1
|
Lama B, Sarma M. Ultrafast Hot Exciton Nonadiabatic Excited-State Dynamics in Green Fluorescent Protein Chromophore Analogue. J Phys Chem B 2024. [PMID: 38959128 DOI: 10.1021/acs.jpcb.4c02733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The ultrafast high-energy nonadiabatic excited-state dynamics of the benzylidenedimethylimidazolinone chromophore dimer has been investigated using an electronic structure method coupled with on-the-fly quantitative wave function analysis to gain insight into the photophysics of hot excitons in biological systems. The dynamical simulation provides a rationalization of the behavior of the exciton in a dimer after the photoabsorption of light to higher-energy states. The results suggest that hot exciton localization within the manifold of excited states is caused by the hindrance of torsional rotation due to imidazolinone (I) or phenolate (P) bonds i.e., ΦI- or ΦP-dihedral rotation, in the monomeric units of a dimer. This hindrance arises due to weak π-π stacking interaction in the dimer, resulting in an energetically uphill excited-state barrier for ΦI- and ΦP-twisted rotation, impeding the isomerization process in the chromophore. Thus, this study highlights the potential impact of the weak π-π interaction in regulating the photodynamics of the green fluorescent protein chromophore derivatives.
Collapse
Affiliation(s)
- 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
| |
Collapse
|
2
|
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).
Collapse
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
| |
Collapse
|
3
|
Choudhury A, Santra S, Ghosh D. Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment. J Chem Theory Comput 2024; 20:4951-4964. [PMID: 38864715 DOI: 10.1021/acs.jctc.4c00027] [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: 06/13/2024]
Abstract
Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.
Collapse
Affiliation(s)
- Arpan Choudhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Kim SS, Rhee YM. Potential energy interpolation with target-customized weighting coordinates: application to excited-state dynamics of photoactive yellow protein chromophore in water. Phys Chem Chem Phys 2024; 26:9021-9036. [PMID: 38440829 DOI: 10.1039/d3cp05643k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Interpolation of potential energy surfaces (PESs) can provide a practical route to performing molecular dynamics simulations with a reliability matching a high-level quantum chemical calculation. An obstacle to its widespread use is perhaps the lack of general and optimal interpolation settings that can be applied in a black-box manner for any given molecular system. How to set up the weights for interpolation is one such task, and we still need to diversify the approaches in order to treat various systems. Here, we develop a new interpolation weighting scheme, which allows us to choose the weighting coordinates in a system-specific manner, by amplifying the contribution from specific internal coordinates. The new weighting scheme with an appropriate selection of coordinates is proved to be effective in reducing the interpolation error along the reaction pathway. As a demonstration, we consider the photoactive yellow protein chromophore system, as it constitutes itself as an interesting target that bears long-standing questions related to excited-state dynamics inside protein environments. We build its two-state diabatic interpolated PES with the new weighting scheme. We indeed see the utility of our scheme by conducting nonadiabatic molecular dynamics simulations with the required semi-global PES based on a limited number of data points.
Collapse
Affiliation(s)
- Seung Soo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Krueger TD, Henderson JN, Breen IL, Zhu L, Wachter RM, Mills JH, Fang C. Capturing excited-state structural snapshots of evolutionary green-to-red photochromic fluorescent proteins. Front Chem 2023; 11:1328081. [PMID: 38144887 PMCID: PMC10748491 DOI: 10.3389/fchem.2023.1328081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/24/2023] [Indexed: 12/26/2023] Open
Abstract
Photochromic fluorescent proteins (FPs) have proved to be indispensable luminous probes for sophisticated and advanced bioimaging techniques. Among them, an interplay between photoswitching and photoconversion has only been observed in a limited subset of Kaede-like FPs that show potential for discovering the key mechanistic steps during green-to-red photoconversion. Various spectroscopic techniques including femtosecond stimulated Raman spectroscopy (FSRS), X-ray crystallography, and femtosecond transient absorption were employed on a set of five related FPs with varying photoconversion and photoswitching efficiencies. A 3-methyl-histidine chromophore derivative, incorporated through amber suppression using orthogonal aminoacyl tRNA synthetase/tRNA pairs, displays more dynamic photoswitching but greatly reduced photoconversion versus the least-evolved ancestor (LEA). Excitation-dependent measurements of the green anionic chromophore reveal that the varying photoswitching efficiencies arise from both the initial transient dynamics of the bright cis state and the final trans-like photoswitched off state, with an exocyclic bridge H-rocking motion playing an active role during the excited-state energy dissipation. This investigation establishes a close-knit feedback loop between spectroscopic characterization and protein engineering, which may be especially beneficial to develop more versatile FPs with targeted mutations and enhanced functionalities, such as photoconvertible FPs that also feature photoswitching properties.
Collapse
Affiliation(s)
- Taylor D. Krueger
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - J. Nathan Henderson
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Isabella L. Breen
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Rebekka M. Wachter
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - Jeremy H. Mills
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| |
Collapse
|
8
|
Rasmusssen AP, Pedersen HB, Andersen LH. Excited-state dynamics and fluorescence lifetime of cryogenically cooled green fluorescent protein chromophore anions. Phys Chem Chem Phys 2023. [PMID: 38048068 DOI: 10.1039/d3cp04696f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Time-resolved action spectroscopy together with a fs-pump probe scheme is used in an electrostatic ion-storage ring to address lifetimes of specific vibrational levels in electronically excited states. Here we specifically consider the excited-state lifetime of cryogenically cooled green fluorescent protein (GFP) chromophore anions which is systematically measured across the S0-S1 spectral region (450-482 nm). A long lifetime of 5.2 ± 0.3 ns is measured at the S0-S1 band origin. When exciting higher vibrational levels in S1, the lifetime changes dramatically. It decreases by more than two orders of magnitude in a narrow energy region ∼250 cm-1 (31 meV) above the 0-0 transition. This is attributed to the opening of internal conversion over an excited-state energy barrier. The applied experimental technique provides a new way to uncover even small energy barriers, which are crucial for excited-state dynamics.
Collapse
Affiliation(s)
- Anne P Rasmusssen
- Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark.
| | - Henrik B Pedersen
- Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark.
| | - Lars H Andersen
- Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark.
| |
Collapse
|
9
|
Krueger TD, Chen C, Fang C. Targeting Ultrafast Spectroscopic Insights into Red Fluorescent Proteins. Chem Asian J 2023; 18:e202300668. [PMID: 37682793 DOI: 10.1002/asia.202300668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/10/2023]
Abstract
Red fluorescent proteins (RFPs) represent an increasingly popular class of genetically encodable bioprobes and biomarkers that can advance next-generation breakthroughs across the imaging and life sciences. Since the rational design of RFPs with improved functions or enhanced versatility requires a mechanistic understanding of their working mechanisms, while fluorescence is intrinsically an ultrafast event, a suitable toolset involving steady-state and time-resolved spectroscopic techniques has become powerful in delineating key structural features and dynamic steps which govern irreversible photoconverting or reversible photoswitching RFPs, and large Stokes shift (LSS)RFPs. The pertinent cis-trans isomerization and protonation state change of RFP chromophores in their local environments, involving key residues in protein matrices, lead to rich and complicated spectral features across multiple timescales. In particular, ultrafast excited-state proton transfer in various LSSRFPs showcases the resolving power of wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) in mapping a photocycle with crucial knowledge about the red-emitting species. Moreover, recent progress in noncanonical RFPs with a site-specifically modified chromophore provides an appealing route for efficient engineering of redder and brighter RFPs, highly desirable for bioimaging. Such an effective feedback loop involving physical chemists, protein engineers, and biomedical microscopists will enable future successes to expand fundamental knowledge and improve human health.
Collapse
Affiliation(s)
- Taylor D Krueger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
| | - Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
| |
Collapse
|
10
|
Ashworth EK, Kao MH, Anstöter CS, Riesco-Llach G, Blancafort L, Solntsev KM, Meech SR, Verlet JRR, Bull JN. Alkylated green fluorescent protein chromophores: dynamics in the gas phase and in aqueous solution. Phys Chem Chem Phys 2023; 25:23626-23636. [PMID: 37649445 DOI: 10.1039/d3cp03250g] [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: 09/01/2023]
Abstract
Fluorescent labelling of macromolecular samples, including using the green fluorescent protein (GFP), has revolutionised the field of bioimaging. The ongoing development of fluorescent proteins require a detailed understanding of the photophysics of the biochromophore, and how chemical derivatisation influences the excited state dynamics. Here, we investigate the photophysical properties associated with the S1 state of three alkylated derivatives of the chromophore in GFP, in the gas phase using time-resolved photoelectron imaging, and in water using femtosecond fluorescence upconversion. The gas-phase lifetimes (1.6-10 ps), which are associated with the intrinsic (environment independent) dynamics, are substantially longer than the lifetimes in water (0.06-3 ps), attributed to stabilisation of both twisted intermediate structures and conical intersection seams in the condensed phase. In the gas phase, alkylation on the 3 and 5 positions of the phenyl ring slows the dynamics due to inertial effects, while a 'pre-twist' of the methine bridge through alkylation on the 2 and 6 positions significantly shortens the excited state lifetimes. Formation of a minor, long-lived (≫ 40 ps) excited state population in the gas phase is attributed to intersystem crossing to a triplet state, accessed because of a T1/S1 degeneracy in the so-called P-trap potential energy minimum associated with torsion of the single-bond in the bridging unit connecting to the phenoxide ring. A small amount of intersystem crossing is supported through TD-DFT molecular dynamics trajectories and MS-CASPT2 calculations. No such intersystem crossing occurs in water at T = 300 K or in ethanol at T ≈ 77 K, due to a significantly altered potential energy surface and P-trap geometry.
Collapse
Affiliation(s)
- Eleanor K Ashworth
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - Min-Hsien Kao
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - Cate S Anstöter
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Gerard Riesco-Llach
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/M.A. Capmany 69, 17003 Girona, Spain
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/M.A. Capmany 69, 17003 Girona, Spain
| | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Stephen R Meech
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - Jan R R Verlet
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - James N Bull
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, NR4 7TJ, UK.
| |
Collapse
|
11
|
Park SW, Kim D, Rhee YM. Overcoming the Limitation of Spin Statistics in Organic Light Emitting Diodes (OLEDs): Hot Exciton Mechanism and Its Characterization. Int J Mol Sci 2023; 24:12362. [PMID: 37569740 PMCID: PMC10418923 DOI: 10.3390/ijms241512362] [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: 06/30/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Triplet harvesting processes are essential for enhancing efficiencies of fluorescent organic light-emitting diodes. Besides more conventional thermally activated delayed fluorescence and triplet-triplet annihilation, the hot exciton mechanism has been recently noticed because it helps reduce the efficiency roll-off and improve device stability. Hot exciton materials enable the conversion of triplet excitons to singlet ones via reverse inter-system crossing from high-lying triplet states and thereby the depopulation of long-lived triplet excitons that are prone to chemical and/or efficiency degradation. Although their anti-Kasha characteristics have not been clearly explained, numerous molecules with behaviors assigned to the hot exciton mechanism have been reported. Indeed, the related developments appear to have just passed the stage of infancy now, and there will likely be more roles that computational elucidations can play. With this perspective in mind, we review some selected experimental studies on the mechanism and the related designs and then on computational studies. On the computational side, we examine what has been found and what is still missing with regard to properly understanding this interesting mechanism. We further discuss potential future points of computational interests toward aiming for eventually presenting in silico design guides.
Collapse
Affiliation(s)
- Soo Wan Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Dongwook Kim
- Department of Chemistry, Kyonggi University, Suwon 16227, Republic of Korea
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| |
Collapse
|
12
|
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.
Collapse
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;
| |
Collapse
|
13
|
Kanagaraj K, Rebek J, Yu Y. Control of reactivity and selectivity in isomerization and rearrangement reactions inside confined spaces. Chem Commun (Camb) 2023. [PMID: 37377149 DOI: 10.1039/d3cc01198d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
In the confined space of supramolecular systems, the substrate can be forced into a reactive conformation and labile intermediates may be stabilized while isolated from the bulk solution. In this highlight, unusual processes mediated by supramolecular hosts are described. These include unfavourable conformational equilibria, unusual product selectivities in bond and ring-chain isomerizations, accelerated rearrangement reactions through labile intermediates, and encapsulated oxidations. In the host, controlled or altered isomerization of the guests can occur via hydrophobic, photochemical and thermal interventions. The inner spaces of the hosts resemble enzyme cavities that stabilize labile intermediates not accessible in the bulk solvent. The effects of confinement and the binding forces involved are discussed and further applications are suggested.
Collapse
Affiliation(s)
- Kuppusamy Kanagaraj
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China.
| | - Julius Rebek
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China.
- Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yang Yu
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China.
| |
Collapse
|
14
|
Ke HW, Sung K. 7-membered-ring effect on fluorescence quantum yield: does metal-complexation-induced twisting-inhibition of an amino GFP chromophore derivative enhance fluorescence? Phys Chem Chem Phys 2023; 25:14627-14634. [PMID: 37194347 DOI: 10.1039/d3cp00467h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To investigate two aspects, namely, (1) the 7-membered-ring effect on fluorescence quantum yield and (2) whether metal-complexation-induced twisting-inhibition of an amino green fluorescent protein (GFP) chromophore derivative is bound to enhance fluorescence, a novel GFP-chromophore-based triamine ligand, (Z)-o-PABDI, is designed and synthesized. Before complexation with metal ions, the S1 excited state of (Z)-o-PABDI undergoes τ-torsion relaxation (Z/E photoisomerization) with a Z/E photoisomerization quantum yield of 0.28, forming both ground-state (Z)- and (E)-o-PABDI isomers. Since (E)-o-PABDI is less stable than (Z)-o-PABDI, it is thermo-isomerized back to (Z)-o-PABDI at room temperature in acetonitrile with a first-order rate constant of (1.366 ± 0.082) × 10-6 s-1. After complexation with a Zn2+ ion, (Z)-o-PABDI as a tridentate ligand forms a 1 : 1 complex with the Zn2+ ion in acetonitrile and in the solid state, resulting in complete inhibition of the φ-torsion and τ-torsion relaxations, which does not enhance fluorescence but causes fluorescence quenching. (Z)-o-PABDI also forms complexes with other first-row transition metal ions Mn2+, Fe3+, Co2+, Ni2+ and Cu2+, generating almost the same fluorescence quenching effect. By comparison with the 2/Zn2+ complex, in which a 6-membered ring of Zn2+-complexation enhances fluorescence significantly (a positive 6-membered-ring effect on fluorescence quantum yield), we find that the flexible 7-membered rings of the (Z)-o-PABDI/Mn+ complexes trigger their S1 excited states to relax through internal conversion at a rate much faster than fluorescence (a negative 7-membered-ring effect on fluorescence quantum yield), leading to fluorescence quenching regardless of the type of transition metal that complexes with (Z)-o-PABDI.
Collapse
Affiliation(s)
- Hao-Wei Ke
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
| | - Kuangsen Sung
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
| |
Collapse
|
15
|
Yang Z, Wang J, Yin B, Liu W, Yin D, Shen J, Wang W, Li L, Guo X. Stimuli-Induced Subconformation Transformation of the PSI-LHCI Protein at Single-Molecule Resolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2205945. [PMID: 37114832 DOI: 10.1002/advs.202205945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/11/2023] [Indexed: 06/19/2023]
Abstract
Photosynthesis is a very important process for the current biosphere which can maintain such a subtle and stable circulatory ecosystem on earth through the transformation of energy and substance. Even though been widely studied in various aspects, the physiological activities, such as intrinsic structural vibration and self-regulation process to stress of photosynthetic proteins, are still not in-depth resolved in real-time. Herein, utilizing silicon nanowire biosensors with ultrasensitive temporal and spatial resolution, real-time responses of a single photosystem I-light harvesting complex I (PSI-LHCI) supercomplex of Pisum sativum to various conditions, including gradient variations in temperature, illumination, and electric field, are recorded. Under different temperatures, there is a bi-state switch process associated with the intrinsic thermal vibration behavior. When the variations of illumination and the bias voltage are applied, two additional shoulder states, probably derived from the self-conformational adjustment, are observed. Based on real-time monitoring of the dynamic processes of the PSI-LHCI supercomplex under various conditions, it is successively testified to promising nanotechnology for protein profiling and biological functional integration in photosynthesis studies.
Collapse
Affiliation(s)
- Zhiheng Yang
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, P. R. China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing, 100871, P. R. China
| | - Jie Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P. R. China
| | - Bing Yin
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing, 100871, P. R. China
| | - Wenzhe Liu
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing, 100871, P. R. China
| | - Dongbao Yin
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing, 100871, P. R. China
| | - Jianren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P. R. China
| | - Wenda Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P. R. China
| | - Lidong Li
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing, 100871, P. R. China
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, P. R. China
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Cruzeiro VWD, Wang Y, Pieri E, Hohenstein EG, Martínez TJ. TeraChem protocol buffers (TCPB): Accelerating QM and QM/MM simulations with a client-server model. J Chem Phys 2023; 158:044801. [PMID: 36725506 DOI: 10.1063/5.0130886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The routine use of electronic structures in many chemical simulation applications calls for efficient and easy ways to access electronic structure programs. We describe how the graphics processing unit (GPU) accelerated electronic structure program TeraChem can be set up as an electronic structure server, to be easily accessed by third-party client programs. We exploit Google's protocol buffer framework for data serialization and communication. The client interface, called TeraChem protocol buffers (TCPB), has been designed for ease of use and compatibility with multiple programming languages, such as C++, Fortran, and Python. To demonstrate the ease of coupling third-party programs with electronic structures using TCPB, we have incorporated the TCPB client into Amber for quantum mechanics/molecular mechanics (QM/MM) simulations. The TCPB interface saves time with GPU initialization and I/O operations, achieving a speedup of more than 2× compared to a prior file-based implementation for a QM region with ∼250 basis functions. We demonstrate the practical application of TCPB by computing the free energy profile of p-hydroxybenzylidene-2,3-dimethylimidazolinone (p-HBDI-)-a model chromophore in green fluorescent proteins-on the first excited singlet state using Hamiltonian replica exchange for enhanced sampling. All calculations in this work have been performed with the non-commercial freely-available version of TeraChem, which is sufficient for many QM region sizes in common use.
Collapse
Affiliation(s)
| | - Yuanheng Wang
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
| | - Elisa Pieri
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
| | - Edward G Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
18
|
Addison K, Roy P, Bressan G, Skudaite K, Robb J, Bulman Page PC, Ashworth EK, Bull JN, Meech SR. Photophysics of the red-form Kaede chromophore. Chem Sci 2023; 14:3763-3775. [PMID: 37035701 PMCID: PMC10074405 DOI: 10.1039/d3sc00368j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
The chromophore responsible for colour switching in the optical highlighting protein Kaede has unexpectedly complicated excited state dynamics, which are measured and analysed here. This will inform the development of new imaging proteins.
Collapse
Affiliation(s)
- Kiri Addison
- School of Chemistry, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Palas Roy
- School of Chemistry, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Giovanni Bressan
- School of Chemistry, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Karolina Skudaite
- School of Chemistry, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Josh Robb
- School of Chemistry, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | | | - Eleanor K. Ashworth
- School of Chemistry, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - James N. Bull
- School of Chemistry, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| |
Collapse
|
19
|
Baxter J, Hutchison CD, Maghlaoui K, Cordon-Preciado V, Morgan RML, Aller P, Butryn A, Axford D, Horrell S, Owen RL, Storm SLS, Devenish NE, van Thor JJ. Observation of Cation Chromophore Photoisomerization of a Fluorescent Protein Using Millisecond Synchrotron Serial Crystallography and Infrared Vibrational and Visible Spectroscopy. J Phys Chem B 2022; 126:9288-9296. [PMID: 36326150 PMCID: PMC9677427 DOI: 10.1021/acs.jpcb.2c06780] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The chromophores of reversibly switchable fluorescent proteins (rsFPs) undergo photoisomerization of both the trans and cis forms. Concurrent with cis/trans photoisomerisation, rsFPs typically become protonated on the phenolic oxygen resulting in a blue shift of the absorption. A synthetic rsFP referred to as rsEospa, derived from EosFP family, displays the same spectroscopic behavior as the GFP-like rsFP Dronpa at pH 8.4 and involves the photoconversion between nonfluorescent neutral and fluorescent anionic chromophore states. Millisecond time-resolved synchrotron serial crystallography of rsEospa at pH 8.4 shows that photoisomerization is accompanied by rearrangements of the same three residues as seen in Dronpa. However, at pH 5.5 we observe that the OFF state is identified as the cationic chromophore with additional protonation of the imidazolinone nitrogen which is concurrent with a newly formed hydrogen bond with the Glu212 carboxylate side chain. FTIR spectroscopy resolves the characteristic up-shifted carbonyl stretching frequency at 1713 cm-1 for the cationic species. Electronic spectroscopy furthermore distinguishes the cationic absorption band at 397 nm from the neutral species at pH 8.4 seen at 387 nm. The observation of photoisomerization of the cationic chromophore state demonstrates the conical intersection for the electronic configuration, where previously fluorescence was proposed to be the main decay route for states containing imidazolinone nitrogen protonation. We present the full time-resolved room-temperature X-ray crystallographic, FTIR, and UV/vis assignment and photoconversion modeling of rsEospa.
Collapse
Affiliation(s)
- James
M. Baxter
- Department
of Life Sciences, Imperial College London, LondonSW7 2AZ, United Kingdom
| | | | - Karim Maghlaoui
- Department
of Life Sciences, Imperial College London, LondonSW7 2AZ, United Kingdom
| | | | - R. Marc L. Morgan
- Department
of Life Sciences, Imperial College London, LondonSW7 2AZ, United Kingdom
| | - Pierre Aller
- Research
Complex at Harwell, Rutherford Appleton
Laboratory, DidcotOX11 0FAUnited Kingdom,Diamond
Light Source, Harwell Science and Innovation
Campus, DidcotOX11 0DE, United Kingdom
| | - Agata Butryn
- Research
Complex at Harwell, Rutherford Appleton
Laboratory, DidcotOX11 0FAUnited Kingdom,Diamond
Light Source, Harwell Science and Innovation
Campus, DidcotOX11 0DE, United Kingdom
| | - Danny Axford
- Diamond
Light Source, Harwell Science and Innovation
Campus, DidcotOX11 0DE, United Kingdom
| | - Sam Horrell
- Diamond
Light Source, Harwell Science and Innovation
Campus, DidcotOX11 0DE, United Kingdom
| | - Robin L. Owen
- Diamond
Light Source, Harwell Science and Innovation
Campus, DidcotOX11 0DE, United Kingdom
| | - Selina L. S. Storm
- Diamond
Light Source, Harwell Science and Innovation
Campus, DidcotOX11 0DE, United Kingdom
| | - Nicholas E. Devenish
- Diamond
Light Source, Harwell Science and Innovation
Campus, DidcotOX11 0DE, United Kingdom
| | - Jasper J. van Thor
- Department
of Life Sciences, Imperial College London, LondonSW7 2AZ, United Kingdom,
| |
Collapse
|
20
|
Rajbongshi BK, Rafiq S, Bhowmik S, Sen P. Ultrafast Excited State Relaxation of a Model Green Fluorescent Protein Chromophore: Femtosecond Fluorescence and Transient Absorption Study. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
21
|
Gautier A. Fluorescence-Activating and Absorption-Shifting Tags for Advanced Imaging and Biosensing. Acc Chem Res 2022; 55:3125-3135. [PMID: 36269101 DOI: 10.1021/acs.accounts.2c00098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Fluorescent labels and biosensors play central roles in biological and medical research. Targeted to specific biomolecules or cells, they allow noninvasive imaging of the machinery that govern cells and organisms in real time. Recently, chemogenetic reporters made of organic dyes specifically anchored to genetic tags have challenged the paradigm of fully genetically encoded fluorescent proteins. Combining the advantage of synthetic fluorophores with the targeting selectivity of genetically encoded tags, these chemogenetic reporters open new exciting prospects for studying cell biochemistry and biology. In this Account, we present the growing toolbox of fluorescence-activating and absorption-shifting tags (FASTs), small monomeric proteins of 14 kDa (125 amino acids residues) that can be used as markers to monitor gene expression and protein localization in live cells and organisms. Engineered by directed protein evolution from the photoactive yellow protein (PYP) from the bacterium Halorhodospira halophila, prototypical FAST binds and stabilizes the fluorescent state of live-cell compatible hydroxybenzylidene rhodanine chromophores. This class of chromophores are normally dark when free in solution or in cells because they dissipate light energy through nonradiative processes. The protein cavity of FAST allows the stabilization of the deprotonated state of the chromophore and blocks the chromophore into a planar conformation, which leads to highly fluorescent protein-chromophore assemblies. The use of such fluorogenic dyes (also called fluorogens) enables the imaging of FAST fusion proteins in cells with high contrast without the need to remove unbound ligands through separate washing steps. Fluorogens with various spectral properties exist nowadays allowing investigators to adjust the spectral properties of FAST to their experimental conditions. Molecular engineering allowed furthermore to generate membrane-impermeant fluorogens for the selective labeling of cell-surface proteins. Over the years, we generated a collection of FAST variants with expanded spectral properties or fluorogen selectivity using a concerted strategy involving molecular engineering and directed protein evolution. Moreover, protein engineering allowed us to adapt FASTs for the design of fluorescent biosensors. Circular permutation enabled the generation of FAST variants with increased conformational flexibility for the design of biosensors in which fluorogen binding is conditioned to the recognition of a given analyte. Bisection of FASTs into two complementary fragments allowed us furthermore to create split variants with reversible complementation that allow the detection and imaging of dynamic protein-protein interactions. We provide, here, a general overview of the current state of development of these different systems and their applications for advanced live cell imaging and biosensing and discuss potential future directions.
Collapse
Affiliation(s)
- Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France.,Institut Universitaire de France, 75005 Paris, France
| |
Collapse
|
22
|
Hostetter ER, Keyes JR, Poon I, Nguyen JP, Nite JM, Jimenez Hoyos CA, Smith CA. Prediction of Fluorophore Brightness in Designed Mini Fluorescence Activating Proteins. J Chem Theory Comput 2022; 18:3190-3203. [PMID: 35417158 DOI: 10.1021/acs.jctc.1c00748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The de novo computational design of proteins with predefined three-dimensional structure is becoming much more routine due to advancements both in force fields and algorithms. However, creating designs with functions beyond folding is more challenging. In that regard, the recent design of small beta barrel proteins that activate the fluorescence of an exogenous small molecule chromophore (DFHBI) is noteworthy. These proteins, termed mini fluorescence activating proteins (mFAPs), have been shown to increase the brightness of the chromophore more than 100-fold upon binding to the designed ligand pocket. The design process created a large library of variants with different brightness levels but gave no rational explanation for why one variant was brighter than another. Here, we use quantum mechanics and molecular dynamics simulations to investigate how molecular flexibility in the ground and excited states influences brightness. We show that the ability of the protein to resist dihedral angle rotation of the chromophore is critical for predicting brightness. Our simulations suggest that the mFAP/DFHBI complex has a rough energy landscape, requiring extensive ground-state sampling to achieve converged predictions of excited-state kinetics. While computationally demanding, this roughness suggests that mFAP protein function can be enhanced by reshaping the energy landscape toward conformations that better resist DFHBI bond rotation.
Collapse
Affiliation(s)
- Emma R Hostetter
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Jeffrey R Keyes
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Ivy Poon
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Justin P Nguyen
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Jacob M Nite
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | -
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Carlos A Jimenez Hoyos
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Colin A Smith
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| |
Collapse
|
23
|
Lin CY, Romei MG, Mathews II, Boxer SG. Energetic Basis and Design of Enzyme Function Demonstrated Using GFP, an Excited-State Enzyme. J Am Chem Soc 2022; 144:3968-3978. [PMID: 35200017 PMCID: PMC9014791 DOI: 10.1021/jacs.1c12305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The past decades have witnessed an explosion of de novo protein designs with a remarkable range of scaffolds. It remains challenging, however, to design catalytic functions that are competitive with naturally occurring counterparts as well as biomimetic or nonbiological catalysts. Although directed evolution often offers efficient solutions, the fitness landscape remains opaque. Green fluorescent protein (GFP), which has revolutionized biological imaging and assays, is one of the most redesigned proteins. While not an enzyme in the conventional sense, GFPs feature competing excited-state decay pathways with the same steric and electrostatic origins as conventional ground-state catalysts, and they exert exquisite control over multiple reaction outcomes through the same principles. Thus, GFP is an "excited-state enzyme". Herein we show that rationally designed mutants and hybrids that contain environmental mutations and substituted chromophores provide the basis for a quantitative model and prediction that describes the influence of sterics and electrostatics on excited-state catalysis of GFPs. As both perturbations can selectively bias photoisomerization pathways, GFPs with fluorescence quantum yields (FQYs) and photoswitching characteristics tailored for specific applications could be predicted and then demonstrated. The underlying energetic landscape, readily accessible via spectroscopy for GFPs, offers an important missing link in the design of protein function that is generalizable to catalyst design.
Collapse
Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
24
|
Ye S, Hsiung CH, Tang Y, Zhang X. Visualizing the Multistep Process of Protein Aggregation in Live Cells. Acc Chem Res 2022; 55:381-390. [PMID: 35040316 PMCID: PMC9098262 DOI: 10.1021/acs.accounts.1c00648] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Protein aggregation is a biological phenomenon in which aberrantly processed or mutant proteins misfold and assemble into a variety of insoluble aggregates. Decades of studies have delineated the structure, interaction, and activity of proteins in either their natively folded structures or insoluble aggregates such as amyloid fibrils. However, a variety of intermediate species exist between these two extreme states in the protein folding landscape. Herein, we collectively term these intermediate species as misfolded protein oligomers, including soluble oligomers and preamyloid oligomers that are formed by unfolded or misfolded proteins. While extensive tools have been developed to study folded proteins or amyloid fibrils, research to understand the properties and activities of misfolded protein oligomers has been limited by the lack of methods to detect and interrogate these species in live cells.In this Account, we describe our efforts in the development of chemical methods that allow for the characterization of the multistep protein aggregation process, in particular the misfolded protein oligomers, in living cells. As the start of this journey, we attempted to develop a fluorogenic method wherein the misfolded oligomers could turn on the fluorescence of chemical probes that are conjugated to the protein-of-interest (POI). To this end, we produced a series of destabilized HaloTag variants, formulating the primary component of the AgHalo sensor, which misfolds and aggregates when cells are subjected to stress. When AgHalo is covalently conjugated with a solvatochromic fluorophore, misfolding of the AgHalo conjugate would activate fluorescence, resulting in the observation of misfolded oligomers. Following this work, we extended the scope of detection from AgHalo to any protein-of-interest via the AggTag method, wherein the POIs are genetically fused to self-labeling protein tags (HaloTag or SNAP-tag). Focusing on the molecular rotor-based fluorophores, we applied the modulated fluorescent protein (FP) chromophore core as a prototype for the AggTag probes, to enable the fluorogenic detection of misfolded soluble oligomers of multiple proteins in live cells. Next, we further developed the AggTag method to distinguish insoluble aggregates from misfolded oligomers, using two classes of probes that activate different fluorescence emission toward these two conformations. To enable this goal, we applied physical organic chemistry and computational chemistry to discover a new category of triode-like fluorophores, wherein the π orbitals of either an electron density regulator or the donor-acceptor linkages are used to control the rotational barriers of fluorophores in the excited states. This mechanism allows us to rationally design molecular rotor-based fluorophores that have desired responses to viscosity, thus extending the application of the AggTag method.In summary, our work allows the direct monitoring of the misfolded protein oligomers and differentiation of insoluble aggregates from other conformations in live cells, thus enabling studies of many currently unanswered questions in protein aggregation. Future directions are to develop methods that enable quantitative analyses of the protein aggregation process. Further, new methods are needed to detect and to quantify the formation and maturation of protein or RNA condensates that form membraneless organelles.
Collapse
Affiliation(s)
- Songtao Ye
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States,Present address: School of Science and School of Life Sciences, Westlake University; Institute of Natural Sciences, Westlake Institute for Advanced Study; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Chia-Heng Hsiung
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States,Present address: School of Science and School of Life Sciences, Westlake University; Institute of Natural Sciences, Westlake Institute for Advanced Study; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Yuqi Tang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States,Present address: School of Science and School of Life Sciences, Westlake University; Institute of Natural Sciences, Westlake Institute for Advanced Study; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Xin Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States,Present address: School of Science and School of Life Sciences, Westlake University; Institute of Natural Sciences, Westlake Institute for Advanced Study; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| |
Collapse
|
25
|
Tau O, Henley A, Boichenko AN, Kleshchina NN, Riley R, Wang B, Winning D, Lewin R, Parkin IP, Ward JM, Hailes HC, Bochenkova AV, Fielding HH. Liquid-microjet photoelectron spectroscopy of the green fluorescent protein chromophore. Nat Commun 2022; 13:507. [PMID: 35082282 PMCID: PMC8791993 DOI: 10.1038/s41467-022-28155-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/11/2022] [Indexed: 01/08/2023] Open
Abstract
Green fluorescent protein (GFP), the most widely used fluorescent protein for in vivo monitoring of biological processes, is known to undergo photooxidation reactions. However, the most fundamental property underpinning photooxidation, the electron detachment energy, has only been measured for the deprotonated GFP chromophore in the gas phase. Here, we use multiphoton ultraviolet photoelectron spectroscopy in a liquid-microjet and high-level quantum chemistry calculations to determine the electron detachment energy of the GFP chromophore in aqueous solution. The aqueous environment is found to raise the detachment energy by around 4 eV compared to the gas phase, similar to calculations of the chromophore in its native protein environment. In most cases, electron detachment is found to occur resonantly through electronically excited states of the chromophore, highlighting their importance in photo-induced electron transfer processes in the condensed phase. Our results suggest that the photooxidation properties of the GFP chromophore in an aqueous environment will be similar to those in the protein. The electronic structures of photoactive proteins underlie many natural photoinduced processes. The authors, using UV liquid-microjet photoelectron spectroscopy and quantum chemistry calculations, determine electron detachment energies of the green fluorescent protein chromophore in aqueous solution, approaching conditions of the protein environment.
Collapse
Affiliation(s)
- Omri Tau
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Alice Henley
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Anton N Boichenko
- Department of Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
| | | | - River Riley
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Bingxing Wang
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.,College of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Eastern Hualan Avenue, Xinxiang, 453003, China
| | - Danielle Winning
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Ross Lewin
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Ivan P Parkin
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - John M Ward
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Helen C Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | | | - Helen H Fielding
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| |
Collapse
|
26
|
List NH, Jones CM, Martínez TJ. Internal conversion of the anionic GFP chromophore: in and out of the I-twisted S 1/S 0 conical intersection seam. Chem Sci 2022; 13:373-385. [PMID: 35126970 PMCID: PMC8729814 DOI: 10.1039/d1sc05849e] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/11/2021] [Indexed: 11/21/2022] Open
Abstract
The functional diversity of the green fluorescent protein (GFP) family is intimately connected to the interplay between competing photo-induced transformations of the chromophore motif, anionic p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI-). Its ability to undergo Z/E-isomerization is of particular importance for super-resolution microscopy and emerging opportunities in optogenetics. Yet, key dynamical features of the underlying internal conversion process in the native HBDI- chromophore remain largely elusive. We investigate the intrinsic excited-state behavior of isolated HBDI- to resolve competing decay pathways and map out the factors governing efficiency and the stereochemical outcome of photoisomerization. Based on non-adiabatic dynamics simulations, we demonstrate that non-selective progress along the two bridge-torsional (i.e., phenolate, P, or imidazolinone, I) pathways accounts for the three decay constants reported experimentally, leading to competing ultrafast relaxation primarily along the I-twisted pathway and S1 trapping along the P-torsion. The majority of the population (∼70%) is transferred to S0 in the vicinity of two approximately enantiomeric minima on the I-twisted intersection seam (MECI-Is). Despite their sloped, reactant-biased topographies (suggesting low photoproduct yields), we find that decay through these intersections leads to products with a surprisingly high quantum yield of ∼30%. This demonstrates that E-isomer generation results at least in part from direct isomerization on the excited state. A photoisomerization committor analysis reveals a difference in intrinsic photoreactivity of the two MECI-Is and that the observed photoisomerization is the combined result of two effects: early, non-statistical dynamics around the less reactive intersection followed by later, near-statistical behavior around the more reactive MECI-I. Our work offers new insight into internal conversion of HBDI- that both establishes the intrinsic properties of the chromophore and enlightens principles for the design of chromophore derivatives and protein variants with improved photoswitching properties.
Collapse
Affiliation(s)
- Nanna H List
- 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
| | - 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
| |
Collapse
|
27
|
Rossano‐Tapia M, Brown A. Quantum mechanical/molecular mechanical studies of photophysical properties of fluorescent proteins. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Alex Brown
- Department of Chemistry University of Alberta Edmonton Alberta Canada
| |
Collapse
|
28
|
Tang L, Fang C. Fluorescence Modulation by Ultrafast Chromophore Twisting Events: Developing a Powerful Toolset for Fluorescent-Protein-Based Imaging. J Phys Chem B 2021; 125:13610-13623. [PMID: 34883016 DOI: 10.1021/acs.jpcb.1c08570] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The advancement of modern life sciences has benefited tremendously from the discovery and development of fluorescent proteins (FPs), widely expressed in live cells to track a myriad of cellular events. The chromophores of various FPs can undergo many ultrafast photophysical and/or photochemical processes in the electronic excited state and emit fluorescence with different colors. However, the chromophore becomes essentially nonfluorescent in solution environment due to its intrinsic twisting capability upon photoexcitation. To study "microscopic" torsional events and their effects on "macroscopic" fluorescence, we have developed an integrated ultrafast characterization platform involving femtosecond transient absorption (fs-TA) and wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS). A wide range of naturally occurring, circularly permuted, non-canonical amino-acid-decorated FPs and FP-based optical highlighters with photochromicity, photoconversion, and/or photoswitching capabilities have been recently investigated in great detail. Twisting conformational motions were elucidated to exist in all of these systems but to various extents. The associated different ultrafast pathways can be monitored via frequency changes of characteristic Raman bands during primary events and functional processes. The mapped electronic and structural dynamics information is crucial and has shown great potential and initial success for the rational design of proteins and other photoreceptors with novel functions and fluorescence properties.
Collapse
Affiliation(s)
- Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, United States
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, United States
| |
Collapse
|
29
|
Liao JW, Sung R, Sung K. Against the NEER principle: the third type of photochromism for GFP chromophore derivatives. Phys Chem Chem Phys 2021; 24:295-304. [PMID: 34889318 DOI: 10.1039/d1cp03581a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochromism is the heart of photochromic fluorescent proteins. Excited-state proton transfer (ESPT) is the major cause of photochromism for the green fluorescent protein (GFP) and Z-E photoisomerization through τ-torsion is the major cause of photochromism for Dronpa (a GFP mutant). In this article, s-E-1 opens a third type of photochromism for GFP chromophore derivatives, which involves light-driven φ-torsion with no τ-torsion, followed by excited-state intramolecular proton transfer (ESIPT), and is gated by environmental polarity. Since s-E-1 does not follow Z-E photoisomerization through τ-torsion but undergoes light-driven φ-torsion, which involves equilibration of the excited-state rotamers, it is clearly against the NEER (Non-Equilibration of Excited-state Rotamers) principle.
Collapse
Affiliation(s)
- Jun-Wei Liao
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
| | - Robert Sung
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
| | - Kuangsen Sung
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Boulanger SA, Chen C, Myasnyanko IN, Sokolov AI, Baranov MS, Fang C. Excited-State Dynamics of a meta-Dimethylamino Locked GFP Chromophore as a Fluorescence Turn-on Water Sensor †. Photochem Photobiol 2021; 98:311-324. [PMID: 34714942 DOI: 10.1111/php.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 12/14/2022]
Abstract
Strategic incorporation of a meta-dimethylamino (-NMe2 ) group on the conformationally locked green fluorescent protein (GFP) model chromophore (m-NMe2 -LpHBDI) has drastically altered molecular electronic properties, counterintuitively enhancing fluorescence of only the neutral and cationic chromophores in aqueous solution. A ˜200-fold decrease in fluorescence quantum yield of m-NMe2 -LpHBDI in alcohols (e.g., MeOH, EtOH and 2-PrOH) supports this GFP-derived compound as a fluorescence turn-on water sensor, with large fluorescence intensity differences between H2 O and ROH emissions in various H2 O/ROH binary mixtures. A combination of steady-state electronic spectroscopy, femtosecond transient absorption, ground-state femtosecond stimulated Raman spectroscopy (FSRS) and quantum calculations elucidates an intermolecular hydrogen-bonding chain between a solvent -OH group and the chromophore phenolic ring -NMe2 and -OH functional groups, wherein fluorescence differences arise from an extended hydrogen-bonding network beyond the first solvation shell, as opposed to fluorescence quenching via a dark twisted intramolecular charge-transfer state. The absence of a meta-NMe2 group twisting coordinate upon electronic excitation was corroborated by experiments on control samples without the meta-NMe2 group or with both meta-NMe2 and para-OH groups locked in a six-membered ring. These deep mechanistic insights stemming from GFP chromophore scaffold will enable rational design of organic, compact and environmentally friendly water sensors.
Collapse
Affiliation(s)
| | - Cheng Chen
- Department of Chemistry, Oregon State University, Corvallis, OR
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anatolii I Sokolov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, OR
| |
Collapse
|
32
|
Kochman MA, Palczewski K, Kubas A. Theoretical Study of the Photoisomerization Mechanism of All- Trans-Retinyl Acetate. J Phys Chem A 2021; 125:8358-8372. [PMID: 34546761 PMCID: PMC8488936 DOI: 10.1021/acs.jpca.1c05533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
The compound 9-cis-retinyl acetate (9-cis-RAc) is a precursor
to 9-cis-retinal,
which has potential application in the treatment of some hereditary
diseases of the retina. An attractive synthetic route to 9-cis-RAc is based on the photoisomerization reaction of the
readily available all-trans-RAc. In the present study,
we examine the mechanism of the photoisomerization reaction with the
use of state-of-the-art electronic structure calculations for two
polyenic model compounds: tEtEt-octatetraene and tEtEtEc-2,6-dimethyl-1,3,5,7,9-decapentaene. The occurrence
of photoisomerization is attributed to a chain-kinking mechanism,
whereby a series of S1/S0 conical intersections
associated with kinking deformations at different positions along
the polyenic chain mediate internal conversion to the S0 state, and subsequent isomerization around one of the double bonds.
Two other possible photoisomerization mechanisms are taken into account,
but they are rejected as incompatible with simulation results and/or
the available spectroscopic data.
Collapse
Affiliation(s)
- Michał Andrzej Kochman
- Institute of Physical Chemistry, Polish Academy of Sciences, Ul. Marcina Kasprzaka 44/52, 01-224 Warszawa, Poland
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, California 92697, United States.,Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States.,Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Adam Kubas
- Institute of Physical Chemistry, Polish Academy of Sciences, Ul. Marcina Kasprzaka 44/52, 01-224 Warszawa, Poland
| |
Collapse
|
33
|
Chen C, Tutol JN, Tang L, Zhu L, Ong WSY, Dodani SC, Fang C. Excitation ratiometric chloride sensing in a standalone yellow fluorescent protein is powered by the interplay between proton transfer and conformational reorganization. Chem Sci 2021; 12:11382-11393. [PMID: 34667546 PMCID: PMC8447875 DOI: 10.1039/d1sc00847a] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Natural and laboratory-guided evolution has created a rich diversity of fluorescent protein (FP)-based sensors for chloride (Cl−). To date, such sensors have been limited to the Aequorea victoria green fluorescent protein (avGFP) family, and fusions with other FPs have unlocked ratiometric imaging applications. Recently, we identified the yellow fluorescent protein from jellyfish Phialidium sp. (phiYFP) as a fluorescent turn-on, self-ratiometric Cl− sensor. To elucidate its working mechanism as a rare example of a single FP with this capability, we tracked the excited-state dynamics of phiYFP using femtosecond transient absorption (fs-TA) spectroscopy and target analysis. The photoexcited neutral chromophore undergoes bifurcated pathways with the twisting-motion-induced nonradiative decay and barrierless excited-state proton transfer. The latter pathway yields a weakly fluorescent anionic intermediate , followed by the formation of a red-shifted fluorescent state that enables the ratiometric response on the tens of picoseconds timescale. The redshift results from the optimized π–π stacking between chromophore Y66 and nearby Y203, an ultrafast molecular event. The anion binding leads to an increase of the chromophore pKa and ESPT population, and the hindrance of conversion. The interplay between these two effects determines the turn-on fluorescence response to halides such as Cl− but turn-off response to other anions such as nitrate as governed by different binding affinities. These deep mechanistic insights lay the foundation for guiding the targeted engineering of phiYFP and its derivatives for ratiometric imaging of cellular chloride with high selectivity. We discovered an interplay between proton transfer and conformational reorganization that powers a standalone fluorescent-protein-based excitation-ratiometric biosensor for chloride imaging.![]()
Collapse
Affiliation(s)
- Cheng Chen
- Department of Chemistry, Oregon State University 153 Gilbert Hall Corvallis OR 97331-4003 USA https://fanglab.oregonstate.edu/
| | - Jasmine N Tutol
- Department of Chemistry and Biochemistry, The University of Texas at Dallas 800 West Campbell Road Richardson TX 75080 USA https://lab.utdallas.edu/dodani/
| | - Longteng Tang
- Department of Chemistry, Oregon State University 153 Gilbert Hall Corvallis OR 97331-4003 USA https://fanglab.oregonstate.edu/
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University 153 Gilbert Hall Corvallis OR 97331-4003 USA https://fanglab.oregonstate.edu/
| | - Whitney S Y Ong
- Department of Chemistry and Biochemistry, The University of Texas at Dallas 800 West Campbell Road Richardson TX 75080 USA https://lab.utdallas.edu/dodani/
| | - Sheel C Dodani
- Department of Chemistry and Biochemistry, The University of Texas at Dallas 800 West Campbell Road Richardson TX 75080 USA https://lab.utdallas.edu/dodani/
| | - Chong Fang
- Department of Chemistry, Oregon State University 153 Gilbert Hall Corvallis OR 97331-4003 USA https://fanglab.oregonstate.edu/
| |
Collapse
|
34
|
Jones CM, List NH, Martínez TJ. Resolving the ultrafast dynamics of the anionic green fluorescent protein chromophore in water. Chem Sci 2021; 12:11347-11363. [PMID: 34667545 PMCID: PMC8447926 DOI: 10.1039/d1sc02508b] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/13/2021] [Indexed: 11/21/2022] Open
Abstract
The chromophore of the green fluorescent protein (GFP) is critical for probing environmental influences on fluorescent protein behavior. Using the aqueous system as a bridge between the unconfined vacuum system and a constricting protein scaffold, we investigate the steric and electronic effects of the environment on the photodynamical behavior of the chromophore. Specifically, we apply ab initio multiple spawning to simulate five picoseconds of nonadiabatic dynamics after photoexcitation, resolving the excited-state pathways responsible for internal conversion in the aqueous chromophore. We identify an ultrafast pathway that proceeds through a short-lived (sub-picosecond) imidazolinone-twisted (I-twisted) species and a slower (several picoseconds) channel that proceeds through a long-lived phenolate-twisted (P-twisted) intermediate. The molecule navigates the non-equilibrium energy landscape via an aborted hula-twist-like motion toward the one-bond-flip dominated conical intersection seams, as opposed to following the pure one-bond-flip paths proposed by the excited-state equilibrium picture. We interpret our simulations in the context of time-resolved fluorescence experiments, which use short- and long-time components to describe the fluorescence decay of the aqueous GFP chromophore. Our results suggest that the longer time component is caused by an energetically uphill approach to the P-twisted intersection seam rather than an excited-state barrier to reach the twisted intramolecular charge-transfer species. Irrespective of the location of the nonadiabatic population events, the twisted intersection seams are inefficient at facilitating isomerization in aqueous solution. The disordered and homogeneous nature of the aqueous solvent environment facilitates non-selective stabilization with respect to I- and P-twisted species, offering an important foundation for understanding the consequences of selective stabilization in heterogeneous and rigid protein environments.
Collapse
Affiliation(s)
- 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
| | - Nanna H List
- 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
| |
Collapse
|
35
|
Boulanger SA, Chen C, Tang L, Zhu L, Baleeva NS, Myasnyanko IN, Baranov MS, Fang C. Shedding light on ultrafast ring-twisting pathways of halogenated GFP chromophores from the excited to ground state. Phys Chem Chem Phys 2021; 23:14636-14648. [PMID: 34212170 DOI: 10.1039/d1cp02140k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since green fluorescent protein (GFP) has revolutionized molecular and cellular biology for about three decades, there has been a keen interest in understanding, designing, and controlling the fluorescence properties of GFP chromophore (i.e., HBDI) derivatives from the protein matrix to solution. Amongst these cross-disciplinary efforts, the elucidation of excited-state dynamics of HBDI derivatives holds the key to correlating the light-induced processes and fluorescence quantum yield (FQY). Herein, we implement steady-state electronic spectroscopy, femtosecond transient absorption (fs-TA), femtosecond stimulated Raman spectroscopy (FSRS), and quantum calculations to study a series of mono- and dihalogenated HBDI derivatives (X = F, Cl, Br, 2F, 2Cl, and 2Br) in basic aqueous solution, gaining new insights into the photophysical reaction coordinates. In the excited state, the halogenated "floppy" chromophores exhibit an anti-heavy atom effect, reflected by strong correlations between FQY vs. Franck-Condon energy (EFC) or Stokes shift, and knrvs. EFC, as well as a swift bifurcation into the I-ring (major) and P-ring (minor) twisting motions. In the ground state, both ring-twisting motions become more susceptible to sterics and exhibit spectral signatures from the halogen-dependent hot ground-state absorption band decay in TA data. We envision this type of systematic analysis of the halogenated HBDI derivatives to provide guiding principles for the site-specific modification of GFP chromophores, and expand design space for brighter and potentially photoswitchable organic chemical probes in aqueous solution with discernible spectral signatures throughout the photocycle.
Collapse
Affiliation(s)
- Sean A Boulanger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA.
| | - Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA.
| | - Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA.
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA.
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia and Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia and Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia and Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA.
| |
Collapse
|
36
|
Chen C, Tachibana SR, Baleeva NS, Myasnyanko IN, Bogdanov AM, Gavrikov AS, Mishin AS, Malyshevskaya KK, Baranov MS, Fang C. Developing Bright Green Fluorescent Protein (GFP)-like Fluorogens for Live-Cell Imaging with Nonpolar Protein-Chromophore Interactions. Chemistry 2021; 27:8946-8950. [PMID: 33938061 DOI: 10.1002/chem.202101250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Indexed: 11/09/2022]
Abstract
Fluorescence-activating proteins (FAPs) that bind a chromophore and activate its fluorescence have gained popularity in bioimaging. The fluorescence-activating and absorption-shifting tag (FAST) is a light-weight FAP that enables fast reversible fluorogen binding, thus advancing multiplex and super-resolution imaging. However, the rational design of FAST-specific fluorogens with large fluorescence enhancement (FE) remains challenging. Herein, a new fluorogen directly engineered from green fluorescent protein (GFP) chromophore by a unique double-donor-one-acceptor strategy, which exhibits an over 550-fold FE upon FAST binding and a high extinction coefficient of approximately 100,000 M-1 cm-1 , is reported. Correlation analysis of the excited state nonradiative decay rates and environmental factors reveal that the large FE is caused by nonpolar protein-fluorogen interactions. Our deep insights into structure-function relationships could guide the rational design of bright fluorogens for live-cell imaging with extended spectral properties such as redder emissions.
Collapse
Affiliation(s)
- Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA
| | - Sean R Tachibana
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Alexey M Bogdanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Kseniya K Malyshevskaya
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA
| |
Collapse
|
37
|
De Zitter E, Hugelier S, Duwé S, Vandenberg W, Tebo AG, Van Meervelt L, Dedecker P. Structure-Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System*. Angew Chem Int Ed Engl 2021; 60:10073-10081. [PMID: 33543524 DOI: 10.1002/anie.202015201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Indexed: 11/05/2022]
Abstract
Anisotropic environments can drastically alter the spectroscopy and photochemistry of molecules, leading to complex structure-function relationships. We examined this using fluorescent proteins as easy-to-modify model systems. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, including the determination of 43 crystal structures. Correlation and principal component analysis confirmed the complex relationship between structure and spectroscopy, but also allowed us to identify consistent trends and to relate these to the spatial organization. We find that changes in spectroscopic properties can come about through multiple underlying mechanisms, of which polarity, hydrogen bonding and presence of water molecules are key modulators. We anticipate that our findings and rich structure/spectroscopy dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.
Collapse
Affiliation(s)
- Elke De Zitter
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium.,Present address: University Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Siewert Hugelier
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium
| | - Sam Duwé
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium.,Present address: Advanced Optical Microscopy Centre, Hasselt University, Agoralaan building C, 3590, Diepenbeek, Belgium
| | - Wim Vandenberg
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium
| | - Alison G Tebo
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA
| | - Luc Van Meervelt
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium
| |
Collapse
|
38
|
De Zitter E, Hugelier S, Duwé S, Vandenberg W, Tebo AG, Van Meervelt L, Dedecker P. Structure–Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elke De Zitter
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
- Present address: University Grenoble Alpes CEA CNRS IBS 71 Avenue des Martyrs 38000 Grenoble France
| | - Siewert Hugelier
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
| | - Sam Duwé
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
- Present address: Advanced Optical Microscopy Centre Hasselt University Agoralaan building C 3590 Diepenbeek Belgium
| | - Wim Vandenberg
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
| | - Alison G. Tebo
- Janelia Research Campus Howard Hughes Medical Institute 19700 Helix Drive Ashburn Virginia 20147 USA
| | - Luc Van Meervelt
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
| | - Peter Dedecker
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
| |
Collapse
|
39
|
Fluorescent Orthopalladated Complexes of 4-Aryliden-5(4 H)-oxazolones from the Kaede Protein: Synthesis and Characterization. Molecules 2021; 26:molecules26051238. [PMID: 33669118 PMCID: PMC7956804 DOI: 10.3390/molecules26051238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 11/18/2022] Open
Abstract
The goal of the work reported here was to amplify the fluorescent properties of 4-aryliden-5(4H)-oxazolones by suppression of the hula-twist non-radiative deactivation pathway. This aim was achieved by simultaneous bonding of a Pd center to the N atom of the heterocycle and the ortho carbon of the arylidene ring. Two different 4-((Z)-arylidene)-2-((E)-styryl)-5(4H)-oxazolones, the structures of which are closely related to the chromophore of the Kaede protein and substituted at the 2- and 4-positions of the arylidene ring (1a OMe; 1b F), were used as starting materials. Oxazolones 1a and 1b were reacted with Pd(OAc)2 to give the corresponding dinuclear orthometalated palladium derivates 2a and 2b by regioselective C–H activation of the ortho-position of the arylidene ring. Reaction of 2a (2b) with LiCl promoted the metathesis of the bridging carboxylate by chloride ligands to afford dinuclear 3a (3b). Mononuclear complexes containing the orthopalladated oxazolone and a variety of ancillary ligands (acetylacetonate (4a, 4b), hydroxyquinolinate (5a), aminoquinoline (6a), bipyridine (7a), phenanthroline (8a)) were prepared from 3a or 3b through metathesis of anionic ligands or substitution of neutral weakly bonded ligands. All species were fully characterized and the X-ray determination of the molecular structure of 7a was carried out. This structure has strongly distorted ligands due to intramolecular interactions. Fluorescence measurements showed an increase in the quantum yield (QY) by up to one order of magnitude on comparing the free oxazolone (QY < 1%) with the palladated oxazolone (QY = 12% for 6a). This fact shows that the coordination of the oxazolone to the palladium efficiently suppresses the hula-twist deactivation pathway.
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
Coppola F, Perrella F, Petrone A, Donati G, Rega N. A Not Obvious Correlation Between the Structure of Green Fluorescent Protein Chromophore Pocket and Hydrogen Bond Dynamics: A Choreography From ab initio Molecular Dynamics. Front Mol Biosci 2020; 7:569990. [PMID: 33195416 PMCID: PMC7653547 DOI: 10.3389/fmolb.2020.569990] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/11/2020] [Indexed: 11/23/2022] Open
Abstract
The Green Fluorescent Protein (GFP) is a widely studied chemical system both for its large amount of applications and the complexity of the excited state proton transfer responsible of the change in the protonation state of the chromophore. A detailed investigation on the structure of the chromophore environment and the influence of chromophore form (either neutral or anionic) on it is of crucial importance to understand how these factors could potentially influence the protein function. In this study, we perform a detailed computational investigation based on the analysis of ab-initio molecular dynamics simulations, to disentangle the main structural quantities determining the fine balance in the chromophore environment. We found that specific hydrogen bonds interactions directly involving the chromophore (or not), are correlated to quantities, such as the volume of the cavity in which the chromophore is embedded and that it is importantly affected by the chromophore protonation state. The cross-correlation analysis performed on some of these hydrogen bonds and the cavity volume, demonstrates a direct correlation among them and we also identified the ones specifically involved in this correlation. We also found that specific interactions among residues far in the space are correlated, demonstrating the complexity of the chromophore environment and that many structural quantities have to be taken into account to properly describe and understand the main factors tuning the active site of the protein. From an overall evaluation of the results obtained in this work, it is shown that the residues which a priori are perceived to be spectators play instead an important role in both influencing the chromophore environment (cavity volume) and its dynamics (cross-correlations among spatially distant residues).
Collapse
Affiliation(s)
- Federico Coppola
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Fulvio Perrella
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Alessio Petrone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Greta Donati
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Nadia Rega
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.,Center for Advanced Biomaterials for Healthcare@CRIB, Naples, Italy
| |
Collapse
|
42
|
Wolstenholme CH, Hu H, Ye S, Funk BE, Jain D, Hsiung CH, Ning G, Liu Y, Li X, Zhang X. AggFluor: Fluorogenic Toolbox Enables Direct Visualization of the Multi-Step Protein Aggregation Process in Live Cells. J Am Chem Soc 2020; 142:17515-17523. [PMID: 32915553 DOI: 10.1021/jacs.0c07245] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aberrantly processed or mutant proteins misfold and assemble into a variety of soluble oligomers and insoluble aggregates, a process that is associated with an increasing number of diseases that are not curable or manageable. Herein, we present a chemical toolbox, AggFluor, that allows for live cell imaging and differentiation of complex aggregated conformations in live cells. Based on the chromophore core of green fluorescent proteins, AggFluor is comprised of a series of molecular rotor fluorophores that span a wide range of viscosity sensitivity. As a result, these compounds exhibit differential turn-on fluorescence when incorporated in either soluble oligomers or insoluble aggregates. This feature allows us to develop, for the first time, a dual-color imaging strategy to distinguish unfolded protein oligomers from insoluble aggregates in live cells. Furthermore, we have demonstrated how small molecule proteostasis regulators can drive formation and disassembly of protein aggregates in both conformational states. In summary, AggFluor is the first set of rationally designed molecular rotor fluorophores that evenly cover a wide range of viscosity sensitivities. This set of fluorescent probes not only change the status quo of current imaging methods to visualize protein aggregation in live cells but also can be generally applied to study other biological processes that involve local viscosity changes with temporal and spatial resolutions.
Collapse
|
43
|
Raucci U, Perrella F, Donati G, Zoppi M, Petrone A, Rega N. Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study. J Comput Chem 2020; 41:2228-2239. [PMID: 32770577 DOI: 10.1002/jcc.26384] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 12/15/2022]
Abstract
Solute-solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical-physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute-solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.
Collapse
Affiliation(s)
- Umberto Raucci
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
| | - Fulvio Perrella
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
| | - Greta Donati
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy.,Dipartimento di Chimica e Biologia "Adolfo Zambelli", Università di Salerno, Fisciano, Italy
| | - Maria Zoppi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
| | - Alessio Petrone
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
| | - Nadia Rega
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy.,Center for Advanced Biomaterials for Healthcare@CRIB, Naples, Italy
| |
Collapse
|
44
|
Romei MG, Lin CY, Mathews II, Boxer SG. Electrostatic control of photoisomerization pathways in proteins. Science 2020; 367:76-79. [PMID: 31896714 DOI: 10.1126/science.aax1898] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/04/2019] [Accepted: 10/31/2019] [Indexed: 12/23/2022]
Abstract
Rotation around a specific bond after photoexcitation is central to vision and emerging opportunities in optogenetics, super-resolution microscopy, and photoactive molecular devices. Competing roles for steric and electrostatic effects that govern bond-specific photoisomerization have been widely discussed, the latter originating from chromophore charge transfer upon excitation. We systematically altered the electrostatic properties of the green fluorescent protein chromophore in a photoswitchable variant, Dronpa2, using amber suppression to introduce electron-donating and electron-withdrawing groups to the phenolate ring. Through analysis of the absorption (color), fluorescence quantum yield, and energy barriers to ground- and excited-state isomerization, we evaluate the contributions of sterics and electrostatics quantitatively and demonstrate how electrostatic effects bias the pathway of chromophore photoisomerization, leading to a generalized framework to guide protein design.
Collapse
Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
45
|
Zagorec-Marks W, Foreman MM, Verlet JRR, Weber JM. Probing the Microsolvation Environment of the Green Fluorescent Protein Chromophore In Vacuo. J Phys Chem Lett 2020; 11:1940-1946. [PMID: 32073271 DOI: 10.1021/acs.jpclett.0c00105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present vibrational and electronic photodissociation spectra of a model chromophore of the green fluorescent protein in complexes with up to two water molecules, prepared in a cryogenic ion trap at 160-180 K. We find the band origin of the singly hydrated chromophore at 20 985 cm-1 (476.5 nm) and observe partially resolved vibrational signatures. While a single water molecule induces only a small shift of the S1 electronic band of the chromophore, without significant change of the Franck-Condon envelope, the spectrum of the dihydrate shows significant broadening and a greater blue shift of the band edge. Comparison of the vibrational spectra with predicted infrared spectra from density functional theory indicates that water molecules can interact with the oxygen atom on the phenolate group or on the imidazole moiety, respectively.
Collapse
Affiliation(s)
- Wyatt Zagorec-Marks
- JILA and Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
| | - Madison M Foreman
- JILA and Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
| | - Jan R R Verlet
- Department of Chemistry, Durham University, Durham DH1 3LE, U.K
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
| |
Collapse
|
46
|
Chen YH, Sung R, Sung K. Dramatic changes in the excited-state behaviour of the green fluorescent protein chromophore by a strong π-donating group through significantly lowering the excited-state potential energy surface with photoinduced intramolecular charge transfer. Phys Chem Chem Phys 2020; 22:2424-2428. [PMID: 31939956 DOI: 10.1039/c9cp06231a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A strong π-donating group like p-NMe2 dramatically changes the excited-state behavior of the green fluorescent protein (GFP) chromophore, such as realizing charge-transfer absorption and executing significant photoinduced intramolecular charge transfer (ICT), which makes a planar first singlet (S1) excited-state minimum disappear and significantly lowers the S1 excited-state potential energy surface (PES), leading to barrierless τ-torsion and φ-torsion excited-state relaxation and eliciting the φ-torsion S1 excited-state minimum. This finding is critical since a strong π-donating group like p-NMe2 may do the same things to other fluorophores.
Collapse
Affiliation(s)
- Yi-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan, Republic of China.
| | - Robert Sung
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan, Republic of China.
| | - Kuangsen Sung
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan, Republic of China.
| |
Collapse
|
47
|
Zagorec-Marks W, Foreman MM, Verlet JRR, Weber JM. Cryogenic Ion Spectroscopy of the Green Fluorescent Protein Chromophore in Vacuo. J Phys Chem Lett 2019; 10:7817-7822. [PMID: 31682445 DOI: 10.1021/acs.jpclett.9b02916] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present the spectrum of the S1 ← S0 transition of an anionic model for the chromophore of the green fluorescent protein in vacuo at cryogenic temperatures, showing previously unresolved vibrational features, and resolving the band origin at 20 930 cm-1 (477.8 nm) with unprecedented accuracy. The vibrational spectrum establishes that the molecule is in the Z isomer at low temperature. At increased temperature, the S1 ← S0 band shifts to the red, which we tentatively attribute to emergent population of the E isomer.
Collapse
Affiliation(s)
- Wyatt Zagorec-Marks
- JILA and Department of Chemistry , University of Colorado , Boulder , Colorado 80309-0440 , United States
| | - Madison M Foreman
- JILA and Department of Chemistry , University of Colorado , Boulder , Colorado 80309-0440 , United States
| | - Jan R R Verlet
- Department of Chemistry , Durham University , Durham , DH1 3LE , U.K
| | - J Mathias Weber
- JILA and Department of Chemistry , University of Colorado , Boulder , Colorado 80309-0440 , United States
| |
Collapse
|
48
|
Influence of the First Chromophore-Forming Residue on Photobleaching and Oxidative Photoconversion of EGFP and EYFP. Int J Mol Sci 2019; 20:ijms20205229. [PMID: 31652505 PMCID: PMC6829896 DOI: 10.3390/ijms20205229] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 12/21/2022] Open
Abstract
Enhanced green fluorescent protein (EGFP)—one of the most widely applied genetically encoded fluorescent probes—carries the threonine-tyrosine-glycine (TYG) chromophore. EGFP efficiently undergoes green-to-red oxidative photoconversion (“redding”) with electron acceptors. Enhanced yellow fluorescent protein (EYFP), a close EGFP homologue (five amino acid substitutions), has a glycine-tyrosine-glycine (GYG) chromophore and is much less susceptible to redding, requiring halide ions in addition to the oxidants. In this contribution we aim to clarify the role of the first chromophore-forming amino acid in photoinduced behavior of these fluorescent proteins. To that end, we compared photobleaching and redding kinetics of EGFP, EYFP, and their mutants with reciprocally substituted chromophore residues, EGFP-T65G and EYFP-G65T. Measurements showed that T65G mutation significantly increases EGFP photostability and inhibits its excited-state oxidation efficiency. Remarkably, while EYFP-G65T demonstrated highly increased spectral sensitivity to chloride, it is also able to undergo redding chloride-independently. Atomistic calculations reveal that the GYG chromophore has an increased flexibility, which facilitates radiationless relaxation leading to the reduced fluorescence quantum yield in the T65G mutant. The GYG chromophore also has larger oscillator strength as compared to TYG, which leads to a shorter radiative lifetime (i.e., a faster rate of fluorescence). The faster fluorescence rate partially compensates for the loss of quantum efficiency due to radiationless relaxation. The shorter excited-state lifetime of the GYG chromophore is responsible for its increased photostability and resistance to redding. In EYFP and EYFP-G65T, the chromophore is stabilized by π-stacking with Tyr203, which suppresses its twisting motions relative to EGFP.
Collapse
|
49
|
Lin CY, Romei MG, Oltrogge LM, Mathews II, Boxer SG. Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins. J Am Chem Soc 2019; 141:15250-15265. [PMID: 31450887 DOI: 10.1021/jacs.9b07152] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Green fluorescent proteins (GFPs) have become indispensable imaging and optogenetic tools. Their absorption and emission properties can be optimized for specific applications. Currently, no unified framework exists to comprehensively describe these photophysical properties, namely the absorption maxima, emission maxima, Stokes shifts, vibronic progressions, extinction coefficients, Stark tuning rates, and spontaneous emission rates, especially one that includes the effects of the protein environment. In this work, we study the correlations among these properties from systematically tuned GFP environmental mutants and chromophore variants. Correlation plots reveal monotonic trends, suggesting that all these properties are governed by one underlying factor dependent on the chromophore's environment. By treating the anionic GFP chromophore as a mixed-valence compound existing as a superposition of two resonance forms, we argue that this underlying factor is defined as the difference in energy between the two forms, or the driving force, which is tuned by the environment. We then introduce a Marcus-Hush model with the bond length alternation vibrational mode, treating the GFP absorption band as an intervalence charge transfer band. This model explains all of the observed strong correlations among photophysical properties; related subtopics are extensively discussed in the Supporting Information. Finally, we demonstrate the model's predictive power by utilizing the additivity of the driving force. The model described here elucidates the role of the protein environment in modulating the photophysical properties of the chromophore, providing insights and limitations for designing new GFPs with desired phenotypes. We argue that this model should also be generally applicable to both biological and nonbiological polymethine dyes.
Collapse
Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Matthew G Romei
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Luke M Oltrogge
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Steven G Boxer
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| |
Collapse
|
50
|
Chen YH, Sung R, Sung K. Why does a para-amino group make the green fluorescent protein chromophore non-fluorescent: coherent intramolecular charge transfer reduces the Z/E-photoisomerization barrier. Chem Commun (Camb) 2019; 55:8991-8994. [PMID: 31290874 DOI: 10.1039/c9cc04156g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A para-N-phenyl-amino group significantly increases the fluorescence quantum yield of N-phenyl-4-aminostilbene by the "amino conjugation effect", but, in contrast, a para-amino group in the para-amino analogue (p-ABDI) of the green fluorescent protein (GFP) chromophore makes p-ABDI non-fluorescent because the coherent photo-induced intramolecular charge transfer reduces the barrier of the Z/E-photoisomerization.
Collapse
Affiliation(s)
- Yi-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
| | - Robert Sung
- Faculty of Family Medicine, Northern Ontario School of Medicine, Ontario, Canada
| | - Kuangsen Sung
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
| |
Collapse
|