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Guo Y, Feng M, Kuang Z, Abeywickrama CS, Pang Y, Xia A. Unveiling Solvation Dynamics of Excited and Ground States via Ultrafast Pump-Dump-Probe Spectroscopy. J Phys Chem B 2023; 127:7764-7771. [PMID: 37656037 DOI: 10.1021/acs.jpcb.3c05450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The conventional ultrafast pump-probe spectroscopy has primarily focused on examining the formation and decay of the excited state intermediates, but it is very difficult to detect those intermediates while the formation is slow and dissipation is much fast because of the limited concentration during the intrinsic photocycle. To address this issue, a multipulse ultrafast pump-dump-probe spectroscopy was employed to generate and probe the short-lived ground state intermediates (GSIs) in an electronic push-pull pyrene derivative (EPP). This particular derivative undergoes planarized intramolecular charge transfer (PICT) in the excited state upon initial femtosecond pulse excitation. After applying the dump pulse once the PICT was formed, the blue-shifted transient absorption GSIs with the ground state dynamics of the structure recovery was directly observed. It is found that GSIs undergo slower reorganization than the PICT formation in the excited state of EPP due to the solvation effect with different dipole moments of ground states and excited states. These findings provide a comprehensive understanding of the full photocycle dynamics of both the ground and excited states, shedding light on the presence of hidden ground state behaviors.
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Affiliation(s)
- Yuanyuan Guo
- School of Science, Beijing University of Posts and Telecommunications (BUPT), Beijing 100876, People's Republic of China
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Minjun Feng
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Zhuoran Kuang
- School of Science, Beijing University of Posts and Telecommunications (BUPT), Beijing 100876, People's Republic of China
| | | | - Yi Pang
- Department of Chemistry, University of Akron, Akron, Ohio 44325, United States
| | - Andong Xia
- School of Science, Beijing University of Posts and Telecommunications (BUPT), Beijing 100876, People's Republic of China
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2
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Direct or Indirect ESPT Mechanism in CFP psamFP488? A Theoretical-Computational Investigation. Int J Mol Sci 2022; 23:ijms232415640. [PMID: 36555282 PMCID: PMC9779432 DOI: 10.3390/ijms232415640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/27/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
Fluorescent Proteins are widely studied for their multiple applications in technological and biotechnological fields. Despite this, they continue to represent a challenge in terms of a complete understanding of all the non-equilibrium photo-induced processes that rule their properties. In this context, a theoretical-computational approach can support experimental results in unveiling and understanding the processes taking place after electronic excitation. A non-standard cyan fluorescent protein, psamFP488, is characterized by an absorption maximum that is blue-shifted in comparison to other cyan fluorescent proteins. This protein is characterized by an extended Stokes shift and an ultrafast (170 fs) excited state proton transfer. In this work, a theoretical-computational study, including excited state ab initio dynamics, is performed to help understanding the reaction mechanism and propose new hypotheses on the role of the residues surrounding the chromophore. Our results suggest that the proton transfer could be indirect toward the acceptor (Glu167) and involves other residues surrounding the chromophore, despite the ultrafast kinetics.
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3
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Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine. Nat Commun 2021; 12:3549. [PMID: 34112799 PMCID: PMC8192780 DOI: 10.1038/s41467-021-23932-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/25/2021] [Indexed: 12/15/2022] Open
Abstract
Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.
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Sun T, Li T, Yi K, Gao X. Structure-guided evolution of Green2 toward photostability and quantum yield enhancement by F145Y substitution. Protein Sci 2020; 29:1964-1974. [PMID: 32715541 DOI: 10.1002/pro.3917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 11/10/2022]
Abstract
Quantum yield is a determinant for fluorescent protein (FP) applications and enhancing FP brightness through gene engineering is still a challenge. Green2, our de novo FP synthesized by microfluidic picoarray and cloning, has a significantly lower quantum yield than enhanced green FP, though they have high homology and share the same chromophore. To increase its quantum yield, we introduced an F145Y substitution into Green2 based on rational structural analysis. Y145 significantly increased the quantum yield (0.22 vs. 0.18) and improved the photostability (t1/2 , 73.0 s vs. 46.0 s), but did not affect the excitation and emission spectra. Further structural analysis showed that the F145Y substitution resulted in a significant electrical field change in the immediate environment of the chromophore. The perturbation of electrostatic charge around the chromophore lead to energy barrier changes between the ground and excited states, which resulted in the enhancement of quantum yield and photostability. Our results illustrate a typical example of engineering an FP based solely on fluorescence efficiency optimization and provide novel insights into the rational evolution of FPs.
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Affiliation(s)
- Tingting Sun
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, Shandong, China
| | - Tianpeng Li
- College of City and Architecture Engineering, Zaozhuang University, Zaozhuang, Shandong, China.,School of Environment, Henan Normal University, Xinxiang, Henan, China.,Shandong Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong, China
| | - Ke Yi
- Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Xiaolian Gao
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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5
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Donati G, Petrone A, Caruso P, Rega N. The mechanism of a green fluorescent protein proton shuttle unveiled in the time-resolved frequency domain by excited state ab initio dynamics. Chem Sci 2018; 9:1126-1135. [PMID: 29675157 PMCID: PMC5890789 DOI: 10.1039/c7sc02803b] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/26/2017] [Indexed: 11/21/2022] Open
Abstract
We simulated an excited state proton transfer in green fluorescent protein by excited state ab initio dynamics, and examined the reaction mechanism in both the time and the frequency domain through a multi resolution wavelet analysis. This original approach allowed us, for the first time, to directly compare the trends of photoactivated vibrations to femtosecond stimulated Raman spectroscopy results, and to give an unequivocal interpretation of the role played by low frequency modes in promoting the reaction. We could attribute the main driving force of the reaction to an important photoinduced softening of the ring-ring orientational motion of the chromophore, thus permitting the tightening of the hydrogen bond network and the opening of the reaction pathway. We also found that both the chromophore (in terms of its inter-ring dihedral angle and phenolic C-O and imidazolinone C-N bond distances) and its pocket (in terms of the inter-molecular oxygen's dihedral angle of the chromophore pocket) relaxations are modulated by low frequency (about 120 cm-1) modes involving the oxygen atoms of the network. This is in agreement with the femtosecond Raman spectroscopy findings in the time-frequency domain. Moreover, the rate in proximity to the Franck Condon region involves a picosecond time scale, with a significant influence from fluctuations of nearby hydrogen bonded residues such as His148. This approach opens a new scenario with ab initio simulations as routinely used tools to understand photoreactivity and the results of advanced time resolved spectroscopy techniques.
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Affiliation(s)
- Greta Donati
- Dipartimento di Scienze Chimiche , Università di Napoli 'Federico II' , Complesso Universitario di M.S.Angelo , via Cintia , I-80126 Napoli , Italy . ; Tel: +39 081 674207
| | - Alessio Petrone
- Dipartimento di Scienze Chimiche , Università di Napoli 'Federico II' , Complesso Universitario di M.S.Angelo , via Cintia , I-80126 Napoli , Italy . ; Tel: +39 081 674207
| | - Pasquale Caruso
- Italian Institute of Technology , IIT@CRIB Center for Advanced Biomaterials for Healthcare , Largo Barsanti e Matteucci , I-80125 Napoli , Italy
| | - Nadia Rega
- Dipartimento di Scienze Chimiche , Università di Napoli 'Federico II' , Complesso Universitario di M.S.Angelo , via Cintia , I-80126 Napoli , Italy . ; Tel: +39 081 674207
- Italian Institute of Technology , IIT@CRIB Center for Advanced Biomaterials for Healthcare , Largo Barsanti e Matteucci , I-80125 Napoli , Italy
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Abstract
Channelrhodopsin (ChR) is a key protein of the optogenetic toolkit. C1C2, a functional chimeric protein of Chlamydomonas reinhardtii ChR1 and ChR2, is the only ChR whose crystal structure has been solved, and thus uniquely suitable for structure-based analysis. We report C1C2 photoreaction dynamics with ultrafast transient absorption and multi-pulse spectroscopy combined with target analysis and structure-based hybrid quantum mechanics/molecular mechanics calculations. Two relaxation pathways exist on the excited (S1) state through two conical intersections CI1 and CI2, that are reached via clockwise and counter-clockwise rotations: (i) the C13=C14 isomerization path with 450 fs via CI1 and (ii) a relaxation path to the initial ground state with 2.0 ps and 11 ps via CI2, depending on the hydrogen-bonding network, hence indicating active-site structural heterogeneity. The presence of the additional conical intersection CI2 rationalizes the relatively low quantum yield of photoisomerization (30 ± 3%), reported here. Furthermore, we show the photoreaction dynamics from picoseconds to seconds, characterizing the complete photocycle of C1C2.
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Tachibana SR, Tang L, Wang Y, Zhu L, Liu W, Fang C. Tuning calcium biosensors with a single-site mutation: structural dynamics insights from femtosecond Raman spectroscopy. Phys Chem Chem Phys 2017; 19:7138-7146. [DOI: 10.1039/c6cp08821j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Structural dynamics governing the emission properties of a single-site mutant of fluorescent-protein-based calcium biosensors are elucidated by femtosecond stimulated Raman spectroscopy.
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Affiliation(s)
- Sean R. Tachibana
- Oregon State University
- Department of Chemistry
- 263 Linus Pauling Science Centre (lab)
- Corvallis
- USA
| | - Longteng Tang
- Oregon State University
- Department of Chemistry
- 263 Linus Pauling Science Centre (lab)
- Corvallis
- USA
| | - Yanli Wang
- Oregon State University
- Department of Chemistry
- 263 Linus Pauling Science Centre (lab)
- Corvallis
- USA
| | - Liangdong Zhu
- Oregon State University
- Department of Chemistry
- 263 Linus Pauling Science Centre (lab)
- Corvallis
- USA
| | - Weimin Liu
- Oregon State University
- Department of Chemistry
- 263 Linus Pauling Science Centre (lab)
- Corvallis
- USA
| | - Chong Fang
- Oregon State University
- Department of Chemistry
- 263 Linus Pauling Science Centre (lab)
- Corvallis
- USA
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8
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Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev 2016; 117:758-795. [PMID: 27754659 DOI: 10.1021/acs.chemrev.6b00238] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.
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Affiliation(s)
- Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
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9
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Mori Y, Masuda Y. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Lv X, Yu Y, Zhou M, Hu C, Gao F, Li J, Liu X, Deng K, Zheng P, Gong W, Xia A, Wang J. Ultrafast photoinduced electron transfer in green fluorescent protein bearing a genetically encoded electron acceptor. J Am Chem Soc 2015; 137:7270-3. [PMID: 26020364 DOI: 10.1021/jacs.5b03652] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transfer (ET) is widely used for driving the processes that underlie the chemistry of life. However, our abilities to probe electron transfer mechanisms in proteins and design redox enzymes are limited, due to the lack of methods to site-specifically insert electron acceptors into proteins in vivo. Here we describe the synthesis and genetic incorporation of 4-fluoro-3-nitrophenylalanine (FNO2Phe), which has similar reduction potentials to NAD(P)H and ferredoxin, the most important biological reductants. Through the genetic incorporation of FNO2Phe into green fluorescent protein (GFP) and femtosecond transient absorption measurement, we show that photoinduced electron transfer (PET) from the GFP chromophore to FNO2Phe occurs very fast (within 11 ps), which is comparable to that of the first electron transfer step in photosystem I, from P700* to A0. This genetically encoded, low-reduction potential unnatural amino acid (UAA) can significantly improve our ability to investigate electron transfer mechanisms in complex reductases and facilitate the design of miniature proteins that mimic their functions.
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Affiliation(s)
- Xiaoxuan Lv
- †Laboratory of RNA Biology and Laboratory of Quantum Biophysics, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Yang Yu
- §Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Meng Zhou
- ‡Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Cheng Hu
- †Laboratory of RNA Biology and Laboratory of Quantum Biophysics, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Feng Gao
- †Laboratory of RNA Biology and Laboratory of Quantum Biophysics, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Jiasong Li
- †Laboratory of RNA Biology and Laboratory of Quantum Biophysics, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Xiaohong Liu
- †Laboratory of RNA Biology and Laboratory of Quantum Biophysics, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Kai Deng
- †Laboratory of RNA Biology and Laboratory of Quantum Biophysics, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Peng Zheng
- †Laboratory of RNA Biology and Laboratory of Quantum Biophysics, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Weimin Gong
- †Laboratory of RNA Biology and Laboratory of Quantum Biophysics, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Andong Xia
- ‡Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiangyun Wang
- †Laboratory of RNA Biology and Laboratory of Quantum Biophysics, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
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11
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Kim H, Zou T, Modi C, Dörner K, Grunkemeyer TJ, Chen L, Fromme R, Matz MV, Ozkan SB, Wachter RM. A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins. Structure 2015; 23:34-43. [PMID: 25565105 PMCID: PMC4370283 DOI: 10.1016/j.str.2014.11.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/20/2014] [Accepted: 11/14/2014] [Indexed: 11/19/2022]
Abstract
In proteins, functional divergence involves mutations that modify structure and dynamics. Here we provide experimental evidence for an evolutionary mechanism driven solely by long-range dynamic motions without significant backbone adjustments, catalytic group rearrangements, or changes in subunit assembly. Crystallographic structures were determined for several reconstructed ancestral proteins belonging to a GFP class frequently employed in superresolution microscopy. Their chain flexibility was analyzed using molecular dynamics and perturbation response scanning. The green-to-red photoconvertible phenotype appears to have arisen from a common green ancestor by migration of a knob-like anchoring region away from the active site diagonally across the β barrel fold. The allosterically coupled mutational sites provide active site conformational mobility via epistasis. We propose that light-induced chromophore twisting is enhanced in a reverse-protonated subpopulation, activating internal acid-base chemistry and backbone cleavage to enlarge the chromophore. Dynamics-driven hinge migration may represent a more general platform for the evolution of novel enzyme activities.
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Affiliation(s)
- Hanseong Kim
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Taisong Zou
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Chintan Modi
- Institute for Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
| | - Katerina Dörner
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Timothy J Grunkemeyer
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Liqing Chen
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Mikhail V Matz
- Section of Integrative Biology, The University of Texas, Austin, TX 78712, USA
| | - S Banu Ozkan
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
| | - Rebekka M Wachter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA; Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, AZ 85287, USA.
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