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Ohmine I, Saito S. Dynamical Behavior of Water; Fluctuation, Reactions and Phase Transitions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Iwao Ohmine
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
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2
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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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3
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Antioxidant flavone analog functionalized fluorescent silica nanoparticles: Synthesis and exploration of their possible use as biomolecule sensor. Colloids Surf B Biointerfaces 2017; 157:286-296. [PMID: 28601757 DOI: 10.1016/j.colsurfb.2017.05.074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/23/2017] [Accepted: 05/29/2017] [Indexed: 12/18/2022]
Abstract
For the first time, a synthetic fluorescent antioxidant flavone analog was successfully anchored onto the surface of the APTES-modified mesoporous silica nanoparticles (NPs) through sulfonamide linkage. The surface chemistry and morphology of the flavone modified fluorescent silica (FMFS) NPs were studied in detail. The flavone moiety when attached onto the FMFS NP surface, imparted its characteristic fluorescence and antioxidant activities to these NPs. Moreover, the NPs are highly biocompatible as evidenced from their cytotoxicity assay on normal lung cell (L132). The fluorescence activity of these biocompatible NPs was further utilized to study their interaction with a biomolecule, BSA (Bovine Serum Albumin). It was interesting to note that the fluorescence behavior of FMFS NPs completely changed on their binding with BSA. On the other hand, the intrinsic fluorescence activity of BSA was also significantly modified due to its interaction with FMFS NPs. Thus, the sensing and detection of biomolecules like BSA in presence of FMFS NPs can be accomplished by monitoring changes in the fluorescence behavior of either FMFS NPs or BSA. Furthermore, these FMFS NPs retained their intrinsic fluorescence behavior in the cellular medium which opens up their possible use as biocompatible cell imaging agents in future.
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4
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Asatkar AK, Panda S, Zade SS. Thiophene-based salen-type new ligands, their structural aspects and a dimeric Cu(II) complex. Polyhedron 2015. [DOI: 10.1016/j.poly.2015.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 743] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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6
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Borase HP, Patil CD, Salunkhe RB, Suryawanshi RK, Salunke BK, Patil SV. Phytolatex synthesized gold nanoparticles as novel agent to enhance sun protection factor of commercial sunscreens. Int J Cosmet Sci 2014; 36:571-8. [PMID: 25124731 DOI: 10.1111/ics.12158] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/26/2014] [Indexed: 01/16/2023]
Abstract
OBJECTIVE To study the potential of phytolatex (latex of Jatropha gossypifolia) fabricated gold nanoparticles as promising candidate in sunscreen formulations for enhancement in sun protection factor. METHODS In this study, plant latex was used as reducing and capping agent to synthesize gold nanoparticles. Latex fabricated gold nanoparticles were characterized by different analytical techniques such as UV-Vis spectroscopy, Fourier transforms infrared spectroscopy, dynamic light scattering, zeta potential, transmission electron microscopy and X-ray diffraction. Potential of sunscreen preparations containing gold nanoparticles to protect skin from UV radiation was investigated by in vitro sun protection factor analysis. Transmission electron microscopy and UV-Vis spectroscopy techniques were used to get insight into mechanism by which AuNPs enhance sun protection factor of sunscreen. RESULTS Monodisperse gold nanoparticles were synthesized using plant latex without need of hazardous chemical reducing and capping agents. Gold nanoparticles showed surface plasmon resonance peak at 550 nm in UV-Vis spectroscopic study. Gold nanoparticles were spherical and triangular in shape with size range of 30-50 nm. The zeta potential of gold nanoparticles was found to be -9.39 ± 0.19 mV. XRD analysis confirmed face-centred cubic (fcc) structure of gold nanoparticles. Incorporation of latex synthesized gold nanoparticles (2 and 4 [% w/w]) into commercial sunscreens increased the sun protection factor from 2.43 ± 0.74 to 24.11 ± 0.46% than sunscreen devoid of gold nanoparticles. From UV-Vis absorption spectroscopy and TEM analysis, it was observed that gold nanoparticles enhance the sun protection factor of commercial sunscreens due to reflection and scattering of UV radiation. CONCLUSION Phytolatex synthesized gold nanoparticle is novel agent to enhance sun protection factor of commercial sunscreens. Gold nanoparticles aggregation in commercial sunscreen was the main factor behind SPF enhancement. This study showed that gold nanoparticles are potent alternative to traditionally used hazardous titanium dioxide and zinc oxide nanoparticles in sunscreen.
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Affiliation(s)
- H P Borase
- School of Life Sciences, North Maharashtra University, PO Box- 80, Jalgaon, 425001, Maharashtra, India
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7
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Wei L, Wang H, Chen X, Fang W, Wang H. A comprehensive study of isomerization and protonation reactions in the photocycle of the photoactive yellow protein. Phys Chem Chem Phys 2014; 16:25263-72. [DOI: 10.1039/c4cp03495c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A comprehensive picture of the overall photocycle was obtained to reveal a wide range of structural signals in the photoactive yellow protein.
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Affiliation(s)
- Lili Wei
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing, China
| | - Hongjuan Wang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing, China
| | - Xuebo Chen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing, China
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing, China
| | - Haobin Wang
- Department of Chemistry and Biochemistry
- New Mexico State University
- Las Cruces, USA
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8
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Pan ZH, Zhou JW, Luo GG. Experimental and theoretical study of enol–keto prototropic tautomerism and photophysics of azomethine–BODIPY dyads. Phys Chem Chem Phys 2014; 16:16290-301. [DOI: 10.1039/c4cp02151g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Enol ↔ keto prototropic tautomerism can be exploited to modulate the photophysics of BODIPY chromophores based on proton-coupled photoinduced electron transfer processes.
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Affiliation(s)
- Zhong-Hua Pan
- College of Materials Science and Engineering
- Huaqiao University
- Xiamen 361021, P. R. China
| | - Jing-Wei Zhou
- School of Pharmaceutical Sciences
- East Campus
- Sun Yat-sen University
- Guangzhou 510006, P. R. China
| | - Geng-Geng Luo
- College of Materials Science and Engineering
- Huaqiao University
- Xiamen 361021, P. R. China
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9
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Thellamurege NM, Cui F, Li H. Quantum mechanical/molecular mechanical/continuum style solvation model: Time-dependent density functional theory. J Chem Phys 2013; 139:084106. [DOI: 10.1063/1.4819139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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10
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Preketes NK, Biggs JD, Ren H, Andricioaei I, Mukamel S. Simulations of Two-dimensional Infrared and Stimulated Resonance Raman Spectra of Photoactive Yellow Protein. Chem Phys 2013; 422. [PMID: 24244064 DOI: 10.1016/j.chemphys.2012.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We present simulations of one and two-dimensional infrared (2DIR) and stimulated resonance Raman (SRR) spectra of the dark state (pG) and early red-shifted intermediate (pR) of photoactive yellow protein (PYP). Shifts in the amide I and Glu46 COOH stretching bands distinguish between pG and pR in the IR absorption and 2DIR spectra. The one-dimensional SRR spectra are similar to the spontaneous RR spectra. The two-dimensional SRR spectra show large changes in cross peaks involving the C=O stretch of the two species and are more sensitive to the chromophore structure than 2DIR spectra.
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11
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Liu J, Yabushita A, Taniguchi S, Chosrowjan H, Imamoto Y, Sueda K, Miyanaga N, Kobayashi T. Ultrafast Time-Resolved Pump–Probe Spectroscopy of PYP by a Sub-8 fs Pulse Laser at 400 nm. J Phys Chem B 2013; 117:4818-26. [DOI: 10.1021/jp4001016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jun Liu
- Advanced Ultrafast Laser Research
Center, University of Electro-Communications, Chofugaoka 1-5-1, Chofu, Tokyo 182-8585 Japan
- State Key Laboratory of High
Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800, China
- Core Research for Evolutional
Science and Technology (CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Atsushi Yabushita
- Department of Electrophysics, National Chiao Tung University, 1001 Ta Hsueh Road,
Hsinchu 300, Taiwan
| | - Seiji Taniguchi
- Institute
for Laser Technology, Osaka University,
Yamadaoka 2-6, Suita Osaka, 565-0871
Japan
| | - Haik Chosrowjan
- Institute
for Laser Technology, Osaka University,
Yamadaoka 2-6, Suita Osaka, 565-0871
Japan
| | - Yasushi Imamoto
- Department of Biophysics,
Graduate
School of Science, Kyoto University, Kitashirakawa-Oiwake,
Sakyo, Kyoto 606-8502 Japan
| | - Keiichi Sueda
- Institute of Laser Engineering, Osaka University, Yamadakami 2-6, Suita 565-0871, Ibaraki
567-0047, Japan
| | - Noriaki Miyanaga
- Institute of Laser Engineering, Osaka University, Yamadakami 2-6, Suita 565-0871, Ibaraki
567-0047, Japan
| | - Takayoshi Kobayashi
- Advanced Ultrafast Laser Research
Center, University of Electro-Communications, Chofugaoka 1-5-1, Chofu, Tokyo 182-8585 Japan
- Core Research for Evolutional
Science and Technology (CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Department of Electrophysics, National Chiao Tung University, 1001 Ta Hsueh Road,
Hsinchu 300, Taiwan
- Institute of Laser Engineering, Osaka University, Yamadakami 2-6, Suita 565-0871, Ibaraki
567-0047, Japan
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12
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Isborn CM, Götz AW, Clark MA, Walker RC, Martínez TJ. Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. J Chem Theory Comput 2012; 8:5092-5106. [PMID: 23476156 PMCID: PMC3590007 DOI: 10.1021/ct3006826] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.
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Affiliation(s)
- Christine M. Isborn
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Matthew A. Clark
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Ross C. Walker
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Todd J. Martínez
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
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Ab initio, density functional theory, and semi-empirical calculations. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 924:3-27. [PMID: 23034743 DOI: 10.1007/978-1-62703-017-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This chapter introduces the theory and applications of commonly used methods of electronic structure calculation, with particular emphasis on methods applicable for modelling biomolecular systems. This chapter is sectioned as follows. We start by presenting ab initio methods, followed by a treatment of density functional theory (DFT) and some recent advances in semi-empirical methods. Treatment of excited states as well as basis sets are also presented.
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14
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Roy N, Alam MN, Mondal S, Sk I, Laskar RA, Das S, Mandal D, Begum NA. Exploring Indian Rosewood as a promising biogenic tool for the synthesis of metal nanoparticles with tailor-made morphologies. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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15
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Han WG, Sandala GM, Giammona DA, Bashford D, Noodleman L. Mössbauer properties of the diferric cluster and the differential iron(II)-binding affinity of the iron sites in protein R2 of class Ia Escherichia coli ribonucleotide reductase: a DFT/electrostatics study. Dalton Trans 2011; 40:11164-75. [PMID: 21837345 PMCID: PMC3604995 DOI: 10.1039/c1dt10950b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The R2 subunit of class-Ia ribonucleotide reductase (RNR) from Escherichia coli (E. coli) contains a diiron active site. Starting from the apo-protein and Fe(II) in solution at low Fe(II)/apoR2 ratios, mononuclear Fe(II) binding is observed indicating possible different Fe(II) binding affinities for the two alternative sites. Further, based on their Mössbauer spectroscopy and two-iron-isotope reaction experiments, Bollinger et al. (J. Am. Chem. Soc., 1997, 119, 5976-5977) proposed that the site Fe1, which bonds to Asp84, should be associated with the higher observed (57)Fe Mössbauer quadrupole splitting (2.41 mm s(-1)) and lower isomer shift (0.45 mm s(-1)) in the Fe(III)Fe(III) state, site Fe2, which is further from Tyr122, should have a greater affinity for Fe(II) binding than site Fe1, and Fe(IV) in the intermediate X state should reside at site Fe2. In this paper, using density functional theory (DFT) incorporated with the conductor-like screening (COSMO) solvation model and with the finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) methodologies, we have demonstrated that the observed large quadrupole splitting for the diferric state R2 does come from site Fe1(III) and it is mainly caused by the binding position of the carboxylate group of the Asp84 sidechain. Further, a series of active site clusters with mononuclear Fe(II) binding at either site Fe1 or Fe2 have been studied, which show that with a single dielectric medium outside the active site quantum region, there is no energetic preference for Fe(II) binding at one site over another. However, when including the explicit extended protein environment in the PB-SCRF model, the reaction field favors the Fe(II) binding at site Fe2 rather than at site Fe1 by ~9 kcal mol(-1). Therefore our calculations support the proposal of the previous Mössbauer spectroscopy and two-iron-isotope reaction experiments by Bollinger et al.
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Affiliation(s)
- Wen-Ge Han
- Department of Molecular Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Gregory M. Sandala
- Department of Molecular Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Debra Ann Giammona
- Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105
| | - Donald Bashford
- Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105
| | - Louis Noodleman
- Department of Molecular Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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16
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Kelly A, Kapral R. Quantum-classical description of environmental effects on electronic dynamics at conical intersections. J Chem Phys 2010; 133:084502. [DOI: 10.1063/1.3475773] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Han WG, Giammona DA, Bashford D, Noodleman L. Density functional theory analysis of structure, energetics, and spectroscopy for the Mn-Fe active site of Chlamydia trachomatis ribonucleotide reductase in four oxidation states. Inorg Chem 2010; 49:7266-81. [PMID: 20604534 PMCID: PMC2919573 DOI: 10.1021/ic902051t] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Models for the Mn-Fe active site structure of ribonucleotide reductase (RNR) from pathogenic bacteria Chlamydia trachomatis (Ct) in different oxidation states have been studied in this paper, using broken-symmetry density functional theory (DFT) incorporated with the conductor like screening (COSMO) solvation model and also with finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) calculations. The detailed structures for the reduced Mn(II)-Fe(II), the met Mn(III)-Fe(III), the oxidized Mn(IV)-Fe(III) and the superoxidized Mn(IV)-Fe(IV) states are predicted. The calculated properties, including geometries, (57)Fe Mossbauer isomer shifts and quadrupole splittings, and (57)Fe and (55)Mn electron nuclear double resonance (ENDOR) hyperfine coupling constants, are compared with the available experimental data. The Mössbauer and energetic calculations show that the (mu-oxo, mu-hydroxo) models better represent the structure of the Mn(IV)-Fe(III) state than the di-mu-oxo models. The predicted Mn(IV)-Fe(III) distances (2.95 and 2.98 A) in the (mu-oxo, mu-hydroxo) models are in agreement with the extended X-ray absorption fine structure (EXAFS) experimental value of 2.92 A (Younker et al. J. Am. Chem. Soc. 2008, 130, 15022-15027). The effect of the protein and solvent environment on the assignment of the Mn metal position is examined by comparing the relative energies of alternative mono-Mn(II) active site structures. It is proposed that if the Mn(II)-Fe(II) protein is prepared with prior addition of Mn(II) or with Mn(II) richer than Fe(II), Mn is likely positioned at metal site 2, which is further from Phe127.
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Affiliation(s)
- Wen-Ge Han
- Department of Molecular Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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18
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Wang Y, Li H. Excited state geometry of photoactive yellow protein chromophore: A combined conductorlike polarizable continuum model and time-dependent density functional study. J Chem Phys 2010; 133:034108. [DOI: 10.1063/1.3462248] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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19
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Coto PB, Roca-Sanjuán D, Serrano-Andrés L, Martín-Pendás A, Martí S, Andrés J. Toward Understanding the Photochemistry of Photoactive Yellow Protein: A CASPT2/CASSCF and Quantum Theory of Atoms in Molecules Combined Study of a Model Chromophore in Vacuo. J Chem Theory Comput 2009; 5:3032-8. [DOI: 10.1021/ct900401z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. B. Coto
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - D. Roca-Sanjuán
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - L. Serrano-Andrés
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - A. Martín-Pendás
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - S. Martí
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - J. Andrés
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
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20
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Andrews BT, Roy M, Jennings PA. Chromophore packing leads to hysteresis in GFP. J Mol Biol 2009; 392:218-27. [PMID: 19577576 DOI: 10.1016/j.jmb.2009.06.072] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 06/26/2009] [Accepted: 06/28/2009] [Indexed: 11/27/2022]
Abstract
Green fluorescent protein (GFP) possesses a unique folding landscape with a dual basin leading to the hysteretic folding behavior observed in experiment. While theoretical data do not have the resolution necessary to observe details of the chromophore during refolding, experimental results point to the chromophore as the cause of the observed hysteresis. With the use of NMR spectroscopy, which probes at the level of the individual residue, the hysteretic intermediate state is further characterized in the context of the loosely folded isomerized native-like state {N(iso)} predicted in simulation. In the present study, several residues located in the lid of GFP indicate heterogeneity of the native states. Some of these residues show chemical shifts when the native-like intermediate {N(iso)} responsible for GFP's hysteretic folding behavior is trapped. Observed changes in the chromophore are consistent with increased flexibility or isomerization in {N(iso)} as predicted in recent theoretical work. Here, we observed that multiple chromophore environments within the native state are averaged in the trapped intermediate, linking chromophore flexibility to mispacking in the trapped intermediate. The present work is experimental evidence for the proposed final "locking" mechanism in GFP folding forming an incorrectly or loosely packed barrel under intermediate (hysteretic) folding conditions.
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Affiliation(s)
- Benjamin T Andrews
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, 92093-0375, USA
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21
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Yang Z, Yang G, Zu Y, Fu Y, Zhou L. The conformational analysis and proton transfer of neuraminidase inhibitors: a theoretical study. Phys Chem Chem Phys 2009; 11:10035-41. [DOI: 10.1039/b909299d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Coto PB, Martí S, Oliva M, Olivucci M, Merchán M, Andrés J. Origin of the Absorption Maxima of the Photoactive Yellow Protein Resolved via Ab Initio Multiconfigurational Methods. J Phys Chem B 2008; 112:7153-6. [DOI: 10.1021/jp711396b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pedro B. Coto
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Sergio Martí
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Mónica Oliva
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Massimo Olivucci
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Manuela Merchán
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Juan Andrés
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
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23
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Theoretical study of 2,5-diphenyl-1,4-distyrylbenzene (A model compound of PPV): A comparison of the electronic structure and photophysical properties of cis- and trans-isomers. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.01.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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24
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Gromov EV, Burghardt I, Hynes JT, Köppel H, Cederbaum LS. Electronic structure of the photoactive yellow protein chromophore: Ab initio study of the low-lying excited singlet states. J Photochem Photobiol A Chem 2007. [DOI: 10.1016/j.jphotochem.2007.04.033] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Gromov EV, Burghardt I, Köppel H, Cederbaum LS. Electronic Structure of the PYP Chromophore in Its Native Protein Environment. J Am Chem Soc 2007; 129:6798-806. [PMID: 17474743 DOI: 10.1021/ja069185l] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report on supermolecular ab initio calculations which clarify the role of the local amino acid environment in determining the unique electronic structure properties of the photoactive yellow protein (PYP) chromophore. The extensive ab initio calculations, at the level of the CC2 and EOM-CCSD methods, allow us to explicitly address how the interactions between the deprotonated p-coumaric thio-methyl ester (pCTM-) chromophore and the surrounding amino acids act together to create a specifically stabilized pCTM- species. Particularly noteworthy is the role of the Arg52 amino acid in stabilizing the chromophore against autoionization, and the role of the Tyr42 and Glu46 amino acids in determining the hydrogen-bonding properties that carry the dominant energetic effects.
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Affiliation(s)
- Evgeniy V Gromov
- Theoretische Chemie, Physikalisch-Chemisches Institut Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany.
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26
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Leenders EJM, Guidoni L, Röthlisberger U, Vreede J, Bolhuis PG, Meijer EJ. Protonation of the chromophore in the photoactive yellow protein. J Phys Chem B 2007; 111:3765-73. [PMID: 17388542 DOI: 10.1021/jp067158b] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photoactive yellow protein (PYP) acts as a light sensor to its bacterial host: it responds to light by changing shape. After excitation by blue light, PYP undergoes several transformations, to partially unfold into its signaling state. One of the crucial steps in this photocycle is the protonation of p-coumaric acid after excitation and isomerization of this chromophore. Experimentalists still debate on the nature of the proton donor and on whether it donates the hydrogen directly or indirectly. To obtain better knowledge of the mechanism, we studied this proton transfer using Car-Parrinello molecular dynamics, classical molecular dynamics, and computer simulations combining these two methods (quantum mechanics/molecular mechanics, QMMM). The simulations reproduce the chromophore structure and hydrogen-bond network of the protein measured by X-ray crystallography and NMR. When the chromophore is protonated, it leaves the assumed proton donor, glutamic acid 46, with a negative charge in a hydrophobic environment. We show that the stabilization of this charge is a very important factor in the mechanism of protonation. Protonation frequently occurs in simplified ab initio simulations of the chromophore binding pocket in vacuum, where amino acids can easily hydrogen bond to Glu46. When the complete protein environment is incorporated in a QMMM simulation on the complete protein, no proton transfer is observed within 14 ps. The hydrogen-bond rearrangements in this time span are not sufficient to stabilize the new protonation state. Force field molecular dynamics simulations on a much longer time scale have shown which internal rearrangements of the protein are needed. Combining these simulations with more QMMM calculations enabled us to check the stability of protonation states and clarify the initial requirements for the proton transfer in PYP.
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Affiliation(s)
- Elske J M Leenders
- Van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
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27
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Kamiya M, Saito S, Ohmine I. Proton Transfer and Associated Molecular Rearrangements in the Photocycle of Photoactive Yellow Protein: Role of Water Molecular Migration on the Proton Transfer Reaction. J Phys Chem B 2007; 111:2948-56. [PMID: 17388419 DOI: 10.1021/jp066256u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of the proton transfer and the concomitant molecular structural and hydrogen bond rearrangements after the photoisomerization of the chromophore in the photocycle of photoactive yellow protein are theoretically investigated by using the QM/MM method and molecular dynamics calculations. The free energy surface along this proton-transfer process is determined. This work suggests the important role of the water molecular migration into the moiety of chromophore, which facilitates proton transfer by the hydrogen bond rearrangement and the hydration of the pB' state.
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Affiliation(s)
- Motoshi Kamiya
- Chemistry Department, Nagoya University, 1 Furocho, Chikusaku, Nagoya 464-8602, Japan
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28
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Burghardt I, Hynes JT. Excited-State Charge Transfer at a Conical Intersection: Effects of an Environment. J Phys Chem A 2006; 110:11411-23. [PMID: 17020251 DOI: 10.1021/jp057569c] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influence of a polar and polarizable environment on charge transfer processes at a conical intersection (CI) can be described by a diabatic free energy model yielding coupled surfaces as a function of both molecular coordinates and a solvent coordinate. We extend and apply this model for the S1-S0 CI in protonated Schiff bases, representing a model for retinal isomerization (Faraday Discuss. 2004, 127, 395, 2004). A dielectric continuum description of the solvent is combined with a minimal, two-electron-two-orbital electronic structure model according to Bonacić-Koutecký, Koutecký, and Michl (Angew. Chem. 1987, 26, 170), which characterizes the charge translocation effects at the CI. The model predicts that the nonequilibrium solvent state resulting from the S0-->S1 Franck-Condon transition can entail the disappearance of the CI, such that solvent motion is necessary to reach the CI seam. The concerted evolution of the intramolecular coordinates and the solvent coordinate is illustrated by an excited-state minimum energy path.
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Affiliation(s)
- Irene Burghardt
- Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France
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29
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Sauer M, Yeung C, Chong JH, Patrick BO, MacLachlan MJ. N-salicylideneanilines: tautomers for formation of hydrogen-bonded capsules, clefts, and chains. J Org Chem 2006; 71:775-88. [PMID: 16408993 DOI: 10.1021/jo052277t] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure: see text] The synthesis, characterization, and solid-state structures of new salicylaldimines are reported. Bis(N-salicylideneaniline)s (BSANs) and tris(N-salicylideneaniline)s (TSANs) are sterically encumbered compounds featuring a central six-membered ring in the keto-enamine tautomer. When extended with additional functional groups, these molecules may form hydrogen-bonded capsules, clefts, and extended structures. A TSAN with N-(t)()BOC-o-phenylenediamine groups has been structurally investigated. The complementary hydrogen-bonding motif in this molecule leads it to form dimers in solution and in the solid state. A BSAN with N-(t)()BOC-o-phenylenediamine substituents forms a hydrogen-bonded cleft in solution but forms an extended hydrogen-bonded ladder assembly of cofacial dimers in the solid state. When N-(t)()BOC-1,8-naphthalenediamine was utilized to extend the cleft, an unusual perimidine structure was obtained with the central core in the enol tautomer. In addition, ab initio calculations have been used to support the assignment of the keto-enamine or enol-imine tautomers of the BSANs and TSANs and to predict tautomerization in related BSANs and TSANs.
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Affiliation(s)
- Marc Sauer
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1 Canada
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30
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Heyne K, Mohammed OF, Usman A, Dreyer J, Nibbering ETJ, Cusanovich MA. Structural evolution of the chromophore in the primary stages of trans/cis isomerization in photoactive yellow protein. J Am Chem Soc 2006; 127:18100-6. [PMID: 16366562 PMCID: PMC2580759 DOI: 10.1021/ja051210k] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have studied the structural changes induced by optical excitation of the chromophore in wild-type photoactive yellow protein (PYP) in liquid solution with a combined approach of polarization-sensitive ultrafast infrared spectroscopy and density functional theory calculations. We identify the nuC8-C9 marker modes for solution phase PYP in the P and I0 states, from which we derive that the first intermediate state I0 that appears with a 3 ps time constant can be characterized to have a cis geometry. This is the first unequivocal demonstration that the formation of I0 correlates with the conversion from the trans to the cis state. For the P and I0 states we compare the experimentally measured vibrational band patterns and anisotropies with calculations and find that for both trans and cis configurations the planarity of the chromophore has a strong influence. The C7=C8-(C9=O)-S moiety of the chromophore in the dark P state has a trans geometry with the C=O group slightly tilted out-of-plane, in accordance with the earlier reported structure obtained in an X-ray diffraction study of PYP crystals. In the case of I0, experiment and theory are only in agreement when the C7=C8-(C9=O)-S moiety has a planar configuration. We find that the carboxylic side group of Glu46 that is hydrogen-bonded to the chromophore phenolate oxygen does not alter its orientation on going from the electronic ground P state, via the electronic excited P state to the intermediate I0 state, providing conclusive experimental evidence that the primary stages of PYP photoisomerization involve flipping of the enone thioester linkage without significant relocation of the phenolate moiety.
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Affiliation(s)
- Karsten Heyne
- : Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Omar F. Mohammed
- : Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Anwar Usman
- : Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - J. Dreyer
- : Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Erik T. J. Nibbering
- : Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Michael A. Cusanovich
- :Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
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31
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Espagne A, Changenet-Barret P, Plaza P, Martin MM. Solvent Effect on the Excited-State Dynamics of Analogues of the Photoactive Yellow Protein Chromophore. J Phys Chem A 2006; 110:3393-404. [PMID: 16526618 DOI: 10.1021/jp0563843] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We previously reported that two analogues of the Photoactive Yellow Protein chromophore, trans-p-hydroxycinnamic acid (pCA(2-)) and its amide derivative (pCM-) in their deprotonated forms, undergo a trans-cis photoisomerization whereas the thioester derivative, trans-p-hydroxythiophenyl cinnamate (pCT-), does not. pCT- is also the only one to exhibit a short-lived intermediate on its excited-state deactivation pathway. We here further stress the existence of two different relaxation mechanisms for these molecules and examine the reaction coordinates involved. We looked at the effect of the solvent properties (viscosity, polarity, solvation dynamics) on their excited-state relaxation dynamics, probed by ultrafast transient absorption spectroscopy. Sensitivity to the solvent properties is found to be larger for pCT- than for pCA(2-) and pCM-. This difference is considered to reveal that either the relaxation pathway or the reaction coordinate is different for these two classes of analogues. It is also found to be correlated to the electron donor-acceptor character of the molecule. We attribute the excited-state deactivation of analogues bearing a weaker acceptor group, pCA(2-) and pCM-, to a stilbene-like photoisomerization mechanism with the concerted rotation of the ethylenic bond and one adjacent single bond. For pCT-, which contains a stronger acceptor group, we consider a photoisomerization mechanism mainly involving the single torsion of the ethylenic bond. The excited-state deactivation of pCT- would lead to the formation of a ground-state intermediate at the "perp" geometry, which would return to the initial trans conformation without net isomerization.
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Affiliation(s)
- Agathe Espagne
- Département de Chimie, Ecole Normale Supérieure (UMR CNRS 8640 PASTEUR), 24 rue Lhomond, 75231 Paris Cedex 05, France
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32
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Lee IR, Lee W, Zewail AH. Primary steps of the photoactive yellow protein: isolated chromophore dynamics and protein directed function. Proc Natl Acad Sci U S A 2006; 103:258-62. [PMID: 16407155 PMCID: PMC1326191 DOI: 10.1073/pnas.0510015103] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cycle of the photoactive yellow protein (PYP) has been extensively studied, but the dynamics of the isolated chromophore responsible for transduction is unknown. Here, we present real-time observation of the dynamics of the negatively charged chromophore and detection of intermediates along the path of trans-to-cis isomerization using femtosecond mass selection/electron detachment techniques. The results show that the role of the protein environment is not in the first step of double-bond twisting (barrier crossing) but in directing efficient conversion to the cis-structure and in impeding radical formation within the protein.
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Affiliation(s)
- I-Ren Lee
- Arthur Amos Noyes Laboratory of Chemical Physics, Laboratory for Molecular Sciences, California Institute of Technology, Pasadena, CA 91125, USA
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33
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Shorokhov D, Park ST, Zewail AH. Ultrafast Electron Diffraction: Dynamical Structures on Complex Energy Landscapes. Chemphyschem 2005; 6:2228-50. [PMID: 16273578 DOI: 10.1002/cphc.200500330] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In this contribution, we report studies in ultrafast electron diffraction (UED), with the aim of exploring new directions. The main focus is on the determination of complex structures and their dynamics with spatial and temporal resolutions sufficient to give an atomic-scale picture for the evolution in chemical or biological change. We also provide the theoretical framework for UED, and compare the experimental findings of UED to those predicted by density functional and charge density calculations. Selected applications are given in order to highlight phenomena related to concepts such as bifurcation of trajectories in dynamics, far-from-equilibrium coherent structures, and conformational robustness in biological structures. For the former two cases, we consider chemical systems, and, for the latter, we examine proteins of 200 atoms (angiotensin I) or more.
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Affiliation(s)
- Dmitry Shorokhov
- Laboratory for Molecular Sciences, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125, USA
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34
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Gromov EV, Burghardt I, Köppel H, Cederbaum LS. Impact of Sulfur vs Oxygen on the Low-Lying Excited States oftrans-p-Coumaric Acid andtrans-p-Coumaric Thio Acid. J Phys Chem A 2005; 109:4623-31. [PMID: 16833801 DOI: 10.1021/jp0447791] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The low-lying excited singlet states of trans-p-coumaric acid (CA) and trans-p-coumaric thio acid (CTA) are investigated in view of characterizing the chromophore of the photoactive yellow protein (PYP), with particular regard to the impact of sulfur on the chromophore's electronic structure. The comparative ab initio study, performed with the highly accurate EOM-CCSD method, shows that the electronic state ordering upon vertical excitation and following in-plane geometry relaxation indeed depends in a very sensitive fashion on the presence of either sulfur or oxygen. The study identifies three relevant excited singlet states, two of which are of pi-pi type while the third state is of n-pi character. The study highlights the role of the latter n-pi state which is shown to be the lowest-lying excited state of CTA at all in-plane geometries under consideration, whereas this is not the case for CA.
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Affiliation(s)
- Evgeniy V Gromov
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany
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35
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Changenet-Barret P, Espagne A, Plaza P, Hellingwerf KJ, Martin MM. Investigations of the primary events in a bacterial photoreceptor for photomotility: photoactive yellow protein (PYP). NEW J CHEM 2005. [DOI: 10.1039/b418134d] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Furche F, Rappoport D. Density Functional Methods for Excited States: Equilibrium Structure and Electronic Spectra. THEORETICAL AND COMPUTATIONAL CHEMISTRY 2005. [DOI: 10.1016/s1380-7323(05)80020-2] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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37
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Itoh K, Sasai M. Dynamical transition and proteinquake in photoactive yellow protein. Proc Natl Acad Sci U S A 2004; 101:14736-41. [PMID: 15466708 PMCID: PMC522019 DOI: 10.1073/pnas.0402978101] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Indexed: 11/18/2022] Open
Abstract
Conformational dynamics in protein functioning covers a wide range of time scales from nanosecond fluctuations around a conformation to the large-amplitude conformational changes of milliseconds or longer. We illustrate a picture of cooperative coupling among such motions of different time scales in a model protein, photoactive yellow protein, by proposing a model that can consistently explain the experimental results on the photocycle of photoactive yellow protein. The model provides a scenario in which the global collective motion induced by the unfolding of the N-terminal domain promotes the loosening of the atomistic packing around the chromophore, which produces the favorable molecular environment for the photoexcited chromophore, thereby stabilizing the partially unfolded intermediate in the photocycle. The proteinquake, the large conformational change triggered by the local structural disturbance, plays a decisive role in controlling the kinetics of functioning.
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Affiliation(s)
- Kazuhito Itoh
- Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Nagoya 464-8601, Japan.
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38
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Noodleman L, Lovell T, Han WG, Li J, Himo F. Quantum chemical studies of intermediates and reaction pathways in selected enzymes and catalytic synthetic systems. Chem Rev 2004; 104:459-508. [PMID: 14871132 DOI: 10.1021/cr020625a] [Citation(s) in RCA: 330] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Louis Noodleman
- Department of Molecular Biology TPC-15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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39
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Chromophore vibrations during isomerization of photoactive yellow protein: analysis of normal modes and energy transfer. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.04.100] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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40
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Premvardhan LL, Buda F, van der Horst MA, Lührs DC, Hellingwerf KJ, van Grondelle R. Impact of Photon Absorption on the Electronic Properties of p-Coumaric Acid Derivatives of the Photoactive Yellow Protein Chromophore. J Phys Chem B 2004. [DOI: 10.1021/jp037469b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lavanya L. Premvardhan
- Department of Biophysics and Physics of Complex Systems, Division of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands, and Laboratory for Microbiology, Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Francesco Buda
- Department of Biophysics and Physics of Complex Systems, Division of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands, and Laboratory for Microbiology, Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Michael A. van der Horst
- Department of Biophysics and Physics of Complex Systems, Division of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands, and Laboratory for Microbiology, Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Daniel C. Lührs
- Department of Biophysics and Physics of Complex Systems, Division of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands, and Laboratory for Microbiology, Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Klaas J. Hellingwerf
- Department of Biophysics and Physics of Complex Systems, Division of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands, and Laboratory for Microbiology, Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Rienk van Grondelle
- Department of Biophysics and Physics of Complex Systems, Division of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands, and Laboratory for Microbiology, Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
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41
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Kort R, Hellingwerf KJ, Ravelli RBG. Initial events in the photocycle of photoactive yellow protein. J Biol Chem 2004; 279:26417-24. [PMID: 15026418 DOI: 10.1074/jbc.m311961200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The light-induced isomerization of a double bond is the key event that allows the conversion of light energy into a structural change in photoactive proteins for many light-mediated biological processes, such as vision, photosynthesis, photomorphogenesis, and photo movement. Cofactors such as retinals, linear tetrapyrroles, and 4-hydroxy-cinnamic acid have been selected by nature that provide the essential double bond to transduce the light signal into a conformational change and eventually, a physiological response. Here we report the first events after light excitation of the latter chromophore, containing a single ethylene double bond, in a low temperature crystallographic study of the photoactive yellow protein. We measured experimental phases to overcome possible model bias, corrected for minimized radiation damage, and measured absorption spectra of crystals to analyze the photoproducts formed. The data show a mechanism for the light activation of photoactive yellow protein, where the energy to drive the remainder of the conformational changes is stored in a slightly strained but fully cis-chromophore configuration. In addition, our data indicate a role for backbone rearrangements during the very early structural events.
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Affiliation(s)
- Remco Kort
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.
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42
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Chong JH, Sauer M, Patrick BO, MacLachlan MJ. Highly Stable Keto-Enamine Salicylideneanilines. Org Lett 2003; 5:3823-6. [PMID: 14535719 DOI: 10.1021/ol0352714] [Citation(s) in RCA: 205] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] Highly stable NH salicylideneanilines have been prepared by reaction of 1,3,5-triformylphloroglucinol with aniline derivatives. The NH form was confirmed by X-ray crystallographic data, as well as by NMR studies. A convenient one-step synthesis of triformylphloroglucinol is also reported.
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Affiliation(s)
- Jonathan H Chong
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
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43
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Getzoff ED, Gutwin KN, Genick UK. Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation. Nat Struct Mol Biol 2003; 10:663-8. [PMID: 12872160 DOI: 10.1038/nsb958] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2002] [Accepted: 06/26/2003] [Indexed: 11/08/2022]
Abstract
Protein photoreceptors use small-molecule cofactors called chromophores to detect light. Only under the influence of the receptors' active sites do these chromophores adopt spectral and photochemical properties that suit the receptors' functional requirements. This protein-induced change in chromophore properties is called photochemical tuning and is a prime example for the general--but poorly understood--process of chemical tuning through which proteins shape the reactivity of their active-site groups. Here we report the 0.82-A resolution X-ray structure of the bacterial light receptor photoactive yellow protein (PYP). The unusually precise structure reveals deviations from expected molecular geometries and anisotropic atomic displacements in the PYP active site. Our analysis of these deviations points directly to the intramolecular forces and active-site dynamics that tune the properties of PYP's chromophore to absorb blue light, suppress fluorescence, and favor the required light-driven double-bond isomerization.
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Affiliation(s)
- Elizabeth D Getzoff
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
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