1
|
Kang BJ, Rohwer EJ, Rohrbach D, Zyaee E, Akbarimoosavi M, Ollmann Z, Sorohhov G, Borgoo A, Cascella M, Cannizzo A, Decurtins S, Stanley RJ, Liu SX, Feurer T. Time-resolved THz Stark spectroscopy of molecules in solution. Nat Commun 2024; 15:4212. [PMID: 38760343 PMCID: PMC11101612 DOI: 10.1038/s41467-024-48164-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/22/2024] [Indexed: 05/19/2024] Open
Abstract
For decades, it was considered all but impossible to perform Stark spectroscopy on molecules in a liquid solution, because their concomitant orientation to the applied electric field results in overwhelming background signals. A way out was to immobilize the solute molecules by freezing the solvent. While mitigating solute orientation, freezing removes the possibility to study molecules in liquid environments at ambient conditions. Here we demonstrate time-resolved THz Stark spectroscopy, utilizing intense single-cycle terahertz pulses as electric field source. At THz frequencies, solute molecules have no time to orient their dipole moments. Hence, dynamic Stark spectroscopy on the time scales of molecular vibrations or rotations in both non-polar and polar solvents at arbitrary temperatures is now possible. We verify THz Stark spectroscopy for two judiciously selected molecular systems and compare the results to conventional Stark spectroscopy and first principle calculations.
Collapse
Affiliation(s)
- Bong Joo Kang
- Institute of Applied Physics, University of Bern, Bern, Switzerland
- Division of Advanced Materials, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
| | - Egmont J Rohwer
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | - David Rohrbach
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | - Elnaz Zyaee
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | | | - Zoltan Ollmann
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | - Gleb Sorohhov
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Alex Borgoo
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - Andrea Cannizzo
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | - Silvio Decurtins
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Robert J Stanley
- Department of Chemistry, Temple University, Philadelphia, PA, USA
| | - Shi-Xia Liu
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Thomas Feurer
- Institute of Applied Physics, University of Bern, Bern, Switzerland.
| |
Collapse
|
2
|
Lin CY, Boxer SG. Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems. J Phys Chem B 2020; 124:9513-9525. [DOI: 10.1021/acs.jpcb.0c07730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
3
|
Gromov EV, Domratcheva T. Four resonance structures elucidate double-bond isomerisation of a biological chromophore. Phys Chem Chem Phys 2020; 22:8535-8544. [DOI: 10.1039/d0cp00814a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Four resonance structures determining the electronic structure of the chromophore’s ground and first excited states. Changing the relative energies of the structures by hydrogen-bonding interactions tunes all chromophore’s photochemical properties.
Collapse
Affiliation(s)
- Evgeniy V. Gromov
- Max-Planck Institute for Medical Research
- Jahnstraße 29
- 69120 Heidelberg
- Germany
| | - Tatiana Domratcheva
- Max-Planck Institute for Medical Research
- Jahnstraße 29
- 69120 Heidelberg
- Germany
| |
Collapse
|
4
|
Lin CY, Romei MG, Oltrogge LM, Mathews II, Boxer SG. Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins. J Am Chem Soc 2019; 141:15250-15265. [PMID: 31450887 DOI: 10.1021/jacs.9b07152] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Green fluorescent proteins (GFPs) have become indispensable imaging and optogenetic tools. Their absorption and emission properties can be optimized for specific applications. Currently, no unified framework exists to comprehensively describe these photophysical properties, namely the absorption maxima, emission maxima, Stokes shifts, vibronic progressions, extinction coefficients, Stark tuning rates, and spontaneous emission rates, especially one that includes the effects of the protein environment. In this work, we study the correlations among these properties from systematically tuned GFP environmental mutants and chromophore variants. Correlation plots reveal monotonic trends, suggesting that all these properties are governed by one underlying factor dependent on the chromophore's environment. By treating the anionic GFP chromophore as a mixed-valence compound existing as a superposition of two resonance forms, we argue that this underlying factor is defined as the difference in energy between the two forms, or the driving force, which is tuned by the environment. We then introduce a Marcus-Hush model with the bond length alternation vibrational mode, treating the GFP absorption band as an intervalence charge transfer band. This model explains all of the observed strong correlations among photophysical properties; related subtopics are extensively discussed in the Supporting Information. Finally, we demonstrate the model's predictive power by utilizing the additivity of the driving force. The model described here elucidates the role of the protein environment in modulating the photophysical properties of the chromophore, providing insights and limitations for designing new GFPs with desired phenotypes. We argue that this model should also be generally applicable to both biological and nonbiological polymethine dyes.
Collapse
Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Matthew G Romei
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Luke M Oltrogge
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Steven G Boxer
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| |
Collapse
|
5
|
Probing the early stages of photoreception in photoactive yellow protein with ultrafast time-domain Raman spectroscopy. Nat Chem 2017. [PMID: 28644485 DOI: 10.1038/nchem.2717] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Unveiling the nuclear motions of photoreceptor proteins in action is a crucial goal in protein science in order to understand their elaborate mechanisms and how they achieve optimal selectivity and efficiency. Previous studies have provided detailed information on the structures of intermediates that appear during the later stages (>ns) of such photoreception cycles, yet the initial events immediately after photoabsorption remain unclear because of experimental challenges in monitoring nuclear rearrangements on ultrafast timescales, including protein-specific low-frequency motions. Using time-domain Raman probing with sub-7-fs pulses, we obtain snapshot vibrational spectra of photoactive yellow protein and a mutant with high sensitivity, providing insights into the key responses that drive photoreception. Our data show a drastic intensity drop of the excited-state marker band at 135 cm-1 within a few hundred femtoseconds, suggesting a rapid weakening of the hydrogen bond that anchors the chromophore. We also track formation of the first ground-state intermediate over the first few picoseconds and fully characterize its vibrational structure, revealing a substantially-twisted cis conformation.
Collapse
|
6
|
Zhu J, Vreede J, Hospes M, Arents J, Kennis JTM, van Stokkum IHM, Hellingwerf KJ, Groot ML. Short Hydrogen Bonds and Negative Charge in Photoactive Yellow Protein Promote Fast Isomerization but not High Quantum Yield. J Phys Chem B 2014; 119:2372-83. [DOI: 10.1021/jp506785q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jingyi Zhu
- Department
of Physics and Astronomy, Faculty of Sciences, LaserLab, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | | | | | | | - John T. M. Kennis
- Department
of Physics and Astronomy, Faculty of Sciences, LaserLab, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Ivo H. M. van Stokkum
- Department
of Physics and Astronomy, Faculty of Sciences, LaserLab, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | | | - Marie Louise Groot
- Department
of Physics and Astronomy, Faculty of Sciences, LaserLab, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| |
Collapse
|
7
|
Creelman M, Kumauchi M, Hoff WD, Mathies RA. Chromophore Dynamics in the PYP Photocycle from Femtosecond Stimulated Raman Spectroscopy. J Phys Chem B 2014; 118:659-67. [DOI: 10.1021/jp408584v] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Mark Creelman
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Masato Kumauchi
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Wouter D. Hoff
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Richard A. Mathies
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| |
Collapse
|
8
|
Jung YO, Lee JH, Kim J, Schmidt M, Moffat K, Srajer V, Ihee H. Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography. Nat Chem 2013; 5:212-20. [PMID: 23422563 PMCID: PMC3579544 DOI: 10.1038/nchem.1565] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/19/2012] [Indexed: 12/23/2022]
Abstract
Trans-to-cis isomerization, the key reaction in photoactive proteins, usually cannot occur through the standard one-bond-flip mechanism. Owing to spatial constraints imposed by a protein environment, isomerization probably proceeds through a volume-conserving mechanism in which highly choreographed atomic motions are expected, the details of which have not yet been observed directly. Here we employ time-resolved X-ray crystallography to visualize structurally the isomerization of the p-coumaric acid chromophore in photoactive yellow protein with a time resolution of 100 ps and a spatial resolution of 1.6 Å. The structure of the earliest intermediate (I(T)) resembles a highly strained transition state in which the torsion angle is located halfway between the trans- and cis-isomers. The reaction trajectory of I(T) bifurcates into two structurally distinct cis intermediates via hula-twist and bicycle-pedal pathways. The bifurcating reaction pathways can be controlled by weakening the hydrogen bond between the chromophore and an adjacent residue through E46Q mutation, which switches off the bicycle-pedal pathway.
Collapse
Affiliation(s)
- Yang Ouk Jung
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, Republic of Korea
| | | | | | | | | | | | | |
Collapse
|
9
|
Nakamura R, Hamada N, Abe K, Yoshizawa M. Ultrafast hydrogen-bonding dynamics in the electronic excited state of photoactive yellow protein revealed by femtosecond stimulated Raman spectroscopy. J Phys Chem B 2012; 116:14768-75. [PMID: 23210980 DOI: 10.1021/jp308433a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ultrafast structural dynamics in the electronic excited state of photoactive yellow protein (PYP) is studied by femtosecond stimulated Raman spectroscopy. Stimulated Raman spectra in the electronic excited state, S(1), can be obtained by using a Raman pump pulse in resonance with the S(1)-S(0) transition. This is confirmed by comparing the experimental results with numerical calculations based on the density matrix treatment. We also investigate the hydrogen-bonding network surrounding the wild-type (WT)-PYP chromophore in the ground and excited states by comparing its stimulated Raman spectra with those of the E46Q-PYP mutant. We focus on the relative intensity of the Raman band at 1555 cm(-1), which includes both vinyl bond C═C stretching and ring vibrations and is sensitive to the hydrogen-bonding network around the phenolic oxygen of the chromophore. The relative intensity for the WT-PYP decreases after actinic excitation within the 150 fs time resolution and reaches a similar intensity to that for E46Q-PYP. These observations indicate that the WT-PYP hydrogen-bonding network is immediately rearranged in the electronic excited state to form a structure similar to that of E46Q-PYP.
Collapse
Affiliation(s)
- Ryosuke Nakamura
- Science and Technology Entrepreneurship Laboratory, Osaka University, Suita, Osaka, Japan.
| | | | | | | |
Collapse
|
10
|
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: 145] [Impact Index Per Article: 12.1] [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.
Collapse
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
| |
Collapse
|
11
|
On the involvement of single-bond rotation in the primary photochemistry of photoactive yellow protein. Biophys J 2011; 101:1184-92. [PMID: 21889456 DOI: 10.1016/j.bpj.2011.06.065] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 06/09/2011] [Accepted: 06/17/2011] [Indexed: 11/21/2022] Open
Abstract
Prior experimental observations, as well as theoretical considerations, have led to the proposal that C(4)-C(7) single-bond rotation may play an important role in the primary photochemistry of photoactive yellow protein (PYP). We therefore synthesized an analog of this protein's 4-hydroxy-cinnamic acid chromophore, (5-hydroxy indan-(1E)-ylidene)acetic acid, in which rotation across the C(4)-C(7) single bond has been locked with an ethane bridge, and we reconstituted the apo form of the wild-type protein and its R52A derivative with this chromophore analog. In PYP reconstituted with the rotation-locked chromophore, 1), absorption spectra of ground and intermediate states are slightly blue-shifted; 2), the quantum yield of photochemistry is ∼60% reduced; 3), the excited-state dynamics of the chromophore are accelerated; and 4), dynamics of the thermal recovery reaction of the protein are accelerated. A significant finding was that the yield of the transient ground-state intermediate in the early phase of the photocycle was considerably higher in the rotation-locked samples than in the corresponding samples reconstituted with p-coumaric acid. In contrast to theoretical predictions, the initial photocycle dynamics of PYP were observed to be not affected by the charge of the amino acid residue at position 52, which was varied by 1), varying the pH of the sample between 5 and 10; and 2), site-directed mutagenesis to construct R52A. These results imply that C(4)-C(7) single-bond rotation in PYP is not an alternative to C(7)=C(8) double-bond rotation, in case the nearby positive charge of R52 is absent, but rather facilitates, presumably with a compensatory movement, the physiological Z/E isomerization of the blue-light-absorbing chromophore.
Collapse
|
12
|
Deshmukh SS, Williams JC, Allen JP, Kálmán L. Light-Induced Conformational Changes in Photosynthetic Reaction Centers: Dielectric Relaxation in the Vicinity of the Dimer. Biochemistry 2010; 50:340-8. [DOI: 10.1021/bi101496c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Sasmit S. Deshmukh
- Department of Physics, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - JoAnn C. Williams
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - James P. Allen
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - László Kálmán
- Department of Physics, Concordia University, Montreal, Quebec H4B 1R6, Canada
| |
Collapse
|
13
|
Usman A, Asahi T, Sugiyama T, Masuhara H, Tohnai N, Miyata M. Photochemical Reaction of p-hydroxycinnamic-thiophenyl Ester in the Microcrystalline State. J Phys Chem B 2010; 114:14233-40. [DOI: 10.1021/jp909850r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Anwar Usman
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan, Department of Applied Physics, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan, Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan, and Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka
| | - Tsuyoshi Asahi
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan, Department of Applied Physics, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan, Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan, and Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka
| | - Teruki Sugiyama
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan, Department of Applied Physics, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan, Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan, and Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka
| | - Hiroshi Masuhara
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan, Department of Applied Physics, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan, Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan, and Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka
| | - Norimitsu Tohnai
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan, Department of Applied Physics, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan, Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan, and Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka
| | - Mikiji Miyata
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan, Department of Applied Physics, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan, Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan, and Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka
| |
Collapse
|
14
|
Kodali G, Siddiqui SU, Stanley RJ. Charge redistribution in oxidized and semiquinone E. coli DNA photolyase upon photoexcitation: stark spectroscopy reveals a rationale for the position of Trp382. J Am Chem Soc 2009; 131:4795-807. [PMID: 19292445 DOI: 10.1021/ja809214r] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The electronic structure of the two lowest excited electronic states of FAD and FADH(*) in folate-depleted E. coli DNA photolyase (PL(OX) and PL(SQ), respectively) was measured using absorption Stark spectroscopy. The experimental analysis was supported by TDDFT calculations of both the charge redistribution and the difference dipole moments for the transitions of both oxidation states using lumiflavin as a model. The difference dipole moments and polarizabilities for PL(OX) are similar to those obtained in our previous work for flavins in simple solvents and in an FMN-containing flavoprotein. No such comparison can be made for PL(SQ), as we believe this to be the first experimental report of the direction and magnitude of excited-state charge redistribution in any flavosemiquinone. The picture that emerges from these studies is discussed in the context of electron transfer in photolyase, particularly for the semiquinone photoreduction process, which involves nearby tryptophan residues as electron donors. The direction of charge displacement derived from an analysis of the Stark spectra rationalizes the positioning of the critical Trp382 residue relative to the flavin for efficient vectorial electron transfer leading to photoreduction. The ramifications of vectorial charge redistribution are discussed in the context of the wider class of flavoprotein blue light photoreceptors.
Collapse
Affiliation(s)
- Goutham Kodali
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | | | | |
Collapse
|
15
|
Hydrogen bond dynamics in the active site of photoactive yellow protein. Proc Natl Acad Sci U S A 2009; 106:9232-7. [PMID: 19470452 DOI: 10.1073/pnas.0900168106] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrogen bonds play major roles in biological structure and function. Nonetheless, hydrogen-bonded protons are not typically observed by X-ray crystallography, and most structural studies provide limited insight into the conformational plasticity of individual hydrogen bonds or the dynamical coupling present within hydrogen bond networks. We report the NMR detection of the hydrogen-bonded protons donated by Tyr-42 and Glu-46 to the chromophore oxygen in the active site of the bacterial photoreceptor, photoactive yellow protein (PYP). We have used the NMR resonances for these hydrogen bonds to probe their conformational properties and ability to rearrange in response to nearby electronic perturbation. The detection of geometric isotope effects transmitted between the Tyr-42 and Glu-46 hydrogen bonds provides strong evidence for robust coupling of their equilibrium conformations. Incorporation of a modified chromophore containing an electron-withdrawing cyano group to delocalize negative charge from the chromophore oxygen, analogous to the electronic rearrangement detected upon photon absorption, results in a lengthening of the Tyr-42 and Glu-46 hydrogen bonds and an attenuated hydrogen bond coupling. The results herein elucidate fundamental properties of hydrogen bonds within the complex environment of a protein interior. Furthermore, the robust conformational coupling and plasticity of hydrogen bonds observed in the PYP active site may facilitate the larger-scale dynamical coupling and signal transduction inherent to the biological function that PYP has evolved to carry out and may provide a model for other coupled dynamic systems.
Collapse
|
16
|
Abstract
Low-barrier hydrogen bonds (LBHBs) have been proposed to play roles in protein functions, including enzymatic catalysis and proton transfer. Transient formation of LBHBs is expected to stabilize specific reaction intermediates. However, based on experimental results and theoretical considerations, arguments against the importance of LBHB in proteins have been raised. The discrepancy is caused by the absence of direct identification of the hydrogen atom position. Here, we show by high-resolution neutron crystallography of photoactive yellow protein (PYP) that a LBHB exists in a protein, even in the ground state. We identified approximately 87% (819/942) of the hydrogen positions in PYP and demonstrated that the hydrogen bond between the chromophore and E46 is a LBHB. This LBHB stabilizes an isolated electric charge buried in the hydrophobic environment of the protein interior. We propose that in the excited state the fast relaxation of the LBHB into a normal hydrogen bond is the trigger for photo-signal propagation to the protein moiety. These results give insights into the novel roles of LBHBs and the mechanism of the formation of LBHBs.
Collapse
|
17
|
Hydrogen bond switching among flavin and amino acid side chains in the BLUF photoreceptor observed by ultrafast infrared spectroscopy. Biophys J 2008; 95:4790-802. [PMID: 18708458 DOI: 10.1529/biophysj.108.139246] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BLUF domains constitute a recently discovered class of photoreceptor proteins found in bacteria and eukaryotic algae. BLUF domains are blue-light sensitive through a FAD cofactor that is involved in an extensive hydrogen-bond network with nearby amino acid side chains, including a highly conserved tyrosine and glutamine. The participation of particular amino acid side chains in the ultrafast hydrogen-bond switching reaction with FAD that underlies photoactivation of BLUF domains is assessed by means of ultrafast infrared spectroscopy. Blue-light absorption by FAD results in formation of FAD(*-) and a bleach of the tyrosine ring vibrational mode on a picosecond timescale, showing that electron transfer from tyrosine to FAD constitutes the primary photochemistry. This interpretation is supported by the absence of a kinetic isotope effect on the fluorescence decay on H/D exchange. Subsequent protonation of FAD(*-) to result in FADH(*) on a picosecond timescale is evidenced by the appearance of a N-H bending mode at the FAD N5 protonation site and of a FADH(*) C=N stretch marker mode, with tyrosine as the likely proton donor. FADH(*) is reoxidized in 67 ps (180 ps in D(2)O) to result in a long-lived hydrogen-bond switched network around FAD. This hydrogen-bond switch shows infrared signatures from the C-OH stretch of tyrosine and the FAD C4=O and C=N stretches, which indicate increased hydrogen-bond strength at all these sites. The results support a previously hypothesized rotation of glutamine by approximately 180 degrees through a light-driven radical-pair mechanism as the determinant of the hydrogen-bond switch.
Collapse
|
18
|
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)
| |
Collapse
|
19
|
Altun A, Yokoyama S, Morokuma K. Quantum mechanical/molecular mechanical studies on spectral tuning mechanisms of visual pigments and other photoactive proteins. Photochem Photobiol 2008; 84:845-54. [PMID: 18331400 DOI: 10.1111/j.1751-1097.2008.00308.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The protein environments surrounding the retinal tune electronic absorption maximum from 350 to 630 nm. Hybrid quantum mechanical/molecular mechanical (QM/MM) methods can be used in calculating excitation energies of retinal in its native protein environments and in studying the molecular basis of spectral tuning. We hereby review recent QM/MM results on the phototransduction of bovine rhodopsin, bacteriorhodopsin, sensory rhodopsin II, nonretinal photoactive yellow protein and their mutants.
Collapse
Affiliation(s)
- Ahmet Altun
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, GA, USA
| | | | | |
Collapse
|
20
|
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]
|
21
|
Mizuno M, Hamada N, Tokunaga F, Mizutani Y. Picosecond Protein Response to the Chromophore Isomerization of Photoactive Yellow Protein: Selective Observation of Tyrosine and Tryptophan Residues by Time-Resolved Ultraviolet Resonance Raman Spectroscopy. J Phys Chem B 2007; 111:6293-6. [PMID: 17523627 DOI: 10.1021/jp072939d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Picosecond time-resolved ultraviolet resonance Raman (UVRR) spectra of photoactive yellow protein (PYP) were measured. UVRR bands attributed to the vibration of tyrosine and tryptophan residues showed a spectral change upon photoreaction. It was found that the hydrogen-bond strength between the chromophore and Y42 increases in the pG* state. The ultrafast change in the tryptophan band revealed that a photoinduced structural change of the chromophore had propagated to the W119 region, located 12 A from the chromophore, within picoseconds.
Collapse
|
22
|
Changenet-Barret P, Plaza P, Martin MM, Chosrowjan H, Taniguchi S, Mataga N, Imamoto Y, Kataoka M. Role of arginine 52 on the primary photoinduced events in the PYP photocycle. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2006.12.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
23
|
Topolancik J, Vollmer F. Photoinduced transformations in bacteriorhodopsin membrane monitored with optical microcavities. Biophys J 2007; 92:2223-9. [PMID: 17208972 PMCID: PMC1861786 DOI: 10.1529/biophysj.106.098806] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photoinduced molecular transformations in a self-assembled bacteriorhodopsin (bR) monolayer are monitored by observing shifts in the near-infrared resonant wavelengths of linearly polarized modes circulating in a microsphere cavity. We quantify the molecular polarizability change upon all-trans to 13-cis isomerization and deprotonation of the chromophore retinal ( approximately -57 A(3)) and determine its orientation relative to the bR membrane ( approximately 61 degrees ). Our observations establish optical microcavities as a sensitive off-resonant spectroscopic tool for probing conformations and orientations of molecular self-assemblies and for measuring changes of molecular polarizability at optical frequencies. We provide a general estimate of the sensitivity of the technique and discuss possible applications.
Collapse
Affiliation(s)
- Juraj Topolancik
- Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts 02142, USA
| | | |
Collapse
|
24
|
van der Horst MA, Arents JC, Kort R, Hellingwerf KJ. Binding, tuning and mechanical function of the 4-hydroxy-cinnamic acid chromophore in photoactive yellow protein. Photochem Photobiol Sci 2007; 6:571-9. [PMID: 17487311 DOI: 10.1039/b701072a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bacterial photoreceptor protein photoactive yellow protein (PYP) covalently binds the chromophore 4-hydroxy coumaric acid, tuning (spectral) characteristics of this cofactor. Here, we study this binding and tuning using a combination of pointmutations and chromophore analogs. In all photosensor proteins studied to date the covalent linkage of the chromophore to the apoprotein is dispensable for light-induced catalytic activation. We analyzed the functional importance of the covalent linkage using an isosteric chromophore-protein variant in which the cysteine is replaced by a glycine residue and the chromophore by thiomethyl-p-coumaric acid (TMpCA). The model compound TMpCA is shown to weakly complex with the C69G protein. This non-covalent binding results in considerable tuning of both the pKa and the color of the chromophore. The photoactivity of this system, however, was strongly impaired, making PYP the first known photosensor protein in which the covalent linkage of the chromophore is of paramount importance for the functional activity of the protein in vitro. We also studied the influence of chromophore analogs on the color and photocycle of PYP, not only in WT, but especially in the E46Q mutant, to test if effects from both chromophore and protein modifications are additive. When the E46Q protein binds the sinapinic acid chromophore, the color of the protein is effectively changed from yellow to orange. The altered charge distribution in this protein also results in a changed pKa value for chromophore protonation, and a strongly impaired photocycle. Both findings extend our knowledge of the photochemistry of PYP for signal generation.
Collapse
Affiliation(s)
- Michael A van der Horst
- Laboratory for Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV, Amsterdam, The Netherlands
| | | | | | | |
Collapse
|
25
|
van Wilderen LJGW, van der Horst MA, van Stokkum IHM, Hellingwerf KJ, van Grondelle R, Groot ML. Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein. Proc Natl Acad Sci U S A 2006; 103:15050-5. [PMID: 17015839 PMCID: PMC1940041 DOI: 10.1073/pnas.0603476103] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photoactive proteins such as PYP (photoactive yellow protein) are generally accepted as model systems for studying protein signal state formation. PYP is a blue-light sensor from the bacterium Halorhodospira halophila. The formation of PYP's signaling state is initiated by trans-cis isomerization of the p-coumaric acid chromophore upon the absorption of light. The quantum yield of signaling state formation is approximately 0.3. Using femtosecond visible pump/mid-IR probe spectroscopy, we investigated the structure of the very short-lived ground state intermediate (GSI) that results from an unsuccessful attempt to enter the photocycle. This intermediate and the first stable GSI on pathway into the photocycle, I0, both have a mid-IR difference spectrum that is characteristic of a cis isomer, but only the I0 intermediate has a chromophore with a broken hydrogen bond with the backbone N atom of Cys-69. We suggest, therefore, that breaking this hydrogen bond is decisive for a successful entry into the photocycle. The chromophore also engages in a hydrogen-bonding network by means of its phenolate group with residues Tyr-42 and Glu-46. We have investigated the role of this hydrogen bond by exchanging the H bond-donating residue Glu-46 with the weaker H bond-donating glutamine (i.e., Gln-46). We have observed that this mutant exhibits virtually identical kinetics and product yields as WT PYP, even though during the I0-to-I1 transition, on the 800-ps time scale, the hydrogen bond of the chromophore with Gln-46 is broken, whereas this hydrogen bond remains intact with Glu-46.
Collapse
Affiliation(s)
- L J G W van Wilderen
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
| | | | | | | | | | | |
Collapse
|
26
|
Kawaguchi K, Yamato T. Theoretical prediction of optical absorption maxima for photosensory receptor mutants. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.08.141] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
27
|
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.
Collapse
Affiliation(s)
- Irene Burghardt
- Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France
| | | |
Collapse
|
28
|
Espagne A, Paik DH, Changenet-Barret P, Martin MM, Zewail AH. Ultrafast Photoisomerization of Photoactive Yellow Protein Chromophore Analogues in Solution: Influence of the Protonation State. Chemphyschem 2006; 7:1717-26. [PMID: 16847839 DOI: 10.1002/cphc.200600137] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We investigate solvent viscosity and polarity effects on the photoisomerization of the protonated and deprotonated forms of two analogues of the photoactive yellow protein (PYP) chromophore. These are trans-p-hydroxybenzylidene acetone and trans-p-hydroxyphenyl cinnamate, studied in solutions of different polarity and viscosity at room temperature, by means of femtosecond fluorescence up-conversion. The fluorescence lifetimes of the protonated forms are found to be barely sensitive to solvent viscosity, and to increase with increasing solvent polarity. In contrast, the fluorescence decays of the deprotonated forms are significantly slowed down in viscous media and accelerated in polar solvents. These results elucidate the dramatic influence of the protonation state of the PYP chromophore analogues on their photoinduced dynamics. The viscosity and polarity effects are, respectively, interpreted in terms of different isomerization coordinates and charge redistribution in S(1). A trans-to-cis isomerization mechanism involving mainly the ethylenic double-bond torsion and/or solvation is proposed for the anionic forms, whereas "concerted" intramolecular motions are proposed for the neutral forms.
Collapse
Affiliation(s)
- Agathe Espagne
- UMR CNRS-ENS 8640 Pasteur, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France
| | | | | | | | | |
Collapse
|
29
|
Abstract
The photoactive yellow protein (PYP) is the photoreceptor protein responsible for initiating the blue-light repellent response of the Halorhodospira halophila bacterium. Optical excitation of the intrinsic chromophore in PYP, p-coumaric acid, leads to the initiation of a photocycle that comprises several distinct intermediates. The dynamical processes responsible for the initiation of the PYP photocycle have been explored with several time-resolved techniques, which include ultrafast electronic and vibrational spectroscopies. Ultrafast electronic spectroscopies, such as pump-visible probe, pump-dump-visible probe, and fluorescence upconversion, are useful in identifying the timescales and connectivity of the transient intermediates, while ultrafast vibrational spectroscopies link these intermediates to dynamic structures. Herein, we present the use of these techniques for exploring the initial dynamics of PYP, and show how these techniques provide the basis for understanding the complex relationship between protein and chromophore, which ultimately results in biological function.
Collapse
Affiliation(s)
- Delmar S Larsen
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
| | | |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
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.
Collapse
Affiliation(s)
- Agathe Espagne
- Département de Chimie, Ecole Normale Supérieure (UMR CNRS 8640 PASTEUR), 24 rue Lhomond, 75231 Paris Cedex 05, France
| | | | | | | |
Collapse
|
32
|
Premvardhan L, van der Horst MA, Hellingwerf KJ, van Grondelle R. How light-induced charge transfer accelerates the receptor-state recovery of photoactive yellow protein from its signaling state. Biophys J 2005; 89:L64-6. [PMID: 16258045 PMCID: PMC1367008 DOI: 10.1529/biophysj.105.075275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stark (electroabsorption) spectra of the M100A mutant of photoactive yellow protein reveal that the neutral, cis cofactor of the pB intermediate undergoes a strikingly large change in the static dipole moment (|Deltamu| = 19 Debye) on photon absorption. The formation of this charge-separated species, in the excited state, precedes the cis --> trans isomerization of the pB cofactor and the regeneration of pG. The large |Deltamu|, reminiscent of that produced on the excitation of pG, we propose, induces twisting of the cis cofactor as a result of translocation of negative charge, from the hydroxyl oxygen, O1, toward the C7-C8 double bond. The biological significance of this photoinduced charge transfer reaction underlies the significantly faster regeneration of pG from pB in vitro, on the absorption of blue light.
Collapse
Affiliation(s)
- L Premvardhan
- Department of Biophysics and Physics of Complex Systems, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands.
| | | | | | | |
Collapse
|
33
|
Premvardhan L, Papagiannakis E, Hiller RG, van Grondelle R. The Charge-Transfer Character of the S0 → S2 Transition in the Carotenoid Peridinin Is Revealed by Stark Spectroscopy. J Phys Chem B 2005; 109:15589-97. [PMID: 16852977 DOI: 10.1021/jp052027g] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peridinin, the carotenoid in the peridinin chlorophyll a protein (PCP), was studied by Stark (electroabsorption) spectroscopy to determine the change in electrostatic properties produced on excitation within the absorption band, in methyl tetrahydrofuran (MeTHF) versus ethylene glycol (EG), at 77 K. Strikingly, a large change in the permanent dipole moment (|Deltamu|) was found between the ground state, S(0) (1(1)A(g)(-)), and the Franck-Condon region of the S(2) (1(1)B(u)(+)) excited state, in both MeTHF (22 D) and EG (approximately 27 D), thus revealing the previously unknown charge transfer (CT) character of this pi-pi transition in peridinin. Such a large |Deltamu| produced on excitation, we suggest, facilitates the bending of the lactone moiety, toward which charge transfer occurs, and the subsequent formation of the previously identified intramolecular CT (ICT) state at lower energy. This unexpectedly large S(2) dipole moment, which has not been predicted even from high-level electronic structure calculations, is supported by calculating the shift of the peridinin absorption band as a function of solvent polarity, using the experimentally derived result. Overall, the photoinduced charge transfer uncovered here is expected to affect the excited-state reactivity of peridinin and, within the protein, be important for efficient energy transfer from the carotenoid S(2) and S(1)/ICT states to the chlorophylls in PCP.
Collapse
Affiliation(s)
- Lavanya 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.
| | | | | | | |
Collapse
|
34
|
Larsen DS, van Stokkum IHM, Vengris M, van Der Horst MA, de Weerd FL, Hellingwerf KJ, van Grondelle R. Incoherent manipulation of the photoactive yellow protein photocycle with dispersed pump-dump-probe spectroscopy. Biophys J 2005; 87:1858-72. [PMID: 15345564 PMCID: PMC1304590 DOI: 10.1529/biophysj.104.043794] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photoactive yellow protein is the protein responsible for initiating the "blue-light vision" of Halorhodospira halophila. The dynamical processes responsible for triggering the photoactive yellow protein photocycle have been disentangled with the use of a novel application of dispersed ultrafast pump-dump-probe spectroscopy, where the photocycle can be started and interrupted with appropriately tuned and timed laser pulses. This "incoherent" manipulation of the photocycle allows for the detailed spectroscopic investigation of the underlying photocycle dynamics and the construction of a fully self-consistent dynamical model. This model requires three kinetically distinct excited-state intermediates, two (ground-state) photocycle intermediates, I(0) and pR, and a ground-state intermediate through which the protein, after unsuccessful attempts at initiating the photocycle, returns to the equilibrium ground state. Also observed is a previously unknown two-photon ionization channel that generates a radical and an ejected electron into the protein environment. This second excitation pathway evolves simultaneously with the pathway containing the one-photon photocycle intermediates.
Collapse
Affiliation(s)
- Delmar S Larsen
- Faculty of Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
35
|
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
| |
Collapse
|
36
|
Groot ML, van Wilderen LJGW, Larsen DS, van der Horst MA, van Stokkum IHM, Hellingwerf KJ, van Grondelle R. Initial steps of signal generation in photoactive yellow protein revealed with femtosecond mid-infrared spectroscopy. Biochemistry 2003; 42:10054-9. [PMID: 12939133 DOI: 10.1021/bi034878p] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photoactive yellow protein (PYP) is a bacterial blue light sensor that induces Halorhodospira halophila to swim away from intense blue light. Light absorption by PYP's intrinsic chromophore, p-coumaric acid, leads to the initiation of a photocycle that comprises several distinct intermediates. Here we describe the initial structural changes of the chromophore and its nearby amino acids, using visible pump/mid-infrared probe spectroscopy. Upon photoexcitation, the trans bands of the chromophore are bleached, and shifts of the phenol ring bands occur. The latter are ascribed to charge translocation, which probably plays an essential role in driving the trans to cis isomerization process. We conclude that breaking of the hydrogen bond of the chromophore's C=O group with amino acid Cys69 and formation of a stable cis ground state occur in approximately 2 ps. Dynamic changes also include rearrangements of the hydrogen-bonding network of the amino acids around the chromophore. Relaxation of the coumaryl tail of the chromophore occurs in 0.9-1 ns, which event we identify with the I(0) to I(1) transition observed in visible spectroscopy.
Collapse
Affiliation(s)
- Marie Louise Groot
- Faculty of Sciences, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|