange. The long-range-corrected CAM-B3LYP functional performs the best, closely followed by BHandHLYP, while BLYP usually significantly underestimates all investigated spectral properties, hence being the worst in reproducing the reference CC2 results. The hybrid B3LYP and B1LYP functionals can be roughly placed in between. We propose that TDDFT may underestimate the TPA intensities for neutral chromophores of fluorescent proteins due to underestimated oscillator strengths between some excited states. In the case of anionic chromophores, we find that B3LYP and B1LYP functionals overcome others in terms of reproducing CC2 excitation energies. On the other hand, however, TPA intensity is usually significantly underestimated, and in this respect, CAM-B3LYP functional seems to be again superior. In contrast to the case of neutral chromophores, it seems that a large magnitude of excited-state dipole moments or changes in dipole moments upon excitation may be the driving force behind high TPA transition moments.
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Affiliation(s)
- Dawid Grabarek
- Advanced Materials Engineering and Modelling Group , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
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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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4
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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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5
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Grigorenko BL, Krylov AI, Nemukhin AV. Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein. J Am Chem Soc 2017; 139:10239-10249. [DOI: 10.1021/jacs.7b00676] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Bella L. Grigorenko
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna I. Krylov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Alexander V. Nemukhin
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
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6
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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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Ma Y, Sun Q, Smith SC. The mechanism of oxidation in chromophore maturation of wild-type green fluorescent protein: a theoretical study. Phys Chem Chem Phys 2017; 19:12942-12952. [DOI: 10.1039/c6cp07983k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DFT calculations suggested that the thermodynamically unfavourable cyclized product was trapped by oxidation.
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Affiliation(s)
- Yingying Ma
- Institue of Mining Technology
- Inner Mongolia University of Technology
- Hohhot 010051
- P. R. China
- Inner Mongolia Key Laboratory of Theoretical and Computational Chemistry Simulation
| | - Qiao Sun
- School of Radiation Medicine and Radiation Protection
- Soochow University
- Suzhou 215123
- P. R. China
| | - Sean C. Smith
- Integrated Materials Design Centre
- School of Chemical Engineering
- The University of New South Wales
- Sydney
- Australia
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8
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Ma Y, Zhang H, Sun Q, Smith SC. New Insights on the Mechanism of Cyclization in Chromophore Maturation of Wild-Type Green Fluorescence Protein: A Computational Study. J Phys Chem B 2016; 120:5386-94. [DOI: 10.1021/acs.jpcb.6b04406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yingying Ma
- Institue
of Mining Technology, Inner Mongolia University of Technology, Hohhot 010051, P. R. China
- Inner Mongolia Key Laboratory of Theoretical and Computational Chemistry Simulation, Hohhot 010051, P. R. China
| | - Hao Zhang
- College
of Life Science and Engineering, Northwest University for Nationalities, Lanzhou 730030, P. R. China
| | - Qiao Sun
- School
of Radiation Medicine and Radiation Protection, Soochow University, Suzhou 215123, P. R. China
| | - Sean C. Smith
- Integrated
Materials Design Centre, School of Chemical Engineering, The University of New South Wales, NSW2052, Sydney, Australia
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9
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Ma Y, Yu JG, Sun Q, Li Z, Smith SC. The mechanism of dehydration in chromophore maturation of wild-type green fluorescent protein: A theoretical study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.04.061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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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: 760] [Impact Index Per Article: 84.4] [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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11
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Vazquez-Duhalt R, Aguila SA, Arrocha AA, Ayala M. QM/MM Molecular Modeling and Marcus Theory in the Molecular Design of Electrodes for Enzymatic Fuel Cells. ChemElectroChem 2013. [DOI: 10.1002/celc.201300096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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12
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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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13
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Zhang H, Ma Y, Liu K, Yu JG. Theoretical studies on the reaction mechanism of PP1 and the effects of different oxidation states of the Mn–Mn center on the mechanism. J Biol Inorg Chem 2013; 18:451-9. [DOI: 10.1007/s00775-013-0989-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 02/13/2013] [Indexed: 01/18/2023]
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14
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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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15
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A theoretical investigation of the mechanism of formation of a simplified analog of the green fluorescent protein (GFP) from a peptide model. Struct Chem 2012. [DOI: 10.1007/s11224-012-0134-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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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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