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Tahara S, Kuramochi H, Takeuchi S, Tahara T. Protein Dynamics Preceding Photoisomerization of the Retinal Chromophore in Bacteriorhodopsin Revealed by Deep-UV Femtosecond Stimulated Raman Spectroscopy. J Phys Chem Lett 2019; 10:5422-5427. [PMID: 31469573 DOI: 10.1021/acs.jpclett.9b02283] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacteriorhodopsin is a prototypical photoreceptor protein that functions as a light-driven proton pump. The retinal chromophore of bacteriorhodopsin undergoes C13═C14 trans-to-cis isomerization upon photoexcitation, and it has been believed to be the first event that triggers the cascaded structural changes in bacteriorhodopsin. We investigated the protein dynamics of bacteriorhodopsin using deep-ultraviolet resonance femtosecond stimulated Raman spectroscopy. It was found that the stimulated Raman signals of tryptophan and tyrosine residues exhibit significant changes within 0.2 ps after photoexcitation while they do not noticeably change during the isomerization process. This result implies that the protein environment changes first, and its change is small during isomerization. The obtained femtosecond stimulated Raman data indicate that ultrafast change is induced in the protein part by the sudden creation of the large dipole of the excited-state chromophore, providing an environment that realizes efficient and selective isomerization.
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Affiliation(s)
- Shinya Tahara
- Molecular Spectroscopy Laboratory , RIKEN , 2-1 Hirosawa , Wako 351-0198 , Japan
| | - Hikaru Kuramochi
- Molecular Spectroscopy Laboratory , RIKEN , 2-1 Hirosawa , Wako 351-0198 , Japan
- Ultrafast Spectroscopy Research Team , RIKEN Center for Advanced Photonics (RAP) , 2-1 Hirosawa , Wako 351-0198 , Japan
- PRESTO , Japan Science and Technology Agency , 4-1-8 Honcho , Kawaguchi 332-0012 , Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory , RIKEN , 2-1 Hirosawa , Wako 351-0198 , Japan
- Ultrafast Spectroscopy Research Team , RIKEN Center for Advanced Photonics (RAP) , 2-1 Hirosawa , Wako 351-0198 , Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory , RIKEN , 2-1 Hirosawa , Wako 351-0198 , Japan
- Ultrafast Spectroscopy Research Team , RIKEN Center for Advanced Photonics (RAP) , 2-1 Hirosawa , Wako 351-0198 , Japan
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52
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Kinoshita SN, Inokuchi Y, Onitsuka Y, Kohguchi H, Akai N, Shiraogawa T, Ehara M, Yamazaki K, Harabuchi Y, Maeda S, Ebata T. The direct observation of the doorway 1nπ* state of methylcinnamate and hydrogen-bonding effects on the photochemistry of cinnamate-based sunscreens. Phys Chem Chem Phys 2019; 21:19755-19763. [PMID: 31259349 DOI: 10.1039/c9cp02914a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electronic states and photochemistry including nonradiative decay (NRD) and trans(E) → cis(Z) isomerization of methylcinnamate (MC) and its hydrogen-bonded complex with methanol have been investigated under jet-cooled conditions. S1(1nπ*) and S2(1ππ*) are directly observed in MC. This is the first direct observation of S1(1nπ*) in cinnamate derivatives. Surprisingly, the order of the energies between the nπ* and ππ* states is opposite to substituted cinnamates. TD-DFT and SAC-CI calculations support the observed result and show that the substitution to the benzene ring largely lowers the 1ππ* energy while the effect on 1nπ* is rather small. The S2(ππ*) state lifetime of MC is determined to be equal to or shorter than 10 ps, and the production of the transient T1 state is observed. The T1(ππ*) state is calculated to have a structure in which propenyl C[double bond, length as m-dash]C is twisted by 90°, suggesting the trans → cis isomerization proceeds via T1. The production of the cis isomer is confirmed by low-temperature matrix-isolated FTIR spectroscopy. The effect of H-bonding is examined for the MC-methanol complex. The S2 lifetime of MC-methanol is determined to be 180 ps, indicating that the H-bonding to the C[double bond, length as m-dash]O group largely prohibits the 1ππ* → 1nπ* internal conversion. This lifetime elongation in the methanol complex also describes well a higher fluorescence quantum yield of MC in methanol solution than in cyclohexane, while such a solvent dependence is not observed in para-substituted MC. Determination of the photochemical reaction pathways of MC and MC-methanol will help us to design photofunctional cinnamate derivatives.
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Affiliation(s)
- Shin-Nosuke Kinoshita
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
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Bera K, Kwang SY, Cassabaum AA, Rich CC, Frontiera RR. Facile Background Discrimination in Femtosecond Stimulated Raman Spectroscopy Using a Dual-Frequency Raman Pump Technique. J Phys Chem A 2019; 123:7932-7939. [DOI: 10.1021/acs.jpca.9b02473] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kajari Bera
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Siu Yi Kwang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Alyssa A. Cassabaum
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christopher C. Rich
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Renee R. Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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54
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Zhao X, Luo J, Liu Y, Pandey P, Yang S, Wei D, Han K. Substitution Dependent Ultrafast Ultraviolet Energy Dissipation Mechanisms of Plant Sunscreens. J Phys Chem Lett 2019; 10:5244-5249. [PMID: 31436992 DOI: 10.1021/acs.jpclett.9b02175] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
An ultraviolet energy dissipation mechanism plays a critical role in the photoprotection effect of sunscreens. In this work, we discovered substitution dependent UV energy dissipation mechanisms of model plant sunscreen methyl sinapate (MS). We found that the initially populated V(ππ*) states of MS and p-OMeMS relax to the ground state nonradiatively along an ultrafast trans-cis photoisomerization in tens of picoseconds. However, for p-HMS, an internal conversion from V(ππ*) to a relative dark V'(ππ*) state occurs in less than 1 ps, leading to a branching of the excited-state relaxations. The V (ππ*) state still relaxes nonradiatively as in the case of MS and p-OMeMS. In contrast, the V'(ππ*) state decays to the ground state mainly by emitting photons, exhibiting a lifetime as long as 5 ns. It is the first time to definitely distinguish the dynamics between V(ππ*) and V'(ππ*) states in the study of sinapates and cinnamates. These results indicate the anticipation of the V'(ππ*) state should be avoided when designing sunscreens.
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Affiliation(s)
- Xi Zhao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 10049, China
| | - Jian Luo
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Yan Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Pramod Pandey
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Songqiu Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Donghui Wei
- College of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, People's Republic of China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao 266237, P. R. China
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Abstract
After presenting the basic theoretical models of excitation energy transfer and charge transfer, I describe some of the novel experimental methods used to probe them. Finally, I discuss recent results concerning ultrafast energy and charge transfer in biological systems, in chemical systems and in photovoltaics based on sensitized transition metal oxides.
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Affiliation(s)
- Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Lausanne Centre for Ultrafast Science (LACUS), FSB, Station 6, CH-1015 Lausanne, Switzerland.
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56
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Thomson B, Both J, Wu Y, Parrish RM, Martínez TJ, Boxer SG. Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation. J Phys Chem B 2019; 123:4844-4849. [PMID: 31117606 PMCID: PMC7061054 DOI: 10.1021/acs.jpcb.9b01571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photoactive yellow protein (PYP) is a small photoreceptor protein that has two unusually short hydrogen bonds between the deprotonated p-coumaric acid chromophore and two amino acids, a tyrosine and a glutamic acid. This has led to considerable debate as to whether the glutamic acid-chromophore hydrogen bond is a low barrier hydrogen bond, with conflicting results in the literature. We have modified the p Ka of the tyrosine by amber suppression and of the chromophore by chemical substitution. X-ray crystal structures of these modified proteins are nearly identical to the wild-type protein, so the heavy atom distance between proton donor and acceptor is maintained, even though these modifications change the relative proton affinity between donor and acceptor. Despite a considerable change in relative proton affinity, the NMR chemical shifts of the hydrogen-bonded protons are only moderately affected. QM/MM calculations were used to explore the protons' potential energy surface and connect the calculated proton position with empirically measured proton chemical shifts. The results are inconsistent with a low barrier hydrogen bond but in all cases are consistent with a localized proton, suggesting an ionic hydrogen bond rather than a low barrier hydrogen bond.
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Affiliation(s)
| | | | | | - Robert M. Parrish
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Todd J. Martínez
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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57
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Kuramochi H, Takeuchi S, Kamikubo H, Kataoka M, Tahara T. Fifth-order time-domain Raman spectroscopy of photoactive yellow protein for visualizing vibrational coupling in its excited state. SCIENCE ADVANCES 2019; 5:eaau4490. [PMID: 31187055 PMCID: PMC6555629 DOI: 10.1126/sciadv.aau4490] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 04/26/2019] [Indexed: 05/15/2023]
Abstract
We report fifth-order time-domain Raman spectroscopy of photoactive yellow protein (PYP), with the aim to visualize vibrational coupling in its excited state. After the ultrashort actinic pump pulse prepared the vibrational coherence and population in the excited state, the evolving vibrational structure was tracked by time-resolved impulsive stimulated Raman spectroscopy using sub-7-fs pulses. The obtained fifth-order time-domain Raman data were translated to a two-dimensional (2D) frequency-frequency correlation map, which visualizes the correlation between low- and high-frequency vibrational modes of the excited state. The 2D map of PYP reveals a cross peak, indicating the coupling between the phenolic C─O stretch mode of the chromophore and the low-frequency modes (~160 cm-1), assignable to the intermolecular motions involving the surrounding hydrogen-bonded amino acids. The unveiled coupling suggests the importance of the low-frequency vibrational motion in the primary photoreaction of PYP, highlighting the unique capability of this spectroscopic approach for studying ultrafast reaction dynamics.
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Affiliation(s)
- Hikaru Kuramochi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
- Corresponding author. (S.T.); (T.T.)
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
- Corresponding author. (S.T.); (T.T.)
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58
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Bull JN, Silva GD, Scholz MS, Carrascosa E, Bieske EJ. Photoinitiated Intramolecular Proton Transfer in Deprotonated para-Coumaric Acid. J Phys Chem A 2019; 123:4419-4430. [DOI: 10.1021/acs.jpca.9b02023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James N. Bull
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Gabriel da Silva
- Department of Chemical Engineering, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael S. Scholz
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Eduardo Carrascosa
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Evan J. Bieske
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
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59
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Blankenburg L, Schroeder L, Habenstein F, Błasiak B, Kottke T, Bredenbeck J. Following local light-induced structure changes and dynamics of the photoreceptor PYP with the thiocyanate IR label. Phys Chem Chem Phys 2019; 21:6622-6634. [PMID: 30855039 DOI: 10.1039/c8cp05399e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoactive Yellow Protein (PYP) is a bacterial blue light receptor that enters a photocycle after excitation. The intermediate states are formed on time scales ranging from femtoseconds up to hundreds of milliseconds, after which the signaling state with a lifetime of about 1 s is reached. To investigate structural changes and dynamics, we incorporated the SCN IR label at distinct positions of the photoreceptor via cysteine mutation and cyanylation. FT-IR measurements of the SCN label at different sites of the well-established dark state structure of PYP characterized the spectral response of the label to differences in the environment. Under constant blue light irradiation, we observed the formation of the signaling state with significant changes of wavenumber and lineshape of the SCN bands. Thereby we deduced light-induced structural changes in the local environment of the labels. These results were supported by molecular dynamics simulations on PYP providing the solvent accessible surface area (SASA) at the different positions. To follow protein dynamics via the SCN label during the photocycle, we performed step-scan FT-IR measurements with a time resolution of 10 μs. Global analysis yielded similar time constants of τ1 = 70 μs, τ2 = 640 μs, and τ3 > 20 ms for the wild type and τ1 = 36 μs, τ2 = 530 μs, and τ3 > 20 ms for the SCN-labeled mutant PYP-A44C*, a mutant which provided a sufficiently large SCN difference signal to measure step-scan FT-IR spectra. In comparison to the protein (amide, E46) and chromophore bands the dynamics of the SCN label show a different behavior. This result indicates that the local kinetics sensed by the label are different from the global protein kinetics.
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Affiliation(s)
- Larissa Blankenburg
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
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60
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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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61
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Abstract
A proposal for building a Free Electron Laser, EuPRAXIA@SPARC_LAB, at the Laboratori Nazionali di Frascati, is at present under consideration. This FEL facility will provide a unique combination of a high brightness GeV-range electron beam generated in a X-band RF linac, a 0.5 PW-class laser system and the first FEL source driven by a plasma accelerator. The FEL will produce ultra-bright pulses, with up to 10 12 photons/pulse, femtosecond timescale and wavelength down to 3 nm, which lies in the so called “water window”. The experimental activity will be focused on the realization of a plasma driven short wavelength FEL able to provide high-quality photons for a user beamline. In this paper, we describe the main classes of experiments that will be performed at the facility, including coherent diffraction imaging, soft X-ray absorption spectroscopy, Raman spectroscopy, Resonant Inelastic X-ray Scattering and photofragmentation measurements. These techniques will allow studying a variety of samples, both biological and inorganic, providing information about their structure and dynamical behavior. In this context, the possibility of inducing changes in samples via pump pulses leading to the stimulation of chemical reactions or the generation of coherent excitations would tremendously benefit from pulses in the soft X-ray region. High power synchronized optical lasers and a TeraHertz radiation source will indeed be made available for THz and pump–probe experiments and a split-and-delay station will allow performing XUV-XUV pump–probe experiments.
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62
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Excited State Structural Evolution of a GFP Single-Site Mutant Tracked by Tunable Femtosecond-Stimulated Raman Spectroscopy. Molecules 2018; 23:molecules23092226. [PMID: 30200474 PMCID: PMC6225354 DOI: 10.3390/molecules23092226] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 12/31/2022] Open
Abstract
Tracking vibrational motions during a photochemical or photophysical process has gained momentum, due to its sensitivity to the progression of reaction and change of environment. In this work, we implemented an advanced ultrafast vibrational technique, femtosecond-stimulated Raman spectroscopy (FSRS), to monitor the excited state structural evolution of an engineered green fluorescent protein (GFP) single-site mutant S205V. This mutation alters the original excited state proton transfer (ESPT) chain. By strategically tuning the Raman pump to different wavelengths (i.e., 801, 539, and 504 nm) to achieve pre-resonance with transient excited state electronic bands, the characteristic Raman modes of the excited protonated (A*) chromophore species and intermediate deprotonated (I*) species can be selectively monitored. The inhomogeneous distribution/population of A* species go through ESPT with a similar ~300 ps time constant, confirming that bridging a water molecule to protein residue T203 in the ESPT chain is the rate-limiting step. Some A* species undergo vibrational cooling through high-frequency motions on the ~190 ps time scale. At early times, a portion of the largely protonated A* species could also undergo vibrational cooling or return to the ground state with a ~80 ps time constant. On the photoproduct side, a ~1330 cm−1 delocalized motion is observed, with dispersive line shapes in both the Stokes and anti-Stokes FSRS with a pre-resonance Raman pump, which indicates strong vibronic coupling, as the mode could facilitate the I* species to reach a relatively stable state (e.g., the main fluorescent state) after conversion from A*. Our findings disentangle the contributions of various vibrational motions active during the ESPT reaction, and offer new structural dynamics insights into the fluorescence mechanisms of engineered GFPs and other analogous autofluorescent proteins.
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63
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Multidimensional Vibrational Coherence Spectroscopy. Top Curr Chem (Cham) 2018; 376:35. [DOI: 10.1007/s41061-018-0213-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/31/2018] [Indexed: 10/28/2022]
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64
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Spectroscopic ruler for measuring active-site distortions based on Raman optical activity of a hydrogen out-of-plane vibration. Proc Natl Acad Sci U S A 2018; 115:8671-8675. [PMID: 30104345 DOI: 10.1073/pnas.1806491115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Photoactive yellow protein (PYP), from the phototrophic bacterium Halorhodospira halophila, is a small water-soluble photoreceptor protein and contains p-coumaric acid (pCA) as a chromophore. PYP has been an attractive model for studying the physical chemistry of protein active sites. Here, we explore how Raman optical activity (ROA) can be used to extract quantitative information on distortions of the pCA chromophore at the active site in PYP. We use 13C8-pCA to assign an intense signal at 826 cm-1 in the ROA spectrum of PYP to a hydrogen out-of-plane vibration of the ethylenic moiety of the chromophore. Quantum-chemical calculations based on density functional theory demonstrate that the sign of this ROA band reports the direction of the distortion in the dihedral angle about the ethylenic C=C bond, while its amplitude is proportional to the dihedral angle. These results document the ability of ROA to quantify structural deformations of a cofactor molecule embedded in a protein moiety.
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65
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Kuramochi H, Takeuchi S, Tahara T. Ultrafast photodissociation dynamics of diphenylcyclopropenone studied by time-resolved impulsive stimulated Raman spectroscopy. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.02.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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66
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Chen C, Zhu LD, Fang C. Femtosecond stimulated Raman line shapes: Dependence on resonance conditions of pump and probe pulses. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1805125] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
| | - Liang-dong Zhu
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
- Department of Physics, Oregon State University, 301 Weniger Hall, Corvallis, Oregon, 97331-6507, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
- Department of Physics, Oregon State University, 301 Weniger Hall, Corvallis, Oregon, 97331-6507, USA
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67
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Kumar A, Nokhrin S, Woloschuk RM, Woolley GA. Duplication of a Single Strand in a β-Sheet Can Produce a New Switching Function in a Photosensory Protein. Biochemistry 2018; 57:4093-4104. [PMID: 29897240 DOI: 10.1021/acs.biochem.8b00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Duplication of a single β-strand that forms part of a β-sheet in photoactive yellow protein (PYP) was found to produce two approximately isoenergetic protein conformations, in which either the first or the second copy of the duplicated β-strand participates in the β-sheet. Whereas one conformation (big-loop) is more stable at equilibrium in the dark, the other conformation (long-tail) is populated after recovery from blue light irradiation. By appending a recognition motif (E-helix) to the C-terminus of the protein, we show that β-strand duplication, and the resulting possibility of β-strand slippage, can lead to a new switchable protein-protein interaction. We suggest that β-strand duplication may be a general means of introducing two-state switching activity into protein structures.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , ON M5S 3H6 , Canada
| | - Sergiy Nokhrin
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , ON M5S 3H6 , Canada
| | - Ryan M Woloschuk
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , ON M5S 3H6 , Canada
| | - G Andrew Woolley
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , ON M5S 3H6 , Canada
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68
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Fang C, Tang L, Oscar BG, Chen C. Capturing Structural Snapshots during Photochemical Reactions with Ultrafast Raman Spectroscopy: From Materials Transformation to Biosensor Responses. J Phys Chem Lett 2018; 9:3253-3263. [PMID: 29799757 DOI: 10.1021/acs.jpclett.8b00373] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Chemistry studies the composition, structure, properties, and transformation of matter. A mechanistic understanding of the pertinent processes is required to translate fundamental knowledge into practical applications. The current development of ultrafast Raman as a powerful time-resolved vibrational technique, particularly femtosecond stimulated Raman spectroscopy (FSRS), has shed light on the structure-energy-function relationships of various photosensitive systems. This Perspective reviews recent work incorporating optical innovations, including the broad-band up-converted multicolor array (BUMA) into a tunable FSRS setup, and demonstrates its resolving power to watch metal speciation and photolysis, leading to high-quality thin films, and fluorescence modulation of chimeric protein biosensors for calcium ion imaging. We discuss advantages of performing FSRS in the mixed time-frequency domain and present strategies to delineate mechanisms by tracking low-frequency modes and systematically modifying chemical structures with specific functional groups. These unique insights at the chemical-bond level have started to enable the rational design and precise control of functional molecular machines in optical, materials, energy, and life sciences.
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Affiliation(s)
- Chong Fang
- Department of Chemistry , Oregon State University , 153 Gilbert Hall , Corvallis , Oregon 97331 , United States
| | - Longteng Tang
- Department of Chemistry , Oregon State University , 153 Gilbert Hall , Corvallis , Oregon 97331 , United States
| | - Breland G Oscar
- Department of Chemistry , Oregon State University , 153 Gilbert Hall , Corvallis , Oregon 97331 , United States
| | - Cheng Chen
- Department of Chemistry , Oregon State University , 153 Gilbert Hall , Corvallis , Oregon 97331 , United States
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69
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Abstract
The first stage in biological signaling is based on changes in the functional state of a receptor protein triggered by interaction of the receptor with its ligand(s). The light-triggered nature of photoreceptors allows studies on the mechanism of such changes in receptor proteins using a wide range of biophysical methods and with superb time resolution. Here, we critically evaluate current understanding of proton and electron transfer in photosensory proteins and their involvement both in primary photochemistry and subsequent processes that lead to the formation of the signaling state. An insight emerging from multiple families of photoreceptors is that ultrafast primary photochemistry is followed by slower proton transfer steps that contribute to triggering large protein conformational changes during signaling state formation. We discuss themes and principles for light sensing shared by the six photoreceptor families: rhodopsins, phytochromes, photoactive yellow proteins, light-oxygen-voltage proteins, blue-light sensors using flavin, and cryptochromes.
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Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Aihua Xie
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Delmar S. Larsen
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, USA
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, USA
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70
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Dhamija S, Thakur B, Guptasarma P, De AK. Probing the excited state dynamics of Venus: origin of dual-emission in fluorescent proteins. Faraday Discuss 2018; 207:39-54. [DOI: 10.1039/c7fd00187h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We present studies on a yellow fluorescent protein variant, Venus, and investigate the photophysics behind the dual emission upon UV excitation in fluorescent proteins.
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Affiliation(s)
- Shaina Dhamija
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Mohali
- India
| | - Bhisham Thakur
- Department of Biological Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Mohali
- India
| | - Purnananda Guptasarma
- Department of Biological Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Mohali
- India
| | - Arijit K. De
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Mohali
- India
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71
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Henley A, Diveky ME, Patel AM, Parkes MA, Anderson JC, Fielding HH. Electronic structure and dynamics of torsion-locked photoactive yellow protein chromophores. Phys Chem Chem Phys 2017; 19:31572-31580. [PMID: 29165495 DOI: 10.1039/c7cp06950b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photocycle of photoactive yellow protein (PYP) begins with small-scale torsional motions of the chromophore leading to large-scale movements of the protein scaffold triggering a biological response. The role of single-bond torsional molecular motions of the chromophore in the initial steps of the PYP photocycle are not fully understood. Here, we employ anion photoelectron spectroscopy measurements and quantum chemistry calculations to investigate the electronic relaxation dynamics following photoexcitation of four model chromophores, para-coumaric acid, its methyl ester, and two analogues with aliphatic bridges hindering torsional motions around the single bonds adjacent to the alkene group. Following direct photoexcitation of S1 at 400 nm, we find that both single bond rotations play a role in steering the PYP chromophore through the S1/S0 conical intersection but that rotation around the single bond between the alkene moiety and the phenoxide group is particularly important. Following photoexcitation of higher lying electronic states in the range 346-310 nm, we find that rotation around the single bond between the alkene and phenoxide groups also plays a key role in the electronic relaxation from higher lying states to the S1 state. These results have potential applications in tuning the photoresponse of photoactive proteins and materials with chromophores based on PYP.
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Affiliation(s)
- Alice Henley
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Matus E Diveky
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Anand M Patel
- 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.
| | - James C Anderson
- 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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72
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Kuramochi H, Fujisawa T, Takeuchi S, Tahara T. Broadband stimulated Raman spectroscopy in the deep ultraviolet region. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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73
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Oscar BG, Chen C, Liu W, Zhu L, Fang C. Dynamic Raman Line Shapes on an Evolving Excited-State Landscape: Insights from Tunable Femtosecond Stimulated Raman Spectroscopy. J Phys Chem A 2017; 121:5428-5441. [DOI: 10.1021/acs.jpca.7b04404] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Breland G. Oscar
- Department
of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Cheng Chen
- Department
of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Weimin Liu
- Department
of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Liangdong Zhu
- Department
of Physics, Oregon State University, 301 Weniger Hall, Corvallis, Oregon 97331, United States
| | - Chong Fang
- Department
of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
- Department
of Physics, Oregon State University, 301 Weniger Hall, Corvallis, Oregon 97331, United States
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74
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Chergui M, Collet E. Photoinduced Structural Dynamics of Molecular Systems Mapped by Time-Resolved X-ray Methods. Chem Rev 2017; 117:11025-11065. [DOI: 10.1021/acs.chemrev.6b00831] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Majed Chergui
- Laboratoire
de Spectroscopie Ultrarapide (LSU), ISIC, and Lausanne Centre for
Ultrafast Science (LACUS), Faculté des Sciences de Base, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Eric Collet
- Univ Rennes 1, CNRS, Institut de Physique de Rennes, UMR 6251, UBL, Rennes F-35042, France
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