1
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Pieri E, Walker AR, Zhu M, Martínez TJ. Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins. J Am Chem Soc 2024; 146:17646-17658. [PMID: 38885641 DOI: 10.1021/jacs.4c00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Red fluorescent protein (RFP) variants are highly sought after for in vivo imaging since longer wavelengths improve depth and contrast in fluorescence imaging. However, the lower energy emission wavelength usually correlates with a lower fluorescent quantum yield compared to their green emitting counterparts. To guide the rational design of bright variants, we have theoretically assessed two variants (mScarlet and mRouge) which are reported to have very different brightness. Using an α-CASSCF QM/MM framework (chromophore and all protein residues within 6 Å of it in the QM region, for a total of more than 450 QM atoms), we identify key points on the ground and first excited state potential energy surfaces. The brighter variant mScarlet has a rigid scaffold, and the chromophore stays largely planar on the ground state. The dimmer variant mRouge shows more flexibility and can accommodate a pretwisted chromophore conformation which provides easier access to conical intersections. The main difference between the variants lies in the intersection seam regions, which appear largely inaccessible in mScarlet but partially accessible in mRouge. This observation is mainly related with changes in the cavity charge distribution, the hydrogen-bonding network involving the chromophore and a key ARG/THR mutation (which changes both charge and steric hindrance).
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Affiliation(s)
- Elisa Pieri
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Alice R Walker
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Mingning Zhu
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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2
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Rajbongshi BK, Abdullah S, Lama B, Bhattacharyya HP, Sarma M. Regioselective and solvent-dependent photoisomerization induced internal conversion in red fluorescent protein chromophore analogues. RSC Adv 2024; 14:18373-18384. [PMID: 38860252 PMCID: PMC11163268 DOI: 10.1039/d4ra00988f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
Photophysical properties of three red fluorescent protein (RFP) chromophore analogues are reported here. The three RFP chromophore analogues differ in the additional conjugation present in the RFP chromophore. The three chromophores do not exhibit any solvent effect in both absorption and fluorescence spectra. The photoirradiation experiments and recording of 1H NMR before and after irradiation on one of the three RFP model chromophores show isomerization of the (Z,E) diastereomer to the (E,E) diastereomer. Calculation of S0 and S1 potential energy curves shows the preference for isomerization through the exocyclic C[double bond, length as m-dash]C bond with Z-stereochemistry, thus corroborating the experimental results. The computational studies also suggest that torsional motion along the exocyclic C[double bond, length as m-dash]C bond pushes the molecules to a conical intersection, thus paving the pathway for radiationless deactivation.
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Affiliation(s)
| | - Sheikh Abdullah
- Department of Chemistry, Cotton University Panbazar Guwahati Assam 781001 India
| | - Bittu Lama
- Department of Chemistry, Indian Institute of Technology Guwahati Assam 781039 India
| | | | - Manabendra Sarma
- Department of Chemistry, Indian Institute of Technology Guwahati Assam 781039 India
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3
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Liu XY, Wang SR, Fang WH, Cui G. Nuclear Quantum Effects on Nonadiabatic Dynamics of a Green Fluorescent Protein Chromophore Analogue: Ring-Polymer Surface-Hopping Simulation. J Chem Theory Comput 2024; 20:3426-3439. [PMID: 38656202 DOI: 10.1021/acs.jctc.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Herein, we have used the "on-the-fly" ring-polymer surface-hopping simulation method with the centroid approximation (RPSH-CA), in combination with the multireference OM2/MRCI electronic structure calculations to study the photoinduced dynamics of a green fluorescent protein (GFP) chromophore analogue in the gas phase, i.e., o-HBI, at 50, 100, and 300 K with 1, 5, 10, and 15 beads (3600 1 ps trajectories). The electronic structure calculations identified five new minimum-energy conical intersection (MECI) structures, which, together with the previous one, play crucial roles in the excited-state decay dynamics of o-HBI. It is also found that the excited-state intramolecular proton transfer (ESIPT) occurs in an ultrafast manner and is completed within 20 fs in all the simulation conditions because there is no barrier associated with this ESIPT process in the S1 state. However, the other excited-state dynamical results are strongly related to the number of beads. At 50 and 100 K, the nuclear quantum effects (NQEs) are very important; therefore, the excited-state dynamical results change significantly with the bead number. For example, the S1 decay time deduced from time-dependent state populations becomes longer as the bead number increases. Nevertheless, an essentially convergent trend is observed when the bead number is close to 10. In contrast, at 300 K, the NQEs become weaker and the above dynamical results converge very quickly even with 1 bead. Most importantly, the NQEs seriously affect the excited-state decay mechanism of o-HBI. At 50 and 100 K, most trajectories decay to the S0 state via perpendicular keto MECIs, whereas, at 300 K, only twisted keto MECIs are responsible for the excited-state decay. The present work not only comprehensively explores the temperature-dependent photoinduced dynamics of o-HBI, but also demonstrates the importance and necessity of NQEs in nonadiabatic dynamics simulations, especially at relatively low temperatures.
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Affiliation(s)
- Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, China
| | - Sheng-Rui Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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4
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List NH, Jones CM, Martínez TJ. Chemical control of excited-state reactivity of the anionic green fluorescent protein chromophore. Commun Chem 2024; 7:25. [PMID: 38316834 PMCID: PMC10844232 DOI: 10.1038/s42004-024-01099-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Controlling excited-state reactivity is a long-standing challenge in photochemistry, as a desired pathway may be inaccessible or compete with other unwanted channels. An important example is internal conversion of the anionic green fluorescent protein (GFP) chromophore where non-selective progress along two competing torsional modes (P: phenolate and I: imidazolinone) impairs and enables Z-to-E photoisomerization, respectively. Developing strategies to promote photoisomerization could drive new areas of applications of GFP-like proteins. Motivated by the charge-transfer dichotomy of the torsional modes, we explore chemical substitution on the P-ring of the chromophore as a way to control excited-state pathways and improve photoisomerization. As demonstrated by methoxylation, selective P-twisting appears difficult to achieve because the electron-donating potential effects of the substituents are counteracted by inertial effects that directly retard the motion. Conversely, these effects act in concert to promote I-twisting when introducing electron-withdrawing groups. Specifically, 2,3,5-trifluorination leads to both pathway selectivity and a more direct approach to the I-twisted intersection which, in turn, doubles the photoisomerization quantum yield. Our results suggest P-ring engineering as an effective approach to boost photoisomerization of the anionic GFP chromophore.
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Affiliation(s)
- Nanna H List
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-10044, Stockholm, Sweden.
| | - Chey M Jones
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, CA, 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, CA, 94305, USA.
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA.
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5
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Zhi X, Sun Y, Cai F, Wang S, Gao H, Wu F, Zhang L, Shen Z. Oxidized Low-Density Lipoprotein (Ox-LDL)-Triggered Double-Lock Probe for Spatiotemporal Lipoprotein Oxidation and Atherosclerotic Plaque Imaging. Adv Healthc Mater 2023; 12:e2301595. [PMID: 37557912 DOI: 10.1002/adhm.202301595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/25/2023] [Indexed: 08/11/2023]
Abstract
Low-density lipoprotein (LDL), especially oxidative modified LDL (Ox-LDL), is the key risk factor for plaque accumulation and the development of cardiovascular disease. Herein, a highly specific Ox-LDL-triggered fluorogenic-colorimetric probe Pro-P1 is developed for visualizing the oxidation and aggregation progress of lipoproteins and plaque. A series of green fluorescent protein chromophores with modified donor-acceptor structures, containing carbazole as an electron donor and various substituents including pyridine-vinyl (P1), phenol-vinyl (P2), N, N-dimethylaniline-vinyl (P3), and thiophene-vinyl (P4), have been synthesized and evaluated. Emission spectroscopy and theoretical calculations of P1-P4 indicate that P1 shows enhanced green fluorescence (λem = 560 nm) by inhibiting its twisted intramolecular charge transfer in the presence of Ox-LDL. This feature allows the selection of P1 as a sensitive probe to directly visualize ferroptosis and Cu2+ -mediated LDL oxidative aggregation via in situ formation of fluorophore-bound Ox-LDL in living cells. The red-emissive probe Pro-P1 (λem = 660 nm) is prepared via borate protection of P1, which can be cleaved into P1 under high expression of HOCl and Ox-LDL condition at the lesion site, resulting in enhanced green emission. The plaque area and size with clear boundaries can be delineated by colorimetric fluorescence imaging and fluorescence lifetime imaging with precise differentiation.
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Affiliation(s)
- Xu Zhi
- State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yufen Sun
- State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Fangjian Cai
- State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Sisi Wang
- State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Hu Gao
- State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Fan Wu
- State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Lei Zhang
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Zhen Shen
- State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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6
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Chen C, Henderson JN, Ruchkin DA, Kirsh JM, Baranov MS, Bogdanov AM, Mills JH, Boxer SG, Fang C. Structural Characterization of Fluorescent Proteins Using Tunable Femtosecond Stimulated Raman Spectroscopy. Int J Mol Sci 2023; 24:11991. [PMID: 37569365 PMCID: PMC10418586 DOI: 10.3390/ijms241511991] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
The versatile functions of fluorescent proteins (FPs) as fluorescence biomarkers depend on their intrinsic chromophores interacting with the protein environment. Besides X-ray crystallography, vibrational spectroscopy represents a highly valuable tool for characterizing the chromophore structure and revealing the roles of chromophore-environment interactions. In this work, we aim to benchmark the ground-state vibrational signatures of a series of FPs with emission colors spanning from green, yellow, orange, to red, as well as the solvated model chromophores for some of these FPs, using wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) in conjunction with quantum calculations. We systematically analyzed and discussed four factors underlying the vibrational properties of FP chromophores: sidechain structure, conjugation structure, chromophore conformation, and the protein environment. A prominent bond-stretching mode characteristic of the quinoidal resonance structure is found to be conserved in most FPs and model chromophores investigated, which can be used as a vibrational marker to interpret chromophore-environment interactions and structural effects on the electronic properties of the chromophore. The fundamental insights gained for these light-sensing units (e.g., protein active sites) substantiate the unique and powerful capability of wavelength-tunable FSRS in delineating FP chromophore properties with high sensitivity and resolution in solution and protein matrices. The comprehensive characterization for various FPs across a colorful palette could also serve as a solid foundation for future spectroscopic studies and the rational engineering of FPs with diverse and improved functions.
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Affiliation(s)
- Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331, USA;
| | - J. Nathan Henderson
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; (J.N.H.); (J.H.M.)
| | - Dmitry A. Ruchkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; (D.A.R.); (M.S.B.); (A.M.B.)
| | - Jacob M. Kirsh
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; (J.M.K.); (S.G.B.)
| | - Mikhail S. Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; (D.A.R.); (M.S.B.); (A.M.B.)
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; (D.A.R.); (M.S.B.); (A.M.B.)
| | - Jeremy H. Mills
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; (J.N.H.); (J.H.M.)
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; (J.M.K.); (S.G.B.)
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331, USA;
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7
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Zhu YH, Liu XX, Fang Q, Liu XY, Fang WH, Cui G. Multiple Photoisomerization Pathways of the Green Fluorescent Protein Chromophore in a Reversibly Photoswitchable Fluorescent Protein: Insights from Quantum Mechanics/Molecular Mechanics Simulations. J Phys Chem Lett 2023; 14:2588-2598. [PMID: 36881005 DOI: 10.1021/acs.jpclett.3c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Herein, we have employed a combined CASPT2//CASSCF approach within the quantum mechanics/molecular mechanics (QM/MM) framework to explore the early time photoisomerization of rsEGFP2 starting from its two OFF trans states, i.e., Trans1 and Trans2. The results show similar vertical excitation energies to the S1 state in their Franck-Condon regions. Considering the clockwise and counterclockwise rotations of the C11-C9 bond, four pairs of the S1 excited-state minima and low-lying S1/S0 conical intersections were optimized, based on which we determined four S1 photoisomerization paths that are essentially barrierless to the relevant S1/S0 conical intersections leading to efficient excited-state deactivation to the S0 state. Most importantly, our work first identified multiple photoisomerization and excited-state decay paths, which must be seriously considered in the future. This work not only sheds significant light on the primary trans-cis photoisomerization of rsEGFP2 but also aids in the understanding of the microscopic mechanism of GFP-like RSFPs and the design of novel GFP-like fluorescent proteins.
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Affiliation(s)
- Yun-Hua Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xin-Xin Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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8
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Zhang J, Li H, Lin B, Luo X, Yin P, Yi T, Xue B, Zhang XL, Zhu H, Nie Z. Development of Near-Infrared Nucleic Acid Mimics of Fluorescent Proteins for In Vivo Imaging of Viral RNA with Turn-On Fluorescence. J Am Chem Soc 2021; 143:19317-19329. [PMID: 34762804 DOI: 10.1021/jacs.1c04577] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
GFP-like fluorescent proteins and their molecular mimics have revolutionized bioimaging research, but their emissions are largely limited in the visible to far-red region, hampering the in vivo applications in intact animals. Herein, we structurally modulate GFP-like chromophores using a donor-acceptor-acceptor (D-A-A') molecular configuration to discover a set of novel fluorogenic derivatives with infrared-shifted spectra. These chromophores can be fluorescently elicited by their specific interaction with G-quadruplex (G4), a unique noncanonical nucleic acid secondary structure, via inhibition of the chromophores' twisted-intramolecular charge transfer. This feature allows us to create, for the first time, FP mimics with tunable emission in the near-infrared (NIR) region (Emmax = 664-705 nm), namely, infrared G-quadruplex mimics of FPs (igMFP). Compared with their FP counterparts, igMFPs exhibit remarkably higher quantum yields, larger Stokes shift, and better photostability. In a proof-of-concept application using pathogen-related G4s as the target, we exploited igMFPs to directly visualize native hepatitis C virus (HCV) RNA genome in living cells via their in situ formation by the chromophore-bound viral G4 structure in the HCV core gene. Furthermore, igMFPs are capable of high contrast HCV RNA imaging in living mice bearing a HCV RNA-presenting mini-organ, providing the first application of FP mimics in whole-animal imaging.
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Affiliation(s)
- Jiaheng Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Huiyi Li
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, People's Republic of China
| | - Bin Lin
- Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Peng Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Ting Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Binbin Xue
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, People's Republic of China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, School of Medicine, Wuhan University, Wuhan 430071, Hubei, People's Republic of China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, People's Republic of China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
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9
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Drobizhev M, Molina RS, Callis PR, Scott JN, Lambert GG, Salih A, Shaner NC, Hughes TE. Local Electric Field Controls Fluorescence Quantum Yield of Red and Far-Red Fluorescent Proteins. Front Mol Biosci 2021; 8:633217. [PMID: 33763453 PMCID: PMC7983054 DOI: 10.3389/fmolb.2021.633217] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
Genetically encoded probes with red-shifted absorption and fluorescence are highly desirable for imaging applications because they can report from deeper tissue layers with lower background and because they provide additional colors for multicolor imaging. Unfortunately, red and especially far-red fluorescent proteins have very low quantum yields, which undermines their other advantages. Elucidating the mechanism of nonradiative relaxation in red fluorescent proteins (RFPs) could help developing ones with higher quantum yields. Here we consider two possible mechanisms of fast nonradiative relaxation of electronic excitation in RFPs. The first, known as the energy gap law, predicts a steep exponential drop of fluorescence quantum yield with a systematic red shift of fluorescence frequency. In this case the relaxation of excitation occurs in the chromophore without any significant changes of its geometry. The second mechanism is related to a twisted intramolecular charge transfer in the excited state, followed by an ultrafast internal conversion. The chromophore twisting can strongly depend on the local electric field because the field can affect the activation energy. We present a spectroscopic method of evaluating local electric fields experienced by the chromophore in the protein environment. The method is based on linear and two-photon absorption spectroscopy, as well as on quantum-mechanically calculated parameters of the isolated chromophore. Using this method, which is substantiated by our molecular dynamics simulations, we obtain the components of electric field in the chromophore plane for seven different RFPs with the same chromophore structure. We find that in five of these RFPs, the nonradiative relaxation rate increases with the strength of the field along the chromophore axis directed from the center of imidazolinone ring to the center of phenolate ring. Furthermore, this rate depends on the corresponding electrostatic energy change (calculated from the known fields and charge displacements), in quantitative agreement with the Marcus theory of charge transfer. This result supports the dominant role of the twisted intramolecular charge transfer mechanism over the energy gap law for most of the studied RFPs. It provides important guidelines of how to shift the absorption wavelength of an RFP to the red, while keeping its brightness reasonably high.
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Affiliation(s)
- Mikhail Drobizhev
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, United States
| | - Rosana S Molina
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, United States
| | - Patrik R Callis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Gerard G Lambert
- Department of Neurosciences, UC San Diego, San Diego, CA, United States
| | - Anya Salih
- Antares & Fluoresci Research, Dangar Island, NSW, Australia
| | - Nathan C Shaner
- Department of Neurosciences, UC San Diego, San Diego, CA, United States
| | - Thomas E Hughes
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, United States
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10
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Moron V, Marazzi M, Wanko M. Far Red Fluorescent Proteins: Where Is the Limit of the Acylimine Chromophore? J Chem Theory Comput 2019; 15:4228-4240. [PMID: 31146524 DOI: 10.1021/acs.jctc.9b00070] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The search for new near-infrared probes for fluorescence imaging applications is a rapidly growing field of research. Monomeric fluorescent proteins that autocatalyze their chromophore are the most versatile markers for in vivo applications, but the development of bright far-red fluorescent proteins (RFPs) has proven difficult. In this contribution, we search for the theoretical limit of the red shift and how it can be reached without sacrificing the fluorescence quantum yield. Through extensive excited-state pathway calculations, molecular dynamics sampling, and statistical modeling using QM/MM schemes, we provide a new understanding of the chromophore's photophysics including the role of its acylimine extension, which is the main difference from other families of fluorescent proteins. The excited-state dynamics of the mPlum RFP and its mutants provide an ideal basis due to mPlum's flexible binding pocket and extended dynamic Stokes shift. We found a large number of structural species with red-shifted emission that differ in rotamer states and H-bonds between key amino acid residues in the binding pocket. By analyzing their spectral and structural features, we derive guidelines for future rational genetic design strategies.
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Affiliation(s)
- Victor Moron
- Nano-Bio Spectroscopy Group and ETSF, Dpto. Fisica de Materiales , Universidad del País Vasco, CFM CSIC-UPV/EHU-MPC and DIPC , Av. Tolosa 72 , 20018 San Sebastián , Spain
| | - Marco Marazzi
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry, KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering , Universidad de Alcalá, Ctra , Madrid-Barcelona Km. 33,600 , E-28805 Alcalá de Henares, Madrid , Spain
- "Andrés M. del Rı́o" (IQAR) , Universidad de Alcalá , E-28871 Alcalá de Henares, Madrid , Spain
| | - Marius Wanko
- Nano-Bio Spectroscopy Group and ETSF, Dpto. Fisica de Materiales , Universidad del País Vasco, CFM CSIC-UPV/EHU-MPC and DIPC , Av. Tolosa 72 , 20018 San Sebastián , Spain
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11
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Molina RS, Qian Y, Wu J, Shen Y, Campbell RE, Drobizhev M, Hughes TE. Understanding the Fluorescence Change in Red Genetically Encoded Calcium Ion Indicators. Biophys J 2019; 116:1873-1886. [PMID: 31054773 PMCID: PMC6531872 DOI: 10.1016/j.bpj.2019.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/02/2019] [Accepted: 04/02/2019] [Indexed: 12/17/2022] Open
Abstract
For over 20 years, genetically encoded Ca2+ indicators have illuminated dynamic Ca2+ signaling activity in living cells and, more recently, whole organisms. We are just now beginning to understand how they work. Various fluorescence colors of these indicators have been developed, including red. Red ones are promising because longer wavelengths of light scatter less in tissue, making it possible to image deeper. They are engineered from a red fluorescent protein that is circularly permuted and fused to a Ca2+-sensing domain. When Ca2+ binds, a conformational change in the sensing domain causes a change in fluorescence. Three factors can contribute to this fluorescence change: 1) a shift in the protonation equilibrium of the chromophore, 2) a change in fluorescence quantum yield, and 3) a change in the extinction coefficient or the two-photon cross section, depending on if it is excited with one or two photons. Here, we conduct a systematic study of the photophysical properties of a range of red Ca2+ indicators to determine which factors are the most important. In total, we analyzed nine indicators, including jRGECO1a, K-GECO1, jRCaMP1a, R-GECO1, R-GECO1.2, CAR-GECO1, O-GECO1, REX-GECO1, and a new variant termed jREX-GECO1. We find that these could be separated into three classes that each rely on a particular set of factors. Furthermore, in some cases, the magnitude of the change in fluorescence was larger with two-photon excitation compared to one-photon because of a change in the two-photon cross section, by up to a factor of two.
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Affiliation(s)
- Rosana S Molina
- Department of Cell Biology & Neuroscience, Montana State University, Bozeman, Montana
| | - Yong Qian
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jiahui Wu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada; Department of Pharmacology, Weill Cornell Medicine, New York, New York
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada; Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Mikhail Drobizhev
- Department of Cell Biology & Neuroscience, Montana State University, Bozeman, Montana
| | - Thomas E Hughes
- Department of Cell Biology & Neuroscience, Montana State University, Bozeman, Montana.
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12
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Li H, Han J, Zhao H, Liu X, Luo Y, Shi Y, Liu C, Jin M, Ding D. Lighting Up the Invisible Twisted Intramolecular Charge Transfer State by High Pressure. J Phys Chem Lett 2019; 10:748-753. [PMID: 30704239 DOI: 10.1021/acs.jpclett.9b00026] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The twisted intramolecular charge transfer (TICT) state plays an important role in determining the performance of optoelectronic devices. However, for some nonfluorescent TICT molecules, the "invisible" TICT state could only be visualized by modifying the molecular structure. Here, we introduce a new facile pressure-induced approach to light up the TICT state through the use of a pressure-related liquid-solid phase transition of the surrounding solvent. Combining ultrafast spectroscopy and quantum chemical calculations, it reveals that the "invisible" TICT state can emit fluorescence when the rotation of a donor group is restricted by the frozen acetonitrile solution. Furthermore, the TICT process can even be effectively regulated by the external pressure. Our study offers a unique strategy to achieve dual fluorescence behavior in charge transfer molecules and is of significance for optoelectronic and biomedical applications.
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Affiliation(s)
- Hui Li
- Institute of Atomic and Molecular Physics , Jilin University , Changchun 130012 , China
| | - Jianhui Han
- Institute of Atomic and Molecular Physics , Jilin University , Changchun 130012 , China
| | - Huifang Zhao
- Institute of Atomic and Molecular Physics , Jilin University , Changchun 130012 , China
| | - Xiaochun Liu
- Institute of Atomic and Molecular Physics , Jilin University , Changchun 130012 , China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Ying Shi
- Institute of Atomic and Molecular Physics , Jilin University , Changchun 130012 , China
| | - Cailong Liu
- Institute of Atomic and Molecular Physics , Jilin University , Changchun 130012 , China
| | - Mingxing Jin
- Institute of Atomic and Molecular Physics , Jilin University , Changchun 130012 , China
| | - Dajun Ding
- Institute of Atomic and Molecular Physics , Jilin University , Changchun 130012 , China
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13
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Chen YH, Sung R, Sung K. Insights into Excited State Intramolecular Proton Transfer: An Alternative Model for Excited State Proton Transfer of Green Fluorescence Protein. J Phys Chem A 2018; 122:5931-5944. [DOI: 10.1021/acs.jpca.8b01799] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yi-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Robert Sung
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Kuangsen Sung
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
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14
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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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15
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Khrenova MG, Polyakov IV, Grigorenko BL, Krylov AI, Nemukhin AV. Improving the Design of the Triple-Decker Motif in Red Fluorescent Proteins. J Phys Chem B 2017; 121:10602-10609. [PMID: 29090574 DOI: 10.1021/acs.jpcb.7b07517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We characterize computationally a red fluorescent protein (RFP) with the chromophore (Chro) sandwiched between two aromatic tyrosine rings in a triple-decker motif. According to the original proposal [ J. Phys. Chem. Lett. 2013 , 4 , 1743 ], such a tyrosine-chromophore-tyrosine π-stacked construct can be accommodated in the green fluorescent protein (GFP). A recent study [ ACS Chem. Biol. 2016 , 11 , 508 ] attempted to realize the triple-decker motif and obtained an RFP variant called mRojoA-VYGV with two tyrosine residues surrounding the chromophore. The crystal structure showed that only a tyrosine-chromophore pair was involved in π-stacking, whereas the second tyrosine was oriented perpendicularly, edge-to-face with respect to the chromophore. We propose a more promising variant of this RFP with a perfect triple-decker unit achieved by introducing additional mutations in mRojoA-VYGV. The structures and optical properties of model proteins based on the structures of mCherry and mRojoA are characterized computationally by QM(DFT)/MM. The electronic transitions in the protein-bound chromophores are computed by high-level quantum chemical methods. According to our calculations, the triple-decker chromophore unit in the new RFP variant is stable within the protein and its optical bands are red-shifted with respect to the parent mCherry and mRojoA species.
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Affiliation(s)
- Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University , Moscow, 119991, Russia
| | - Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University , Moscow, 119991, Russia
| | - 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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16
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Feng G, Luo C, Yi H, Yuan L, Lin B, Luo X, Hu X, Wang H, Lei C, Nie Z, Yao S. DNA mimics of red fluorescent proteins (RFP) based on G-quadruplex-confined synthetic RFP chromophores. Nucleic Acids Res 2017; 45:10380-10392. [PMID: 28981852 PMCID: PMC5737560 DOI: 10.1093/nar/gkx803] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/26/2017] [Accepted: 08/31/2017] [Indexed: 12/29/2022] Open
Abstract
Red fluorescent proteins (RFPs) have emerged as valuable biological markers for biomolecule imaging in living systems. Developing artificial fluorogenic systems that mimic RFPs remains an unmet challenge. Here, we describe the design and synthesis of six new chromophores analogous to the chromophores in RFPs. We demonstrate, for the first time, that encapsulating RFP chromophore analogues in canonical DNA G-quadruplexes (G4) can activate bright fluorescence spanning red and far-red spectral regions (Em = 583-668 nm) that nearly match the entire RFP palette. Theoretical calculations and molecular dynamics simulations reveal that DNA G4 greatly restricts radiationless deactivation of chromophores induced by a twisted intramolecular charge transfer (TICT). These DNA mimics of RFP exhibit attractive photophysical properties comparable or superior to natural RFPs, including high quantum yield, large Stokes shifts, excellent anti-photobleaching properties, and two-photon fluorescence. Moreover, these RFP chromophore analogues are a novel and distinctive type of topology-selective G4 probe specific to parallel G4 conformation. The DNA mimics of RFP have been further exploited for imaging of target proteins. Using cancer-specific cell membrane biomarkers as targets, long-term real-time monitoring in single live cell and two-photon fluorescence imaging in tissue sections have been achieved without the need for genetic coding.
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Affiliation(s)
- Guangfu Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Chao Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Haibo Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Bin Lin
- Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiaoxiao Hu
- Molecular Science and Biomedicine laboratory, Hunan University, Changsha 410082, PR China
| | - Honghui Wang
- College of Biology, Hunan University, Changsha 410082, PR China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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17
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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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18
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Chatterjee T, Mandal M, Das A, Bhattacharyya K, Datta A, Mandal PK. Dual Fluorescence in GFP Chromophore Analogues: Chemical Modulation of Charge Transfer and Proton Transfer Bands. J Phys Chem B 2016; 120:3503-10. [PMID: 26998908 DOI: 10.1021/acs.jpcb.6b01993] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Tanmay Chatterjee
- Department
of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West-Bengal 741246, India
| | - Mrinal Mandal
- Department
of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West-Bengal 741246, India
| | - Ananya Das
- Department
of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West-Bengal 741246, India
| | - Kalishankar Bhattacharyya
- Department
of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Ayan Datta
- Department
of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Prasun K. Mandal
- Department
of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West-Bengal 741246, India
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19
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Xu J, Chen J, Dong S, Fu A, Li H, Chu T. Excited-state hydrogen bond strengthening of coumarin 153 in ethanol solvent: a TDDFT study. J PHYS ORG CHEM 2016. [DOI: 10.1002/poc.3537] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jinmei Xu
- College of Information Science and Engineering; Ocean University of China; Qingdao 266100 China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 China
| | - Junsheng Chen
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 China
| | - Shunle Dong
- College of Information Science and Engineering; Ocean University of China; Qingdao 266100 China
| | - Aiping Fu
- Institute for Computational Sciences and Engineering, Laboratory of New Fiber Materials and Modern Textile, The Growing Base for State Key Laboratory and College of Physics, College of Chemistry; Qingdao University; Qingdao 266071 People's Republic of China
| | - Hongliang Li
- Institute for Computational Sciences and Engineering, Laboratory of New Fiber Materials and Modern Textile, The Growing Base for State Key Laboratory and College of Physics, College of Chemistry; Qingdao University; Qingdao 266071 People's Republic of China
| | - Tianshu Chu
- Institute for Computational Sciences and Engineering, Laboratory of New Fiber Materials and Modern Textile, The Growing Base for State Key Laboratory and College of Physics, College of Chemistry; Qingdao University; Qingdao 266071 People's Republic of China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 China
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20
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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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21
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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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22
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Chatterjee T, Mandal M, Gude V, Bag PP, Mandal PK. Strong electron donation induced differential nonradiative decay pathways for para and meta GFP chromophore analogues. Phys Chem Chem Phys 2015; 17:20515-21. [PMID: 26176350 DOI: 10.1039/c5cp03086b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Z-E Isomerisation because of rotation around the exocyclic double bond (known as the τ-twist) and not any other internal conversion has been reported to be the major nonradiative decay channel for non-hydroxylic unconstrained para and meta GFP chromophore analogues. The equation Φf + 2ΦZE = 1 has been shown to hold well for both para and meta GFP chromophore analogues. If the above equation holds true, then upon reducing the extent of Z-E isomerisation (ΦZE), the fluorescence quantum yield (Φf) should increase. To probe the above proposition two sets of non-hydroxylic unconstrained para and meta GFP chromophore analogues were synthesized. Quite interestingly by introducing the strongly electron donating -NEt2 group to the benzenic moiety these para and meta GFP chromophore analogues were shown to exhibit differential optical behaviour w.r.t. the extent of the solvatochromic shift, Φf, ΦZE, and τf. For the first time it has been shown that the well accepted equation Φf + 2ΦZE = 1 does not hold at all for these non-hydroxylic unconstrained meta analogues. Although ΦZE has been shown to be <10%, Φf is much lower than the expected near unity value for these meta analogues. After detailed investigation into the nonradiative excited state decay channel, contrary to literature reports, energy gap law governed internal conversion and not Z-E isomerisation was shown to be the major nonradiative decay channel for these meta analogues. Two models are put forward to understand the differential optical behaviour of these para and meta GFP chromophore analogues. Support from X-ray crystal structures, NMR experiments, and computational calculations has also been provided.
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Affiliation(s)
- Tanmay Chatterjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohanpur, Kolkata, West-Bengal 741246, India.
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23
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Chen Y, Wang Y, Yuan Y, Jiao Y, Pu X, Lu Z. Deactivation mechanism of a novel AIE-active naphthalimide derivative in more polar solutions. Phys Chem Chem Phys 2015; 17:1309-16. [DOI: 10.1039/c4cp04213a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We used experimental and computational methods to unveil the deactivation mechanism of a new AIE-active naphthalimide derivative in polar solutions.
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Affiliation(s)
- Yunqing Chen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yi Wang
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yuan Yuan
- College of Management
- Southwest University for Nationalities
- Chengdu
- People's Republic of China
| | - Yan Jiao
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Xuemei Pu
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Zhiyun Lu
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
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24
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SAKAGUCHI M, MOCHIZUKI Y, WATANABE C, FUKUZAWA K. Effects of Water Molecules and Configurations of Neighboring Amino Acid Residues Surrounding DsRed Chromophore on Its Excitation Energy. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2015. [DOI: 10.2477/jccj.2015-0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Masataka SAKAGUCHI
- Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Yuji MOCHIZUKI
- Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Chiduru WATANABE
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Kaori FUKUZAWA
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- School of Dentistry at Matsudo, Nihon University, 2-870-1 Sakaemachi-Nishi, Matsudo 271-8571, Japan
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25
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Zhao L, Zhou PW, Li B, Gao AH, Han KL. Non-adiabatic dynamics of isolated green fluorescent protein chromophore anion. J Chem Phys 2014; 141:235101. [DOI: 10.1063/1.4903241] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Li Zhao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of the Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Pan-Wang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Bin Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Ai-Hua Gao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of the Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Ke-Li Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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26
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Tanha M, Chakraborty SK, Gabris B, Waggoner AS, Salama G, Yaron D. Computational and experimental characterization of a fluorescent dye for detection of potassium ion concentration. J Phys Chem A 2014; 118:9837-43. [PMID: 25216181 PMCID: PMC4207556 DOI: 10.1021/jp507552q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The fluorescence of the SKC-513 ((E)-N-(9-(4-(1,4,7,10,13-pentaoxa-16-azacyclooctadecan-16-yl)phenyl)-6-(butyl(3-sulfopropyl)amino)-3H-xanthen-3-ylidene)-N-(3-sulfopropyl)butan-1-aminium)
dye is shown experimentally to have high sensitivity to binding of
the K+ ion. Computations are used to explore the potential
origins of this sensitivity and to make some suggestions regarding
structural improvements. In the absence of K+, excitation
is to two nearly degenerate states, a neutral (N) excited state with
a high oscillator strength, and a charge-transfer (CT) state with
a lower oscillator strength. Binding of K+ destabilizes
the CT state, raising its energy far above the N state. The increase
in fluorescence quantum yield upon binding of K+ is attributed
to the increased energy of the CT state suppressing a nonradiative
pathway mediated by the CT state. The near degeneracy of the N and
CT excited states can be understood by considering SKC-513 as a reduced
symmetry version of a parent molecule with 3-fold symmetry. Computations
show that acceptor–donor substituents can be used to alter
the relative energies of the N and CT state, whereas a methylene spacer
between the heterocycle and phenylene groups can be used to increase
the coupling between these states. These modifications provide synthetic
handles with which to optimize the dye for K+ detection.
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Affiliation(s)
- Matteus Tanha
- Chemistry Departmentand ‡Molecular Biosensor and Imaging Center, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
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27
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Zhang Q, Chen X, Cui G, Fang WH, Thiel W. Concerted Asynchronous Hula-Twist Photoisomerization in the S65T/H148D Mutant of Green Fluorescent Protein. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405303] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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28
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Zhang Q, Chen X, Cui G, Fang WH, Thiel W. Concerted Asynchronous Hula-Twist Photoisomerization in the S65T/H148D Mutant of Green Fluorescent Protein. Angew Chem Int Ed Engl 2014; 53:8649-53. [DOI: 10.1002/anie.201405303] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Indexed: 01/24/2023]
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29
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Mironov VA, Khrenova MG, Grigorenko BL, Savitsky AP, Nemukhin AV. Thermal isomerization of the chromoprotein asFP595 and its kindling mutant A143G: QM/MM molecular dynamics simulations. J Phys Chem B 2013; 117:13507-14. [PMID: 24079704 DOI: 10.1021/jp407406k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chromoprotein asFP595 and its A143G variant called kindling fluorescent protein (KFP) are among the chronologically first species for which trans-cis chromophore isomerization has been proposed as a driving force of photoswitching. In spite of long-lasting efforts to characterize the route between protein conformations referring to the trans and cis forms of the chromophore, the molecular mechanism of this transformation is still under debate. We report the results of computational studies of the trans-cis isomerization of the anionic and neutral chromophore inside the protein matrices in the ground electronic state for both variants, asFP595 and KFP. Corresponding free energy profiles (potentials of mean force) were evaluated by using molecular dynamics simulations with the quantum mechanical-molecular mechanical (QM/MM) forces. The computed free energy barrier for the cis-trans ground state (thermal) isomerization reaction is about 2 kcal/mol higher in KFP than that in asFP595. These results provide interpretation of experimental studies on thermal relaxation from the light-induced activation of fluorescence of these proteins and correctly show that the A143G mutation in asFP595 noticeably increases the lifetime of the fluorescence species.
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Affiliation(s)
- Vladimir A Mironov
- Department of Chemistry, M.V. Lomonosov Moscow State University , Leninskie Gory, 1/3, Moscow, 119991, Russian Federation
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30
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Ai Y, Tian G, Luo Y. Role of non-Condon vibronic coupling and conformation change on two-photon absorption spectra of green fluorescent protein. Mol Phys 2013. [DOI: 10.1080/00268976.2013.771800] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Yuejie Ai
- a Theoretical Chemistry and Biology, School of Biotechnology , Royal Institute of Technology , Stockholm , Sweden
| | - Guangjun Tian
- a Theoretical Chemistry and Biology, School of Biotechnology , Royal Institute of Technology , Stockholm , Sweden
| | - Yi Luo
- a Theoretical Chemistry and Biology, School of Biotechnology , Royal Institute of Technology , Stockholm , Sweden
- b Heifei National Laboratory for Physical Science at the Microscale , University of Science and Technology of China , Hefei , P.R. China
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31
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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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32
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Addison K, Heisler IA, Conyard J, Dixon T, Bulman Page PC, Meech SR. Ultrafast excited state dynamics of the green fluorescent protein chromophore and its kindling fluorescent protein analogue. Faraday Discuss 2013; 163:277-96; discussion 393-432. [DOI: 10.1039/c3fd00019b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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33
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Olsen S, McKenzie RH. A two-state model of twisted intramolecular charge-transfer in monomethine dyes. J Chem Phys 2012; 137:164319. [DOI: 10.1063/1.4762561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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34
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Battad JM, Traore DAK, Byres E, Rossjohn J, Devenish RJ, Olsen S, Wilce MCJ, Prescott M. A green fluorescent protein containing a QFG tri-peptide chromophore: optical properties and X-ray crystal structure. PLoS One 2012; 7:e47331. [PMID: 23071789 PMCID: PMC3468514 DOI: 10.1371/journal.pone.0047331] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/12/2012] [Indexed: 01/07/2023] Open
Abstract
Rtms5 is an deep blue weakly fluorescent GFP-like protein ([Formula: see text], 592 nm; [Formula: see text], 630nm; Φ(F), 0.004) that contains a (66)Gln-Tyr-Gly chromophore tripeptide sequence. We investigated the optical properties and structure of two variants, Rtms5(Y67F) and Rtms5(Y67F/H146S) in which the tyrosine at position 67 was substituted by a phenylalanine. Compared to the parent proteins the optical spectra for these new variants were significantly blue-shifted. Rtms5(Y67F) spectra were characterised by two absorbing species ([Formula: see text], 440 nm and 513 nm) and green fluorescence emission ([Formula: see text], 440 nm; [Formula: see text], 508 nm; Φ(F), 0.11), whilst Rtms5(Y67F/H146S) spectra were characterised by a single absorbing species ([Formula: see text], 440 nm) and a relatively high fluorescence quantum yield (Φ(F,) 0.75; [Formula: see text], 440 nm; [Formula: see text], 508 nm). The fluorescence emissions of each variant were remarkably stable over a wide range of pH (3-11). These are the first GFP-like proteins with green emissions (500-520 nm) that do not have a tyrosine at position 67. The X-ray crystal structure of each protein was determined to 2.2 Å resolution and showed that the benzylidine ring of the chromophore, similar to the 4-hydroxybenzylidine ring of the Rtms5 parent, is non-coplanar and in the trans conformation. The results of chemical quantum calculations together with the structural data suggested that the 513 nm absorbing species in Rtms5(Y67F) results from an unusual form of the chromophore protonated at the acylimine oxygen. These are the first X-ray crystal structures for fluorescent proteins with a functional chromophore containing a phenylalanine at position 67.
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Affiliation(s)
- Jion M. Battad
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Daouda A. K. Traore
- The Structural Biology Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Emma Byres
- The Structural Biology Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- The Structural Biology Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Rodney J. Devenish
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Seth Olsen
- School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthew C. J. Wilce
- The Structural Biology Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
- * E-mail: (MP); (MW)
| | - Mark Prescott
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
- * E-mail: (MP); (MW)
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35
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Drobizhev M, Hughes TE, Stepanenko Y, Wnuk P, O'Donnell K, Scott JN, Callis PR, Mikhaylov A, Dokken L, Rebane A. Primary role of the chromophore bond length alternation in reversible photoconversion of red fluorescence proteins. Sci Rep 2012; 2:688. [PMID: 23008753 PMCID: PMC3449290 DOI: 10.1038/srep00688] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 09/05/2012] [Indexed: 11/08/2022] Open
Abstract
Rapid photobleaching of fluorescent proteins can limit their use in imaging applications. The underlying kinetics is multi-exponential and strongly depends on the local chromophore environment. The first, reversible, step may be attributed to a rotation around one of the two exocyclic C-C bonds bridging phenol and imidazolinone groups in the chromophore. However it is not clear how the protein environment controls this motion - either by steric hindrances or by modulating the electronic structure of the chromophore through electrostatic interactions. Here we study the first step of the photobleaching kinetics in 13 red fluorescent proteins (RFPs) with different chromophore environment and show that the associated rate strongly correlates with the bond length alternation (BLA) of the two bridge bonds. The sign of the BLA appears to determine which rotation is activated. Our results present experimental evidence for the dominance of electronic effects in the conformational dynamics of the RFP chromophore.
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Affiliation(s)
- Mikhail Drobizhev
- Department of Physics, Montana State University, Bozeman, MT 59717, USA.
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36
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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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37
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Affiliation(s)
- Fedor V. Subach
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Vladislav V. Verkhusha
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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38
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Absorption and fluorescence spectra of the neutral and anionic green fluorescent protein chromophore: Franck–Condon simulation. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.05.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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39
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Gao F, Ye X, Li H, Zhong X, Wang Q. Evidence for Two-Photon Absorption-Induced ESIPT of Chromophores Containing Hydroxyl and Imino Groups. Chemphyschem 2012; 13:1313-24. [DOI: 10.1002/cphc.201100885] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Indexed: 11/09/2022]
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40
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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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41
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Cui G, Lan Z, Thiel W. Intramolecular hydrogen bonding plays a crucial role in the photophysics and photochemistry of the GFP chromophore. J Am Chem Soc 2012; 134:1662-72. [PMID: 22175658 DOI: 10.1021/ja208496s] [Citation(s) in RCA: 177] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In commonly studied GFP chromophore analogues such as 4-(4-hydroxybenzylidene)-1,2-dimethyl-1H-imidazol-5(4H)-one (PHBDI), the dominant photoinduced processes are cis-trans isomerization and subsequent S(1) → S(0) decay via a conical intersection characterized by a highly twisted double bond. The recently synthesized 2-hydroxy-substituted isomer (OHBDI) shows an entirely different photochemical behavior experimentally, since it mainly undergoes ultrafast intramolecular excited-state proton transfer, followed by S(1) → S(0) decay and ground-state reverse hydrogen transfer. We have chosen 4-(2-hydroxybenzylidene)-1H-imidazol-5(4H)-one (OHBI) to model the gas-phase photodynamics of such 2-hydroxy-substituted chromophores. We first use various electronic structure methods (DFT, TDDFT, CC2, DFT/MRCI, OM2/MRCI) to explore the S(0) and S(1) potential energy surfaces of OHBI and to locate the relevant minima, transition state, and minimum-energy conical intersection. These static calculations suggest the following decay mechanism: upon photoexcitation to the S(1) state, an ultrafast adiabatic charge-transfer induced excited-state intramolecular proton transfer (ESIPT) occurs that leads to the S(1) minimum-energy structure. Nearby, there is a S(1)/S(0) minimum-energy conical intersection that allows for an efficient nonadiabatic S(1) → S(0) internal conversion, which is followed by a fast ground-state reverse hydrogen transfer (GSHT). This mechanism is verified by semiempirical OM2/MRCI surface-hopping dynamics simulations, in which the successive ESIPT-GSTH processes are observed, but without cis-trans isomerization (which is a minor path experimentally with less than 5% yield). These gas-phase simulations of OHBI give an estimated first-order decay time of 476 fs for the S(1) state, which is larger but of the same order as the experimental values measured for OHBDI in solution: 270 fs in CH(3)CN and 230 fs in CH(2)Cl(2). The differences between the photoinduced processes of the 2- and 4-hydroxy-substituted chromophores are attributed to the presence or absence of intramolecular hydrogen bonding between the two rings.
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Affiliation(s)
- Ganglong Cui
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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42
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Choudhary A, Kamer KJ, Raines RT. A conserved interaction with the chromophore of fluorescent proteins. Protein Sci 2011; 21:171-7. [PMID: 22057893 DOI: 10.1002/pro.762] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 10/25/2011] [Accepted: 10/28/2011] [Indexed: 01/29/2023]
Abstract
The chromophore of fluorescent proteins, including the green fluorescent protein (GFP), contains a highly conjugated imidazolidinone ring. In many fluorescent proteins, the carbonyl group of the imidazolidinone ring engages in a hydrogen bond with the side chain of an arginine residue. Prior studies have indicated that such an electrophilic carbonyl group in a protein often accepts electron density from a main-chain oxygen. A survey of high-resolution structures of fluorescent proteins indicates that electron lone pairs of a main-chain oxygen-Thr62 in GFP-donate electron density into an antibonding orbital of the imidazolidinone carbonyl group. This n→π* electron delocalization prevents structural distortion during chromophore excitation that could otherwise lead to fluorescence quenching. In addition, this interaction is present in on-pathway intermediates leading to the chromophore, and thus could direct its biogenesis. Accordingly, this n→π* interaction merits inclusion in computational and photophysical analyses of the chromophore, and in speculations about the molecular evolution of fluorescent proteins.
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Affiliation(s)
- Amit Choudhary
- Graduate Program in Biophysics, University of Wisconsin-Madison, Madison, WI 53706, USA
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43
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Hasegawa JY, Fujimoto KJ, Nakatsuji H. Color tuning in photofunctional proteins. Chemphyschem 2011; 12:3106-15. [PMID: 21990164 DOI: 10.1002/cphc.201100452] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/24/2011] [Indexed: 11/11/2022]
Abstract
Depending on protein environment, a single photofunctional chromophore shows a wide variation of photoabsorption/emission energies. This photobiological phenomenon, known as color tuning, is observed in human visual cone pigments, firefly luciferase, and red fluorescent protein. We investigate the origin of color tuning by quantum chemical calculations on the excited states: symmetry-adapted cluster-configuration interaction (SAC-CI) method for excited states and a combined quantum mechanical (QM)/molecular mechanical (MM) method for protein environments. This Minireview summarizes our theoretical studies on the above three systems and explains a common feature of their color-tuning mechanisms. It also discuss the possibility of artificial color tuning toward a rational design of photoabsorption/emission properties.
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Affiliation(s)
- Jun-ya Hasegawa
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan.
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44
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Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein. Amino Acids 2011; 43:557-65. [DOI: 10.1007/s00726-011-1150-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 11/04/2011] [Indexed: 10/15/2022]
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45
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Zhang MY, Wang JY, Lin CS, Cheng WD. First-principles study of one- and two-photon absorption of the H-bonding complexes from monomeric red fluorescent proteins with large Stokes shifts. J Phys Chem B 2011; 115:10750-7. [PMID: 21827203 DOI: 10.1021/jp203977m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
LSSmKate1 and LSSmKate2 are monomeric red fluorescent proteins (RFPs) with large Stokes shifts (LSS). The hydrogen-bonding (H-bonding) network within LSSmKate1 or LSSmKate2, which is composed of a chromophore and some surrounding amino acid residues, supports their special spectral properties. In this work, we propose H-bonding complex models to simulate the H-bonding network of LSSmKate1 and LSSmKate2 and employ the time-dependent density functional theory combining with the sum-overstates method to calculate their one- and two-photon absorption characters. We discuss the influence of the hydrogen bond on the one- and two-photon absorption properties of these H-bonding complexes through intermolecular hyperconjugation of the hydrogen-bond form.
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Affiliation(s)
- Min-Yi Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
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46
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Wang H, Wang M, Liu E, Xin M, Yang C. DFT/TDDFT study on the excited-state hydrogen bonding dynamics of hydrogen-bonded complex formed by methyl cyanide and methanol. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.12.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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47
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Conyard J, Kondo M, Heisler IA, Jones G, Baldridge A, Tolbert LM, Solntsev KM, Meech SR. Chemically modulating the photophysics of the GFP chromophore. J Phys Chem B 2011; 115:1571-7. [PMID: 21268624 DOI: 10.1021/jp111593x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
There is growing interest in engineering the properties of fluorescent proteins through modifications to the chromophore structure utilizing mutagenesis with either natural or unnatural amino acids. This entails an understanding of the photophysical and photochemical properties of the modified chromophore. In this work, a range of GFP chromophores with different alkyl substituents are synthesized and their electronic spectra, pH dependence, and ultrafast fluorescence decay kinetics are investigated. The weakly electron donating character of the alkyl substituents leads to dramatic red shifts in the electronic spectra of the anions, which are accompanied by increased fluorescence decay times. This high sensitivity of electronic structure to substitution is also characteristic of some fluorescent proteins. The solvent viscosity dependence of the decay kinetics are investigated, and found to be consistent with a bimodal radiationless relaxation coordinate. Some substituents are shown to distort the planar structure of the chromophore, which results in a blue shift in the electronic spectra and a strong enhancement of the radiationless decay. The significance of these data for the rational design of novel fluorescent proteins is discussed.
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Affiliation(s)
- Jamie Conyard
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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48
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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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49
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Chica RA, Moore MM, Allen BD, Mayo SL. Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries. Proc Natl Acad Sci U S A 2010; 107:20257-62. [PMID: 21059931 PMCID: PMC2996648 DOI: 10.1073/pnas.1013910107] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The longer emission wavelengths of red fluorescent proteins (RFPs) make them attractive for whole-animal imaging because cells are more transparent to red light. Although several useful RFPs have been developed using directed evolution, the quest for further red-shifted and improved RFPs continues. Herein, we report a structure-based rational design approach to red-shift the fluorescence emission of RFPs. We applied a combined computational and experimental approach that uses computational protein design as an in silico prescreen to generate focused combinatorial libraries of mCherry mutants. The computational procedure helped us identify residues that could fulfill interactions hypothesized to cause red-shifts without destabilizing the protein fold. These interactions include stabilization of the excited state through H-bonding to the acylimine oxygen atom, destabilization of the ground state by hydrophobic packing around the charged phenolate, and stabilization of the excited state by a π-stacking interaction. Our methodology allowed us to identify three mCherry mutants (mRojoA, mRojoB, and mRouge) that display emission wavelengths > 630 nm, representing red-shifts of 20-26 nm. Moreover, our approach required the experimental screening of a total of ∼5,000 clones, a number several orders of magnitude smaller than those previously used to achieve comparable red-shifts. Additionally, crystal structures of mRojoA and mRouge allowed us to verify fulfillment of the interactions hypothesized to cause red-shifts, supporting their contribution to the observed red-shifts.
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Affiliation(s)
- Roberto A. Chica
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125; and
| | - Matthew M. Moore
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125
| | - Benjamin D. Allen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125
| | - Stephen L. Mayo
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125; and
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125
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50
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Samma AA, Johnson CK, Song S, Alvarez S, Zimmer M. On the origin of fluorescence in bacteriophytochrome infrared fluorescent proteins. J Phys Chem B 2010; 114:15362-9. [PMID: 21047084 DOI: 10.1021/jp107119q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tsien et al. (Science, 2009, 324, 804-807) recently reported the creation of the first infrared fluorescent protein (IFP). It was engineered from bacterial phytochrome by removing the PHY and histidine kinase-related domains, by optimizing the protein to prevent dimerization, and by limiting the biliverdins conformational freedom, especially around its D ring. We have used database analyses and molecular dynamics simulations with freely rotating chromophoric dihedrals in order to model the dihedral freedom available to the biliverdin D ring in the excited state and to show that the tetrapyrrole ligands in phytochromes are flexible and can adopt many conformations; however, their conformational space is limited/defined by the chemospatial characteristics of the protein cavity. Our simulations confirm that the reduced accessibility to conformations geared to an excited state proton transfer may be responsible for the fluorescence in IFP, just as has been suggested by Kennis et al. (Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 9170-9175) for fluorescent bacteriophytochrome from Rhodopseudomonas palustris.
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Affiliation(s)
- Alex A Samma
- Chemistry Department, Connecticut College, New London, CT 06320, USA
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