51
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Francés‐Monerris A, Gros PC, Assfeld X, Monari A, Pastore M. Toward Luminescent Iron Complexes: Unravelling the Photophysics by Computing Potential Energy Surfaces. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900100] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Antonio Francés‐Monerris
- Laboratoire de Physique et Chimie Théoriques (LPCT)Université de Lorraine, CNRS 54000 Nancy France
| | - Philippe C. Gros
- Laboratoire Lorrain de Chimie Moléculaire (L2CM)Université de Lorraine, CNRS 54000 Nancy France
| | - Xavier Assfeld
- Laboratoire de Physique et Chimie Théoriques (LPCT)Université de Lorraine, CNRS 54000 Nancy France
| | - Antonio Monari
- Laboratoire de Physique et Chimie Théoriques (LPCT)Université de Lorraine, CNRS 54000 Nancy France
| | - Mariachiara Pastore
- Laboratoire de Physique et Chimie Théoriques (LPCT)Université de Lorraine, CNRS 54000 Nancy France
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52
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Park JW, Al-Saadon R, Strand NE, Shiozaki T. Imaginary Shift in CASPT2 Nuclear Gradient and Derivative Coupling Theory. J Chem Theory Comput 2019; 15:4088-4098. [DOI: 10.1021/acs.jctc.9b00368] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, United States
- Department of Chemistry, Chungbuk National University, Chungdae-ro 1, Cheongju, Chungbuk 28644, Korea
| | - Rachael Al-Saadon
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, United States
| | - Nils E. Strand
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, United States
| | - Toru Shiozaki
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, United States
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53
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Taylor MA, Zhu L, Rozanov ND, Stout KT, Chen C, Fang C. Delayed vibrational modulation of the solvated GFP chromophore into a conical intersection. Phys Chem Chem Phys 2019; 21:9728-9739. [PMID: 31032505 DOI: 10.1039/c9cp01077g] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Green fluorescent protein (GFP) has revolutionized bioimaging and life sciences. Its successes have inspired modification of the chromophore structure and environment to tune emission properties, but outside the protein cage, the chromophore is essentially non-fluorescent. In this study, we employ the tunable femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption (TA) to map the energy dissipation pathways of GFP model chromophore (HBDI) in basic aqueous solution. Strategic tuning of the Raman pump to 550 nm exploits the stimulated emission band to enhance excited state vibrational motions as HBDI navigates the non-equilibrium potential energy landscape to pass through a conical intersection. The time-resolved FSRS uncovers prominent anharmonic couplings between a global out-of-plane bending mode of ∼227 cm-1 and two modes at ∼866 and 1572 cm-1 before HBDI reaches the twisted intramolecular charge transfer (TICT) state on the ∼3 ps time scale. Remarkably, the wavelet transform analysis reveals a ∼500 fs delayed onset of the coupling peaks, in correlation with the emergence of an intermediate charge-separated state en route to the TICT state. This mechanism is corroborated by the altered coupling matrix for the HBDI Raman modes in the 50% (v/v) water-glycerol mixture, and a notable lengthening of the picosecond time constant. The real-time molecular "movie" of the general rotor-like HBDI isomerization reaction following photoexcitation represents a significant advance in comprehending the photochemical reaction pathways of the solvated GFP chromophore, therefore providing a crucial foundation to enable rational design of diverse nanomachines from efficient molecular rotors to bright fluorescent probes.
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Affiliation(s)
- Miles A Taylor
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA.
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54
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Park JW. Single-State Single-Reference and Multistate Multireference Zeroth-Order Hamiltonians in MS-CASPT2 and Conical Intersections. J Chem Theory Comput 2019; 15:3960-3973. [DOI: 10.1021/acs.jctc.9b00067] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Chungbuk National University (CBNU), Cheongju 28644, Korea
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55
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Gao A, Wang M. Volume-conserving photoisomerization of a nonplanar GFP chromophore derivative: Nonadiabatic dynamics simulation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 214:86-94. [PMID: 30769155 DOI: 10.1016/j.saa.2019.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/17/2019] [Accepted: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Nonadiabatic dynamics of a nonplanar green fluorescent protein (GFP) chromophore derivative was examined theoretically by trajectory surface hopping approach at the CASSCF level based on Zhu-Nakamura theory. The geometry optimizations show that there are four ground-state minima and four conical intersections between the ground (S0) and first excited (S1) states. Four S1-state minima were found at a perpendicularly twisted conformation around the imidazolinone-bridged bond. Upon excitation to S1 state, the main decay pathways of four isomers involve different S0/S1 potential energy surface conical intersections. The dominant excited-state relaxation mechanism of this GFP chromophore derivative is the twists of two bridging bonds and the methyl group in the bridge combined with the pyramidalization character of the central carbon atom. Further twists of two bridging bonds and the methyl group occur sequentially in the S0 state. It is worth to mention that the special volume-conserving motion of this molecule is attributed to twists of two bridging bonds in the same direction during the whole photoisomerization processes. The theoretical investigation presented herein provides important insights into the volume-conserving photoisomerization mechanisms of a nonplanar GFP chromophore derivative. We believe that the present work can benefit the design of the photochromic molecule devices in confined media.
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Affiliation(s)
- Aihua Gao
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.
| | - Meishan Wang
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.
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56
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Takaba K, Tai Y, Eki H, Dao HA, Hanazono Y, Hasegawa K, Miki K, Takeda K. Subatomic resolution X-ray structures of green fluorescent protein. IUCRJ 2019; 6:387-400. [PMID: 31098020 PMCID: PMC6503917 DOI: 10.1107/s205225251900246x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/17/2019] [Indexed: 05/06/2023]
Abstract
Green fluorescent protein (GFP) is a light-emitting protein that does not require a prosthetic group for its fluorescent activity. As such, GFP has become indispensable as a molecular tool in molecular biology. Nonetheless, there has been no subatomic elucidation of the GFP structure owing to the structural polymorphism around the chromophore. Here, subatomic resolution X-ray structures of GFP without the structural polymorphism are reported. The positions of H atoms, hydrogen-bonding network patterns and accurate geometric parameters were determined for the two protonated forms. Compared with previously determined crystal structures and theoretically optimized structures, the anionic chromophores of the structures represent the authentic resonance state of GFP. In addition, charge-density analysis based on atoms-in-molecules theory and noncovalent interaction analysis highlight weak but substantial interactions between the chromophore and the protein environment. Considered with the derived chemical indicators, the lone pair-π interactions between the chromophore and Thr62 should play a sufficient role in maintaining the electronic state of the chromophore. These results not only reveal the fine structural features that are critical to understanding the properties of GFP, but also highlight the limitations of current quantum-chemical calculations.
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Affiliation(s)
- Kiyofumi Takaba
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yang Tai
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Haruhiko Eki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hoang-Anh Dao
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuya Hanazono
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuya Hasegawa
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- Correspondence e-mail:
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57
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Nemukhin AV, Grigorenko BL, Khrenova MG, Krylov AI. Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes. J Phys Chem B 2019; 123:6133-6149. [DOI: 10.1021/acs.jpcb.9b00591] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Alexander V. Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Bella L. Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria G. Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Federal Research Center of Biotechnology, Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russian
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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58
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Zhao L, Liu J, Zhou P. Does the wavelength dependent photoisomerization process of the p‑coumaric acid come out from the electronic state dependent pathways? SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 211:203-211. [PMID: 30544011 DOI: 10.1016/j.saa.2018.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Similar to the anion photoactive yellow protein (PYP) chromophore, the neutral form of the PYP chromophore was also found to exhibit a the wavelength-dependent photoisomerization quantum yield. The isomerization quantum yield increases with the increasing excitation energy on the S1 state, while decreases when being excited to the S2 state. Does this wavelength dependent product yield come out from the specific reaction pathways of the S1 and S2 states? This would mean that, the relaxation pathway of the S2 state is distinct from that of the S1 state and does not involve twisting motion. Does it break Kasha's rule by exhibiting a direct transition from the S2 state to the ground state? The underlying mechanism needs further in. In this article, we employed the on-the-fly dynamics simulations and static electronic structure calculations to reveal the deactivation mechanism of the neutral form of the PYP chromophore. Our results indicated that the CC twisting motion dominates the S1 state decay process. In contrast, for the decay process of the S2 state, an ultrafast transition from the S2 to the S1 state through a planar conical intersection is observed, and the excess energy activates a new reaction channel to the ground state characterized by a puckering distortion of the ring. This pathway competes with the photoisomerization channel. No direct transition from S2 to S0 is observed, hence Kasha's rule is valid for this process. Our calcualtions can provide a reasonable explanation of the wavelength-dependent isomerization quantum yield of neutral PYP chromophore, and we hope it can provide theoretical foundations for comparing the effect of protonation state on the dynamcal behaviors of PYP chromophore.
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Affiliation(s)
- Li Zhao
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Jianyong Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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59
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Gudem M, Hazra A. Mechanism of the Chemiluminescent Reaction between Nitric Oxide and Ozone. J Phys Chem A 2019; 123:715-722. [PMID: 30380861 DOI: 10.1021/acs.jpca.8b08812] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The gas phase reaction of nitric oxide with ozone to give chemiluminescence is used extensively for detection of nitrogen oxides. The molecular mechanism of chemiluminescence in this reaction is not known. So far, the only chemiluminescent systems studied in depth are certain cycloperoxides, which emit light following decomposition. Given our understanding of the mechanism of chemiluminescence in those molecules, one would expect by extension that in the NO + O3 reaction the chemiluminescent species (NO2 in this case) is formed in the excited state through a reaction pathway that diverges from the ground state pathway near the transition state. A systematic search for such a pathway leads us to conclude that such a mechanism is unlikely. Instead, our study suggests that chemiluminescence in the NO + O3 reaction is due to emission from the NO2 vibronic states associated with the ground (X̃ 2A1) and first excited (à 2B2) electronic states, which are populated in the nascent NO2 produced in the reaction. The vibronic coupling between the X̃ 2A1 and à 2B2 states of NO2 is due to a conical intersection (CI), which is geometrically and energetically close to the à 2B2 minimum energy geometry and only 1.3 eV higher than ground state NO2. Further, the CI is 1.2 eV lower than the energy of the NO + O3 reactants and therefore thermodynamically accessible following the reaction. An analysis of the product energy distribution indicates that the major fraction of the reaction energy is channeled into the vibrational modes of NO2, sufficient to populate the vibronic states of NO2 around the X̃/à CI. These vibronic states show dipole-allowed emission in a frequency range that is consistent with the observed broad chemiluminescence spectrum.
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Affiliation(s)
- Mahesh Gudem
- Department of Chemistry , Indian Institute of Science Education and Research Pune , Dr. Homi Bhabha Road , Pune 411008 , Maharashtra , India
| | - Anirban Hazra
- Department of Chemistry , Indian Institute of Science Education and Research Pune , Dr. Homi Bhabha Road , Pune 411008 , Maharashtra , India
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60
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Affiliation(s)
- Alice Henley
- Department of Chemistry, University College London, London, UK
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61
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Schramm S, Weiß D. Fluorescent heterocycles: Recent trends and new developments. ADVANCES IN HETEROCYCLIC CHEMISTRY 2019. [DOI: 10.1016/bs.aihch.2018.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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62
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Collado S, Pueyo A, Baudequin C, Bischoff L, Jiménez AI, Cativiela C, Hoarau C, Urriolabeitia EP. Orthopalladation of GFP-Like Fluorophores Through C-H Bond Activation: Scope and Photophysical Properties. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800966] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Sandra Collado
- INSA Rouen, CNRS, COBRA; Normandie Univ, UNIROUEN; 1 rue Tesnière 76821 Mont Saint Aignan France
| | - Alejandro Pueyo
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); CSIC-Universidad de Zaragoza; Pedro Cerbuna 12 50009 Zaragoza Spain
| | - Christine Baudequin
- INSA Rouen, CNRS, COBRA; Normandie Univ, UNIROUEN; 1 rue Tesnière 76821 Mont Saint Aignan France
| | - Laurent Bischoff
- INSA Rouen, CNRS, COBRA; Normandie Univ, UNIROUEN; 1 rue Tesnière 76821 Mont Saint Aignan France
| | - Ana Isabel Jiménez
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); CSIC-Universidad de Zaragoza; Pedro Cerbuna 12 50009 Zaragoza Spain
| | - Carlos Cativiela
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); CSIC-Universidad de Zaragoza; Pedro Cerbuna 12 50009 Zaragoza Spain
| | - Christophe Hoarau
- INSA Rouen, CNRS, COBRA; Normandie Univ, UNIROUEN; 1 rue Tesnière 76821 Mont Saint Aignan France
| | - Esteban P. Urriolabeitia
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); CSIC-Universidad de Zaragoza; Pedro Cerbuna 12 50009 Zaragoza Spain
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63
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Ai Y, Xing J, Zhang A, Zhao C, Liu Y, Xie B, Chen W, Cui G, Lu Z, Wang X. Computational Study on the Excited-State Decay of 5-Methylcytosine and 5-Hydroxymethylcytosine: The Common Form of DNA Methylation and Its Oxidation Product. J Phys Chem B 2018; 122:10424-10434. [DOI: 10.1021/acs.jpcb.8b07830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | | | | | - Binbin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | | | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | | | - Xiangke Wang
- NAAM Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, School for Radiological and Interdisciplinary Sciences, Soochow University, Suzhou 215123, P. R. China
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64
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Gao A, Wang M, Ding J. Ultrafasttrans-cisphotoisomerization of the neutral chromophore in green fluorescent proteins: Surface-hopping dynamics simulation. J Chem Phys 2018; 149:074304. [DOI: 10.1063/1.5043246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Aihua Gao
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Meishan Wang
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Junxia Ding
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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65
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Storti B, Margheritis E, Abbandonato G, Domenichini G, Dreier J, Testa I, Garau G, Nifosì R, Bizzarri R. Role of Gln222 in Photoswitching of Aequorea Fluorescent Proteins: A Twisting and H-Bonding Affair? ACS Chem Biol 2018; 13:2082-2093. [PMID: 29878744 DOI: 10.1021/acschembio.8b00267] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Reversibly photoswitchable fluorescent proteins (RSFPs) admirably combine the genetic encoding of fluorescence with the ability to repeatedly toggle between a bright and dark state, adding a new temporal dimension to the fluorescence signal. Accordingly, in recent years RSFPs have paved the way to novel applications in cell imaging that rely on their reversible photoswitching, including many super-resolution techniques such as F-PALM, RESOLFT, and SOFI that provide nanoscale pictures of the living matter. Yet many RSFPs have been engineered by a rational approach only to a limited extent, in the absence of clear structure-property relationships that in most cases make anecdotic the emergence of the photoswitching. We reported [ Bizzarri et al. J. Am Chem Soc. 2010 , 102 , 85 ] how the E222Q replacement is a single photoswitching mutation, since it restores the intrinsic cis-trans photoisomerization properties of the chromophore in otherwise nonswitchable Aequorea proteins of different color and mutation pattern (Q-RSFPs). We here investigate the subtle role of Q222 on the excited-state photophysics of the two simplest Q-RSFPs by a combined experimental and theoretical approach, using their nonswitchable anacestor EGFP as benchmark. Our findings link indissolubly photoswitching and Q222 presence, by a simple yet elegant scenario: largely twisted chromophore structures around the double bond (including hula-twist configurations) are uniquely stabilized by Q222 via H-bonds. Likely, these H-bonds subtly modulate the electronic properties of the chromophore, enabling the conical intersection that connects the excited cis to ground trans chromophore. Thus, Q222 belongs to a restricted family of single mutations that change dramatically the functional phenotype of a protein. The capability to distinguish quantitatively T65S/E222Q EGFP ("WildQ", wQ) from the spectrally identical EGFP by quantitative Optical Lock-In Detection (qOLID) witnesses the relevance of this mutation for cell imaging.
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Affiliation(s)
- Barbara Storti
- NEST, Scuola Normale Superiore and NANO-CNR, 56127 Pisa, Italy
| | - Eleonora Margheritis
- Center for Nanotechnology Innovation @ NEST, Istituto Italiano di Tecnologia, 56127 Pisa, Italy
| | | | | | - Jes Dreier
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
| | - Gianpiero Garau
- Center for Nanotechnology Innovation @ NEST, Istituto Italiano di Tecnologia, 56127 Pisa, Italy
| | - Riccardo Nifosì
- NEST, Scuola Normale Superiore and NANO-CNR, 56127 Pisa, Italy
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66
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Zaitseva SO, Golodukhina SV, Baleeva NS, Levina EA, Smirnov AY, Zagudaylova MB, Baranov MS. Azidoacetic Acid Amides in the Synthesis of Substituted Arylidene‐1‐
H
‐imidazol‐5‐(4
H
)‐ones. ChemistrySelect 2018. [DOI: 10.1002/slct.201801349] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Snizhana O. Zaitseva
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Svetlana V. Golodukhina
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Nadezhda S. Baleeva
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Evgenia A. Levina
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander Yu. Smirnov
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Marina B. Zagudaylova
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1 117997 Moscow Russia
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67
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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68
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Chen YH, Sung R, Sung K. Insights into Excited State Intramolecular Proton Transfer: An Alternative Model for Excited State Proton Transfer of Green Fluorescence Protein. J Phys Chem A 2018; 122:5931-5944. [DOI: 10.1021/acs.jpca.8b01799] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yi-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Robert Sung
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Kuangsen Sung
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
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69
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Snyder JW, Fales BS, Hohenstein EG, Levine BG, Martínez TJ. A direct-compatible formulation of the coupled perturbed complete active space self-consistent field equations on graphical processing units. J Chem Phys 2018; 146:174113. [PMID: 28477593 DOI: 10.1063/1.4979844] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We recently developed an algorithm to compute response properties for the state-averaged complete active space self-consistent field method (SA-CASSCF) that capitalized on sparsity in the atomic orbital basis. Our original algorithm was limited to treating small to moderate sized active spaces, but the recent development of graphical processing unit (GPU) based direct-configuration interaction algorithms provides an opportunity to extend this to large active spaces. We present here a direct-compatible version of the coupled perturbed equations, enabling us to compute response properties for systems treated with arbitrary active spaces (subject to available memory and computation time). This work demonstrates that the computationally demanding portions of the SA-CASSCF method can be formulated in terms of seven fundamental operations, including Coulomb and exchange matrix builds and their derivatives, as well as, generalized one- and two-particle density matrix and σ vector constructions. As in our previous work, this algorithm exhibits low computational scaling and is accelerated by the use of GPUs, making possible optimizations and nonadiabatic dynamics on systems with O(1000) basis functions and O(100) atoms, respectively.
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Affiliation(s)
- James W Snyder
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
| | - B Scott Fales
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Edward G Hohenstein
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, USA
| | - Benjamin G Levine
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Todd J Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
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70
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Smyrnova D, Marín MDC, Olivucci M, Ceulemans A. Systematic Excited State Studies of Reversibly Switchable Fluorescent Proteins. J Chem Theory Comput 2018; 14:3163-3172. [PMID: 29772175 DOI: 10.1021/acs.jctc.8b00050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The reversibly switchable fluorescent proteins Dronpa, rsFastLime, rsKame, Padron, and bsDronpa feature the same chromophore but display a 40 nm variation in absorption maxima and an only 18 nm variation in emission maxima. In the present contribution, we employ QM/MM models to investigate the mechanism of such remarkably different spectral variations, which are caused by just a few amino acid replacements. We show that the models, which are based on CASPT2//CASSCF level of QM theory, reproduce the observed trends in absorption maxima, with only a 3.5 kcal/mol blue-shift, and in emission maxima, with an even smaller 1.5 kcal/mol blue-shift with respect to the observed quantities. In order to explain the variations across the series, we look at the chromophore's electronic structure change during absorption and emission. Such analysis indicates that a change in charge-transfer character, which is more pronounced during absorption, triggers a cascade of hydrogen-bond-network rearrangements, suggesting preparation to an isomerization event. We also show how the contribution of Arg 89 and Arg 64 residues to the chromophore conformational changes correlate with the spectral variations in absorption and emission. Furthermore, we describe how the conical intersection stability is related to the protein's photophysical properties. While for the Dronpa, rsFastLime, and rsKame triad, the stability correlates with the photoswitching speed, this does not happen for bsDronpa and Padron, suggesting a less obvious photoisomerization mechanism.
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Affiliation(s)
- Daryna Smyrnova
- Quantum Chemistry and Physical Chemistry Division, Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Heverlee , Belgium
| | - María Del Carmen Marín
- Department of Biotechnology, Chemistry, and Pharmacy , Universitá di Siena , via A. Moro 2 , I-53100 Siena , Italy.,Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry, and Pharmacy , Universitá di Siena , via A. Moro 2 , I-53100 Siena , Italy.,Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - Arnout Ceulemans
- Quantum Chemistry and Physical Chemistry Division, Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Heverlee , Belgium
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71
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Langeland J, Kjær C, Andersen LH, Brøndsted Nielsen S. The Effect of an Electric Field on the Spectroscopic Properties of the Isolated Green Fluorescent Protein Chromophore Anion. Chemphyschem 2018; 19:1686-1690. [DOI: 10.1002/cphc.201800225] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Jeppe Langeland
- Department of Physics and AstronomyAarhus University Denmark
| | - Christina Kjær
- Department of Physics and AstronomyAarhus University Denmark
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72
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Chen F, Zhao X, Liang W. One- and two-photon absorption spectra of the yellow fluorescent protein citrine: effects of intramolecular electron-vibrational coupling and intermolecular interactions. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1426130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Fasheng Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, China
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xinyi Zhao
- Department of Science and Technology for Inspection, Xiamen Huaxia University, Xiamen, China
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, China
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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73
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Yang M, Zhang T, Xue J, Zheng X. Ab Initio Study of Decay Dynamics of 1-Nitronaphthalene Initiated from the S 2(ππ* + n NOπ*) State. J Phys Chem A 2018; 122:2732-2738. [PMID: 29488758 DOI: 10.1021/acs.jpca.7b11003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Irradiation of nitro-PAHs in solution at ambient conditions leads to formation of its lowest excited triplet, dissociation intermediates nitrogen oxide (NO•) and aryloxy radical (Ar-O•). Experimental and theoretical studies demonstrated that Franck-Condon excited singlet state SFC(ππ*) to a receiver, higher-energy triplet state Tn(nπ*) controlled the ultrafast population of the triplet state and, hence, the slight fluorescence yield of nitronaphthalenes. However, the detailed information about the curve-crossings of potential energy surfaces and the major channels for forming T1 species and Ar-O• radical were unclear. Here, by using the CASSCF//CASPT2 method, an efficient decay channel is revealed: S2-FC-1NN → S2-MIN-1NN or S2T3-MIN-1NN → T3-MIN-1NN or T3T2-MIN-1NN→ T2-MIN-1NN or T2T1-MIN-1NN → T1-MIN-1NN. This explains the high yield of T1-1NN species and minor yield of Ar-O• and NO• radicals. The calculation results suggest the bifurcation processes take place predominantly after the internal conversion to the T1-1NN state via T2T1-MIN-1NN, one leads to T1-MIN-1NN, while the other to T1-MIN-ISO to produce Ar-O• and NO• radicals.
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Affiliation(s)
- Meng Yang
- Department of Chemistry , Zhejiang Sci-Tech University , Hangzhou 310018 , P. R. China
| | - Tengshuo Zhang
- Department of Chemistry , Zhejiang Sci-Tech University , Hangzhou 310018 , P. R. China
| | - Jiadan Xue
- Department of Chemistry , Zhejiang Sci-Tech University , Hangzhou 310018 , P. R. China
| | - Xuming Zheng
- Department of Chemistry , Zhejiang Sci-Tech University , Hangzhou 310018 , P. R. China
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74
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Xing J, Ai Y, Liu Y, Du J, Chen W, Lu Z, Wang X. Theoretical Studies on the Photophysics and Photochemistry of 5-Formylcytosine and 5-Carboxylcytosine: The Oxidative Products of Epigenetic Modification of Cytosine in DNA. J Phys Chem B 2018; 122:2704-2714. [DOI: 10.1021/acs.jpcb.7b10218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jinlu Xing
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
- School of Mathematics and Physical Science, North China Electric Power University, Beijing 102206, P. R. China
| | - Yuejie Ai
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
| | - Yang Liu
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
| | - Jia Du
- School of Mathematics and Physical Science, North China Electric Power University, Beijing 102206, P. R. China
| | - Weiqiang Chen
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
- School of Mathematics and Physical Science, North China Electric Power University, Beijing 102206, P. R. China
| | - Zhanhui Lu
- School of Mathematics and Physical Science, North China Electric Power University, Beijing 102206, P. R. China
| | - Xiangke Wang
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
- NAAM Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, School for Radiological and Interdisciplinary Sciences, Soochow University, Suzhou 215123, P. R. China
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75
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Simine L, Lammert H, Sun L, Onuchic JN, Rossky PJ. Fluorescent Proteins Detect Host Structural Rearrangements via Electrostatic Mechanism. J Am Chem Soc 2018; 140:1203-1206. [PMID: 29328673 DOI: 10.1021/jacs.7b10851] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The rational design of genetically encoded fluorescent biosensors, which can detect rearrangements of target proteins via interdomain allostery, is hindered by the absence of mechanistic understanding of the underlying photophysics. Here, we focus on the modulation of fluorescence by mechanical perturbation in a popular biological probe: enhanced Green Fluorescent Protein (eGFP). Using a combination of molecular dynamics (MD) simulations and quantum chemistry, and a set of physically motivated assumptions, we construct a map of fluorescence quantum yield as a function of a 2D electric field imposed by the protein environment on the fluorophore. This map is transferable between Tsien's Class 2 GFP's, and it allows one to estimate the shifts in fluorescence intensity due to mechanical perturbations directly from MD simulations. We use it in combination with steered MD simulations to put forward a hypothesis for the mechanism of a genetically encoded voltage probe (ArcLight) whose mechanism is currently under debate.
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Affiliation(s)
- Lena Simine
- Departments of Chemistry, and ‡Physics, and §the Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States
| | - Heiko Lammert
- Departments of Chemistry, and ‡Physics, and §the Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States
| | - Li Sun
- Departments of Chemistry, and ‡Physics, and §the Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States
| | - José N Onuchic
- Departments of Chemistry, and ‡Physics, and §the Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States
| | - Peter J Rossky
- Departments of Chemistry, and ‡Physics, and §the Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States
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76
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Conyard J, Heisler IA, Chan Y, Bulman Page PC, Meech SR, Blancafort L. A new twist in the photophysics of the GFP chromophore: a volume-conserving molecular torsion couple. Chem Sci 2018; 9:1803-1812. [PMID: 29675225 PMCID: PMC5892128 DOI: 10.1039/c7sc04091a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/30/2017] [Indexed: 01/19/2023] Open
Abstract
Dynamics of a nonplanar GFP chromophore are studied experimentally and theoretically. Coupled torsional motion is responsible for the ultrafast decay.
The simple structure of the chromophore of the green fluorescent protein (GFP), a phenol and an imidazolone ring linked by a methyne bridge, supports an exceptionally diverse range of excited state phenomena. Here we describe experimentally and theoretically the photochemistry of a novel sterically crowded nonplanar derivative of the GFP chromophore. It undergoes an excited state isomerization reaction accompanied by an exceptionally fast (sub 100 fs) excited state decay. The decay dynamics are essentially independent of solvent polarity and viscosity. Excited state structural dynamics are probed by high level quantum chemical calculations revealing that the fast decay is due to a conical intersection characterized by a twist of the rings and pyramidalization of the methyne bridge carbon. The intersection can be accessed without a barrier from the pre-twisted Franck–Condon structure, and the lack of viscosity dependence is due to the fact that the rings twist in the same direction, giving rise to a volume-conserving decay coordinate. Moreover, the rotation of the phenyl, methyl and imidazolone groups is coupled in the sterically crowded structure, with the methyl group translating the rotation of one ring to the next. As a consequence, the excited state dynamics can be viewed as a torsional couple, where the absorbed photon energy leads to conversion of the out-of-plane orientation from one ring to the other in a volume conserving fashion. A similar modification of the range of methyne dyes may provide a new family of devices for molecular machines, specifically torsional couples.
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Affiliation(s)
- Jamie Conyard
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Ismael A Heisler
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Yohan Chan
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Philip C Bulman Page
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Stephen R Meech
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , UK .
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi , Departament de Química , Facultat de Ciències , Universitat de Girona , C/ M. A. Capmany 69 , 17003 Girona , Spain .
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77
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Guo WW, Fang YG, Fang Q, Cui GL. Mechanistic Insights into the Photophysics of Ortho-hydroxyl GFP Core Chromophores. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1709179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Wei-wei Guo
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ye-guang Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Gang-long Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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78
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Khrenova MG, Polyakov IV, Grigorenko BL, Krylov AI, Nemukhin AV. Improving the Design of the Triple-Decker Motif in Red Fluorescent Proteins. J Phys Chem B 2017; 121:10602-10609. [PMID: 29090574 DOI: 10.1021/acs.jpcb.7b07517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We characterize computationally a red fluorescent protein (RFP) with the chromophore (Chro) sandwiched between two aromatic tyrosine rings in a triple-decker motif. According to the original proposal [ J. Phys. Chem. Lett. 2013 , 4 , 1743 ], such a tyrosine-chromophore-tyrosine π-stacked construct can be accommodated in the green fluorescent protein (GFP). A recent study [ ACS Chem. Biol. 2016 , 11 , 508 ] attempted to realize the triple-decker motif and obtained an RFP variant called mRojoA-VYGV with two tyrosine residues surrounding the chromophore. The crystal structure showed that only a tyrosine-chromophore pair was involved in π-stacking, whereas the second tyrosine was oriented perpendicularly, edge-to-face with respect to the chromophore. We propose a more promising variant of this RFP with a perfect triple-decker unit achieved by introducing additional mutations in mRojoA-VYGV. The structures and optical properties of model proteins based on the structures of mCherry and mRojoA are characterized computationally by QM(DFT)/MM. The electronic transitions in the protein-bound chromophores are computed by high-level quantum chemical methods. According to our calculations, the triple-decker chromophore unit in the new RFP variant is stable within the protein and its optical bands are red-shifted with respect to the parent mCherry and mRojoA species.
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Affiliation(s)
- Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University , Moscow, 119991, Russia
| | - Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University , Moscow, 119991, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, 119991, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, 119991, Russia
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79
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Sung R, Sung K. TICT excited states of o
- and p
-N
,N
-dimethylamino analogues of GFP chromophore. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3791] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Robert Sung
- Department of Chemistry; National Cheng Kung University; Tainan Taiwan
| | - Kuangsen Sung
- Department of Chemistry; National Cheng Kung University; Tainan Taiwan
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80
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Kajita K, Nakano H, Sato H. A theoretical study on the optical absorption of green fluorescent protein chromophore in solutions. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1315769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ken Kajita
- Department of Molecular Engineering, Kyoto University, Kyoto, Japan
| | - Hiroshi Nakano
- Department of Molecular Engineering, Kyoto University, Kyoto, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto, Japan
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81
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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82
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Feng G, Luo C, Yi H, Yuan L, Lin B, Luo X, Hu X, Wang H, Lei C, Nie Z, Yao S. DNA mimics of red fluorescent proteins (RFP) based on G-quadruplex-confined synthetic RFP chromophores. Nucleic Acids Res 2017; 45:10380-10392. [PMID: 28981852 PMCID: PMC5737560 DOI: 10.1093/nar/gkx803] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/26/2017] [Accepted: 08/31/2017] [Indexed: 12/29/2022] Open
Abstract
Red fluorescent proteins (RFPs) have emerged as valuable biological markers for biomolecule imaging in living systems. Developing artificial fluorogenic systems that mimic RFPs remains an unmet challenge. Here, we describe the design and synthesis of six new chromophores analogous to the chromophores in RFPs. We demonstrate, for the first time, that encapsulating RFP chromophore analogues in canonical DNA G-quadruplexes (G4) can activate bright fluorescence spanning red and far-red spectral regions (Em = 583-668 nm) that nearly match the entire RFP palette. Theoretical calculations and molecular dynamics simulations reveal that DNA G4 greatly restricts radiationless deactivation of chromophores induced by a twisted intramolecular charge transfer (TICT). These DNA mimics of RFP exhibit attractive photophysical properties comparable or superior to natural RFPs, including high quantum yield, large Stokes shifts, excellent anti-photobleaching properties, and two-photon fluorescence. Moreover, these RFP chromophore analogues are a novel and distinctive type of topology-selective G4 probe specific to parallel G4 conformation. The DNA mimics of RFP have been further exploited for imaging of target proteins. Using cancer-specific cell membrane biomarkers as targets, long-term real-time monitoring in single live cell and two-photon fluorescence imaging in tissue sections have been achieved without the need for genetic coding.
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Affiliation(s)
- Guangfu Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Chao Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Haibo Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Bin Lin
- Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiaoxiao Hu
- Molecular Science and Biomedicine laboratory, Hunan University, Changsha 410082, PR China
| | - Honghui Wang
- College of Biology, Hunan University, Changsha 410082, PR China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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83
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Merabti KE, Azizi S, Ridard J, Lévy B, Demachy I. π-Stacking interactions in YFP, quantum mechanics and force field evaluations in the S 0 and S 1 states. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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84
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Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Toru Shiozaki
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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85
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Pirojsirikul T, Götz AW, Weare J, Walker RC, Kowalski K, Valiev M. Combined quantum-mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution. J Comput Chem 2017; 38:1631-1639. [PMID: 28470855 DOI: 10.1002/jcc.24804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/19/2017] [Indexed: 11/07/2022]
Abstract
Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well-known codes-NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore. Using a systematic approach, which involves comparison of gas phase and aqueous phase results for different protonation states and conformations, we resolve existing uncertainties regarding the theoretical interpretation of experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts of the absorption spectra, but the magnitude of the effect is sensitive to both protonation state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likely coming from the phenol protonated form. Our results also show that the high level electron correlated method is essential for a proper description of excited states of GFP. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Teerapong Pirojsirikul
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - John Weare
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - Ross C Walker
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093.,GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania, 19426
| | - Karol Kowalski
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P. O. Box 999, Richland, Washington, 99352
| | - Marat Valiev
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P. O. Box 999, Richland, Washington, 99352
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86
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Svendsen A, Kiefer HV, Pedersen HB, Bochenkova AV, Andersen LH. Origin of the Intrinsic Fluorescence of the Green Fluorescent Protein. J Am Chem Soc 2017; 139:8766-8771. [PMID: 28595004 DOI: 10.1021/jacs.7b04987] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Green fluorescent protein, GFP, has revolutionized biology, due to its use in bioimaging. It is widely accepted that the protein environment makes its chromophore fluoresce, whereas the fluorescence is completely lost when the native chromophore is taken out of GFP. By the use of a new femtosecond pump-probe scheme, based on time-resolved action spectroscopy, we demonstrate that the isolated deprotonated GFP chromophore can be trapped in the first excited state when cooled to 100 K. The trapping is shown to last for 1.2 ns, which is long enough to establish conditions for fluorescence and consistent with calculated trapping barriers in the electronically excited state. Thus, GFP fluorescence is traced back to an intrinsic chromophore property, and by improving excited-state trapping, protein interactions enhance the molecular fluorescence.
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Affiliation(s)
- Annette Svendsen
- Department of Physics and Astronomy, Aarhus University , DK-8000 Aarhus C, Denmark
| | - Hjalte V Kiefer
- Department of Physics and Astronomy, Aarhus University , DK-8000 Aarhus C, Denmark
| | - Henrik B Pedersen
- Department of Physics and Astronomy, Aarhus University , DK-8000 Aarhus C, Denmark
| | | | - Lars H Andersen
- Department of Physics and Astronomy, Aarhus University , DK-8000 Aarhus C, Denmark
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87
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Park JW, Shiozaki T. Analytical Derivative Coupling for Multistate CASPT2 Theory. J Chem Theory Comput 2017; 13:2561-2570. [DOI: 10.1021/acs.jctc.7b00018] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Toru Shiozaki
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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88
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Georgieva I, Aquino AJA, Trendafilova N, Lischka H. High-level Ab Initio Absorption Spectra Simulations of Neutral, Anionic and Neutral+ Chromophore of Green Fluorescence Protein Chromophore Models in Gas Phase and Solution. Photochem Photobiol 2017; 93:1356-1367. [PMID: 28436037 DOI: 10.1111/php.12778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/29/2017] [Indexed: 12/01/2022]
Abstract
Semiclassical ab initio simulations of the absorption spectra of neutral and anionic p-hydroxybenzylidene-2,3-dimethylimidazolinone (p-HBDI), a model chromophore of green fluorescent protein (GFP) and of a positively charged neutral (N+)-HBDI chromophore model, were performed in gas phase with the resolution-of-identity algebraic diagrammatic construction through second-order (RI-ADC(2)) method. The calculated absorption spectra in gas phase are composed of one band centered at 3.51 eV (HBDI), 2.50 eV (HBDI- ) and 3.02 eV ((N+)-HBDI) owing to the absorption of the first 1 ππ* transition. Band maxima are redshifted by ~0.1 eV with respect to the corresponding vertical energies. The COSMO-RI-ADC(2) calculations of the first vertical excitation energy of HBDI, HBDI- and (N+)-HBDI forms in polar solution including microsolvation simulate the observed solvent redshift for neutral HBDI and the solvent blueshift of the HBDI- and (N+)-HBDI forms. The state-specific solvation approach applied to TDDFT calculations reproduced the experimental solvent shifts for the three HBDI forms, demonstrating a more accurate theoretical description as compared to the linear-response TDDFT approach.
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Affiliation(s)
- Ivelina Georgieva
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Adelia J A Aquino
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX.,School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Natasha Trendafilova
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Hans Lischka
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX.,School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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89
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Lin CY, Both J, Do K, Boxer SG. Mechanism and bottlenecks in strand photodissociation of split green fluorescent proteins (GFPs). Proc Natl Acad Sci U S A 2017; 114:E2146-E2155. [PMID: 28242710 PMCID: PMC5358378 DOI: 10.1073/pnas.1618087114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Split GFPs have been widely applied for monitoring protein-protein interactions by expressing GFPs as two or more constituent parts linked to separate proteins that only fluoresce on complementing with one another. Although this complementation is typically irreversible, it has been shown previously that light accelerates dissociation of a noncovalently attached β-strand from a circularly permuted split GFP, allowing the interaction to be reversible. Reversible complementation is desirable, but photodissociation has too low of an efficiency (quantum yield <1%) to be useful as an optogenetic tool. Understanding the physical origins of this low efficiency can provide strategies to improve it. We elucidated the mechanism of strand photodissociation by measuring the dependence of its rate on light intensity and point mutations. The results show that strand photodissociation is a two-step process involving light-activated cis-trans isomerization of the chromophore followed by light-independent strand dissociation. The dependence of the rate on temperature was then used to establish a potential energy surface (PES) diagram along the photodissociation reaction coordinate. The resulting energetics-function model reveals the rate-limiting process to be the transition from the electronic excited-state to the ground-state PES accompanying cis-trans isomerization. Comparisons between split GFPs and other photosensory proteins, like photoactive yellow protein and rhodopsin, provide potential strategies for improving the photodissociation quantum yield.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
| | - Johan Both
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
| | - Keunbong Do
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
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90
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Barnett LM, Hughes TE, Drobizhev M. Deciphering the molecular mechanism responsible for GCaMP6m's Ca2+-dependent change in fluorescence. PLoS One 2017; 12:e0170934. [PMID: 28182677 PMCID: PMC5300113 DOI: 10.1371/journal.pone.0170934] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/12/2017] [Indexed: 11/19/2022] Open
Abstract
The goal of this work is to determine how GCaMP6m's fluorescence is altered in response to Ca2+-binding. Our detailed spectroscopic study reveals the simplest explanation for how GCaMP6m changes fluorescence in response to Ca2+ is with a four-state model, in which a Ca2+-dependent change of the chromophore protonation state, due to a shift in pKa, is the predominant factor. The pKa shift is quantitatively explained by a change in electrostatic potential around the chromophore due to the conformational changes that occur in the protein when calmodulin binds Ca2+ and interacts with the M13 peptide. The absolute pKa values for the Ca2+-free and Ca2+-saturated states of GCaMP6m are critical to its high signal-to-noise ratio. This mechanism has important implications for further improvements to GCaMP6m and potentially for other similarly designed biosensors.
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Affiliation(s)
- Lauren M. Barnett
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States
| | - Thomas E. Hughes
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States
| | - Mikhail Drobizhev
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States
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91
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McLaughlin C, Assmann M, Parkes MA, Woodhouse JL, Lewin R, Hailes HC, Worth GA, Fielding HH. ortho and para chromophores of green fluorescent protein: controlling electron emission and internal conversion. Chem Sci 2017; 8:1621-1630. [PMID: 29780449 PMCID: PMC5933426 DOI: 10.1039/c6sc03833f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/05/2016] [Indexed: 12/22/2022] Open
Abstract
Green fluorescent protein (GFP) continues to play an important role in the biological and biochemical sciences as an efficient fluorescent probe and is also known to undergo light-induced redox transformations. Here, we employ photoelectron spectroscopy and quantum chemistry calculations to investigate how the phenoxide moiety controls the competition between electron emission and internal conversion in the isolated GFP chromophore anion, following photoexcitation with ultraviolet light in the range 400-230 nm. We find that moving the phenoxide group from the para position to the ortho position enhances internal conversion back to the ground electronic state but that adding an additional OH group to the para chromophore, at the ortho position, impedes internal conversion. Guided by quantum chemistry calculations, we interpret these observations in terms of torsions around the C-C-C bridge being enhanced by electrostatic repulsions or impeded by the formation of a hydrogen-bonded seven-membered ring. We also find that moving the phenoxide group from the para position to the ortho position reduces the energy required for detachment processes, whereas adding an additional OH group to the para chromophore at the ortho position increases the energy required for detachment processes. These results have potential applications in tuning light-induced redox processes of this biologically and technologically important fluorescent protein.
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Affiliation(s)
- Conor McLaughlin
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Mariana Assmann
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Michael A Parkes
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Joanne L Woodhouse
- 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 .
| | - Helen C Hailes
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Graham A Worth
- 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 .
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92
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Xu L, Ren N, Pang J, Deng H, Zhu X, Sun M, Yan D. Fluorescent and “breathable” CO2 responsive vesicles inspired from green fluorescent protein. Polym Chem 2017. [DOI: 10.1039/c7py00963a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CO2 responsive fluorescent vesicles from a GFP chromophore labeled block-copolymer could change their size and fluorescence to mimic jellyfish breathing.
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Affiliation(s)
- Lei Xu
- School of Chemistry and Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Ning Ren
- School of Chemistry and Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Ji Pang
- School of Chemistry and Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Hongping Deng
- School of Chemistry and Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Mo Sun
- School of Chemistry and Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Deyue Yan
- School of Chemistry and Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- China
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93
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Smyrnova D, Zinovjev K, Tuñón I, Ceulemans A. Thermal Isomerization Mechanism in Dronpa and Its Mutants. J Phys Chem B 2016; 120:12820-12825. [PMID: 28002952 DOI: 10.1021/acs.jpcb.6b10859] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photoswitching speed of the reversibly switchable fluorescent proteins (RSFPs) from the family of green fluorescent proteins (GFPs) changes upon mutation which is of direct importance for various high-resolution techniques. Dronpa is one of the most used RSFPs. Its point mutants rsFastLime (Dronpa V157G) and rsKame (Dronpa V157L) exhibit a striking difference in their photoswitching speed. Here the QM/MM on-the-fly string method is used in order to explore the details of the thermal isomerization mechanism. The four principal ways in which isomerization may occur have been scrutinized for each of the three proteins. It has been shown that thermal isomerization occurs via a one-bond-flip mechanism in all three proteins, although, in rsKame, where the chromophore is constrained more, the activation free energy difference between hula-twist and one-bond-flip is significantly smaller. Functional mode analysis has been applied to examine the motions of the amino acids during the isomerization. It clearly identifies the importance of Val/Leu 157 as well as the amino acids in the α-helix during the isomerization.
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Affiliation(s)
- Daryna Smyrnova
- Quantum Chemistry and Physical Chemistry Division, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Kirill Zinovjev
- Departament de Química Física, Universitat de València , 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València , 46100 Burjassot, Spain
| | - Arnout Ceulemans
- Quantum Chemistry and Physical Chemistry Division, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Heverlee, Belgium
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94
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Peccati F, Pantaleone S, Solans-Monfort X, Sodupe M. Fluorescent Markers for Amyloid-β Detection: Computational Insights. Isr J Chem 2016. [DOI: 10.1002/ijch.201600114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Francesca Peccati
- Departament de Química; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
| | - Stefano Pantaleone
- Departament de Química; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
| | | | - Mariona Sodupe
- Departament de Química; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
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95
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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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96
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Li X, Chung LW, Li G. Multiscale Simulations on Spectral Tuning and the Photoisomerization Mechanism in Fluorescent RNA Spinach. J Chem Theory Comput 2016; 12:5453-5464. [PMID: 27685000 DOI: 10.1021/acs.jctc.6b00578] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Fluorescent RNA aptamer Spinach can bind and activate a green fluorescent protein (GFP)-like chromophore (an anionic DFHBDI chromophore) displaying green fluorescence. Spectroscopic properties, spectral tuning, and the photoisomerization mechanism in the Spinach-DFHBDI complex have been investigated by high-level QM and hybrid ONIOM(QM:AMBER) methods (QM method: (TD)DFT, SF-BHHLYP, SAC-CI, LT-DF-LCC2, CASSCF, or MS-CASPT2), as well as classical molecular dynamics (MD) simulations. First, our benchmark calculations have shown that TD-DFT and spin-flip (SF) TD-DFT (SF-BHHLYP) failed to give a satisfactory description of absorption and emission of the anionic DFHBDI chromophore. Comparatively, SAC-CI, LT-DF-LCC2, and MS-CASPT2 can give more reliable transition energies and are mainly used to further study the spectra of the anionic DFHBDI chromophore in Spinach. The RNA environmental effects on the spectral tuning and the photoisomerization mechanism have been elucidated. Our simulations show that interactions of the anionic cis-DFHBDI chromophore with two G-quadruplexes as well as a UAU base triple suppress photoisomerization of DFHBDI. In addition, strong hydrogen bonds between the anionic cis-DFHBDI chromophore and nearby nucleotides facilitate its binding to Spinach and further inhibit the cis-trans photoisomerization of DFHBDI. Solvent molecules, ions, and loss of key hydrogen bonds with nearby nucleotides could induce dissociation of the anionic trans-DFHBDI chromophore from the binding site. These results provide new insights into fluorescent RNA Spinach and may help rational design of other fluorescent RNAs.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Lung Wa Chung
- Department of Chemistry, South University of Science and Technology of China , Shenzhen 518055, China
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
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97
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Park JW, Rhee YM. Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in Green Fluorescent Protein. J Am Chem Soc 2016; 138:13619-13629. [PMID: 27662359 DOI: 10.1021/jacs.6b06833] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The green fluorescent protein and its designed variants fluoresce efficiently. Because the isolated chromophore is not fluorescent in a practical sense, it is apparent that the protein environment plays a crucial role in its efficiency. Because of various obstacles in studying excited state dynamics of complex systems, however, the detailed mechanism of this efficiency enhancement is not yet clearly elucidated. Here, by adopting excited state nonadiabatic molecular dynamics simulations together with an interpolated quantum chemical potential model of the chromophore, we find that the strong electric field from the protein matrix contributes dominantly to the motional restriction of the chromophore. The delay in twisting motion subsequently obstructs the nonradiative decay that competes with fluorescence, leading naturally to an enhancement in light-emitting efficiency. Surprisingly, steric constraints make only a minor contribution to these aspects. Through residue specific analyses, we identify a group of key residues that control the excited state behavior. Testing a series of mutant GFPs with different brightnesses also supports the view regarding the importance of protein electrostatics. Our findings may provide a useful guide toward designing new fluorescent chemical systems in the future.
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Affiliation(s)
- Jae Woo Park
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS) , Pohang 37673, Korea.,Department of Chemistry, Pohang University of Science and Technology (POSTECH) , Pohang 37673, Korea
| | - Young Min Rhee
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS) , Pohang 37673, Korea.,Department of Chemistry, Pohang University of Science and Technology (POSTECH) , Pohang 37673, Korea
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98
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Bhaskaran-Nair K, Valiev M, Deng SHM, Shelton WA, Kowalski K, Wang XB. Probing microhydration effect on the electronic structure of the GFP chromophore anion: Photoelectron spectroscopy and theoretical investigations. J Chem Phys 2016; 143:224301. [PMID: 26671369 DOI: 10.1063/1.4936252] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The photophysics of the Green Fluorescent Protein (GFP) chromophore is critically dependent on its local structure and on its environment. Despite extensive experimental and computational studies, there remain many open questions regarding the key fundamental variables that govern this process. One outstanding problem is the role of autoionization as a possible relaxation pathway of the excited state under different environmental conditions. This issue is considered in our work through combined experimental and theoretical studies of microsolvated clusters of the deprotonated p-hydroxybenzylidene-2,3-dimethylimidazolinone anion (HBDI(-)), an analog of the GFP chromophore. Through selective generation of microsolvated structures of predetermined size and subsequent analysis of experimental photoelectron spectra by high level ab initio methods, we are able to precisely identify the structure of the system, establish the accuracy of theoretical data, and provide reliable description of auto-ionization process as a function of hydrogen-bonding environment. Our study clearly illustrates the first few water molecules progressively stabilize the excited state of the chromophore anion against the autodetached neutral state, which should be an important trait for crystallographic water molecules in GFPs that has not been fully explored to date.
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Affiliation(s)
- Kiran Bhaskaran-Nair
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Marat Valiev
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - S H M Deng
- Physical Sciences Division, Pacific Northwest National Laboratory, K8-88, P.O. Box 999, Richland, Washington 99352, USA
| | - William A Shelton
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Karol Kowalski
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, K8-88, P.O. Box 999, Richland, Washington 99352, USA
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99
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Chatterjee T, Lacombat F, Yadav D, Mandal M, Plaza P, Espagne A, Mandal PK. Ultrafast Dynamics of a Green Fluorescent Protein Chromophore Analogue: Competition between Excited-State Proton Transfer and Torsional Relaxation. J Phys Chem B 2016; 120:9716-22. [DOI: 10.1021/acs.jpcb.6b05795] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tanmay Chatterjee
- Department
of Chemical Sciences, Indian Institute of Science Education and Research (IISER) - Kolkata, Mohanpur, West-Bengal 741246, India
| | - Fabien Lacombat
- Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24, rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06,
ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Dheerendra Yadav
- Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24, rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06,
ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Mrinal Mandal
- Department
of Chemical Sciences, Indian Institute of Science Education and Research (IISER) - Kolkata, Mohanpur, West-Bengal 741246, India
| | - Pascal Plaza
- Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24, rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06,
ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Agathe Espagne
- Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24, rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06,
ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Prasun K. Mandal
- Department
of Chemical Sciences, Indian Institute of Science Education and Research (IISER) - Kolkata, Mohanpur, West-Bengal 741246, India
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100
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Ai Y, Xia S, Liao RZ. Theoretical Studies on the Photochemistry of Pentose Aminooxazoline, a Hypothetical Intermediate Product in the Prebiotic Synthetic Scenario of RNA Nucleotides. J Phys Chem B 2016; 120:9329-37. [PMID: 27525736 DOI: 10.1021/acs.jpcb.6b06061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2-Aminooxazole is generally considered a prebiotic precursor of ribonucleotides on the early earth. Its pentose compound, pentose aminooxazoline, has been suggested to be a key intermediate in the prebiotic synthetic scenario. In this article, detailed mechanism of the photochemistry of pentose aminooxazoline has been studied by performing density functional theory and multireference complete active space self-consistent field calculations. Parallel to the "ring-puckering" process, which leads to ultrafast nonradiative deactivation, several other photodissociation channels are explored in detail. In addition, the influences of the pentose structure and solvation effects with both implicit and explicit water models have been uncovered for both neutral and protonated forms. The current theoretical results provide very important information not only for the photostability of RNA nucleotides but also for an in-depth understanding of the synthesis of other prebiotic nucleotides.
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Affiliation(s)
- Yuejie Ai
- School of Environmental and Chemical Engineering, North China Electric Power University , Beijing 102206, China
| | - Shuhua Xia
- College of Life and Environmental Science, Minzu University of China , Beijing 100081, China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
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