1
|
Konold PE, Arik E, Weißenborn J, Arents JC, Hellingwerf KJ, van Stokkum IHM, Kennis JTM, Groot ML. Confinement in crystal lattice alters entire photocycle pathway of the Photoactive Yellow Protein. Nat Commun 2020; 11:4248. [PMID: 32843623 PMCID: PMC7447820 DOI: 10.1038/s41467-020-18065-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 07/31/2020] [Indexed: 11/27/2022] Open
Abstract
Femtosecond time-resolved crystallography (TRC) on proteins enables resolving the spatial structure of short-lived photocycle intermediates. An open question is whether confinement and lower hydration of the proteins in the crystalline state affect the light-induced structural transformations. Here, we measured the full photocycle dynamics of a signal transduction protein often used as model system in TRC, Photoactive Yellow Protein (PYP), in the crystalline state and compared those to the dynamics in solution, utilizing electronic and vibrational transient absorption measurements from 100 fs over 12 decades in time. We find that the photocycle kinetics and structural dynamics of PYP in the crystalline form deviate from those in solution from the very first steps following photon absorption. This illustrates that ultrafast TRC results cannot be uncritically extrapolated to in vivo function, and that comparative spectroscopic experiments on proteins in crystalline and solution states can help identify structural intermediates under native conditions. Protein structural dynamics can be studied by time-resolved crystallography (TRC) and ultrafast transient spectroscopic methods. Here, the authors perform electronic and vibrational transient absorption measurements to characterise the full photocycle of Photoactive Yellow Protein (PYP) both in the crystalline and solution state and find that the photocycle kinetics and structural intermediates of PYP deviate in the crystalline state, which must be taken into consideration when planning TRC experiments.
Collapse
Affiliation(s)
- Patrick E Konold
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Enis Arik
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Jörn Weißenborn
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Jos C Arents
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park, 1098, XH, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park, 1098, XH, Amsterdam, The Netherlands
| | - Ivo H M van Stokkum
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - John T M Kennis
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Marie Louise Groot
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
| |
Collapse
|
2
|
Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
Collapse
Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| |
Collapse
|
3
|
Yang C, Kim TW, Kim Y, Choi J, Lee SJ, Ihee H. Kinetics of the E46Q mutant of photoactive yellow protein investigated by transient grating spectroscopy. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
4
|
Kim TW, Yang C, Kim Y, Kim JG, Kim J, Jung YO, Jun S, Lee SJ, Park S, Kosheleva I, Henning R, van Thor JJ, Ihee H. Combined probes of X-ray scattering and optical spectroscopy reveal how global conformational change is temporally and spatially linked to local structural perturbation in photoactive yellow protein. Phys Chem Chem Phys 2017; 18:8911-8919. [PMID: 26960811 DOI: 10.1039/c6cp00476h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Real-time probing of structural transitions of a photoactive protein is challenging owing to the lack of a universal time-resolved technique that can probe the changes in both global conformation and light-absorbing chromophores of the protein. In this work, we combine time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) spectroscopy to investigate how the global conformational changes involved in the photoinduced signal transduction of photoactive yellow protein (PYP) is temporally and spatially related to the local structural change around the light-absorbing chromophore. In particular, we examine the role of internal proton transfer in developing a signaling state of PYP by employing its E46Q mutant (E46Q-PYP), where the internal proton transfer is inhibited by the replacement of a proton donor. The comparison of TRXSS and TA spectroscopy data directly reveals that the global conformational change of the protein, which is probed by TRXSS, is temporally delayed by tens of microseconds from the local structural change of the chromophore, which is probed by TA spectroscopy. The molecular shape of the signaling state reconstructed from the TRXSS curves directly visualizes the three-dimensional conformations of protein intermediates and reveals that the smaller structural change in E46Q-PYP than in wild-type PYP suggested by previous studies is manifested in terms of much smaller protrusion, confirming that the signaling state of E46Q-PYP is only partially developed compared with that of wild-type PYP. This finding provides direct evidence of how the environmental change in the vicinity of the chromophore alters the conformational change of the entire protein matrix.
Collapse
Affiliation(s)
- Tae Wu Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Cheolhee Yang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Youngmin Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Jong Goo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, Incheon 402-751, Korea
| | - Yang Ouk Jung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Sunhong Jun
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Sang Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Sungjun Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago IL 60637, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago IL 60637, USA
| | - Jasper J van Thor
- Division of Molecular Biosciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| |
Collapse
|
5
|
Naseem S, Laurent AD, Carroll EC, Vengris M, Kumauchi M, Hoff WD, Krylov AI, Larsen DS. Photo-isomerization upshifts the pKa of the Photoactive Yellow Protein chromophore to contribute to photocycle propagation. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.06.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
6
|
Liu J, Yabushita A, Taniguchi S, Chosrowjan H, Imamoto Y, Sueda K, Miyanaga N, Kobayashi T. Ultrafast Time-Resolved Pump–Probe Spectroscopy of PYP by a Sub-8 fs Pulse Laser at 400 nm. J Phys Chem B 2013; 117:4818-26. [DOI: 10.1021/jp4001016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jun Liu
- Advanced Ultrafast Laser Research
Center, University of Electro-Communications, Chofugaoka 1-5-1, Chofu, Tokyo 182-8585 Japan
- State Key Laboratory of High
Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800, China
- Core Research for Evolutional
Science and Technology (CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Atsushi Yabushita
- Department of Electrophysics, National Chiao Tung University, 1001 Ta Hsueh Road,
Hsinchu 300, Taiwan
| | - Seiji Taniguchi
- Institute
for Laser Technology, Osaka University,
Yamadaoka 2-6, Suita Osaka, 565-0871
Japan
| | - Haik Chosrowjan
- Institute
for Laser Technology, Osaka University,
Yamadaoka 2-6, Suita Osaka, 565-0871
Japan
| | - Yasushi Imamoto
- Department of Biophysics,
Graduate
School of Science, Kyoto University, Kitashirakawa-Oiwake,
Sakyo, Kyoto 606-8502 Japan
| | - Keiichi Sueda
- Institute of Laser Engineering, Osaka University, Yamadakami 2-6, Suita 565-0871, Ibaraki
567-0047, Japan
| | - Noriaki Miyanaga
- Institute of Laser Engineering, Osaka University, Yamadakami 2-6, Suita 565-0871, Ibaraki
567-0047, Japan
| | - Takayoshi Kobayashi
- Advanced Ultrafast Laser Research
Center, University of Electro-Communications, Chofugaoka 1-5-1, Chofu, Tokyo 182-8585 Japan
- Core Research for Evolutional
Science and Technology (CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Department of Electrophysics, National Chiao Tung University, 1001 Ta Hsueh Road,
Hsinchu 300, Taiwan
- Institute of Laser Engineering, Osaka University, Yamadakami 2-6, Suita 565-0871, Ibaraki
567-0047, Japan
| |
Collapse
|
7
|
Nakamura R, Hamada N, Abe K, Yoshizawa M. Structural Evolution in Photoactive Yellow Protein Studied by Femtosecond Stimulated Raman Spectroscopy. EPJ WEB OF CONFERENCES 2013. [DOI: 10.1051/epjconf/20134107008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
8
|
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
|
9
|
Nakamura R, Hamada N, Ichida H, Tokunaga F, Kanematsu Y. Transient Vibronic Structure in Ultrafast Fluorescence Spectra of Photoactive Yellow Protein. Photochem Photobiol 2008; 84:937-40. [DOI: 10.1111/j.1751-1097.2008.00329.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
10
|
Kühn O, Wöste L. Biological systems: Applications and perspectives. ANALYSIS AND CONTROL OF ULTRAFAST PHOTOINDUCED REACTIONS 2007. [PMCID: PMC7122019 DOI: 10.1007/978-3-540-68038-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Oliver Kühn
- Institut f. Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, D-14195 Berlin, Germany
| | - Ludger Wöste
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| |
Collapse
|
11
|
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
|
12
|
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
|
13
|
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
|
14
|
Yeremenko S, van Stokkum IHM, Moffat K, Hellingwerf KJ. Influence of the crystalline state on photoinduced dynamics of photoactive yellow protein studied by ultraviolet-visible transient absorption spectroscopy. Biophys J 2006; 90:4224-35. [PMID: 16513787 PMCID: PMC1459521 DOI: 10.1529/biophysj.105.074765] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Time-resolved ultraviolet-visible spectroscopy was used to characterize the photocycle transitions in single crystals of wild-type and the E-46Q mutant of photoactive yellow protein (PYP) with microsecond time resolution. The results were compared with the results of similar measurements on aqueous solutions of these two variants of PYP, with and without the components present in the mother liquor of crystals. The experimental data were analyzed with global and target analysis. Distinct differences in the reaction path of a PYP molecule are observed between these conditions when it progresses through its photocycle. In the crystalline state i), much faster relaxation of the late blue-shifted photocycle intermediate back to the ground state is observed; ii), this intermediate in crystalline PYP absorbs at 380 nm, rather than at 350-360 nm in solution; and iii), for various intermediates of this photocycle the forward reaction through the photocycle directly competes with a branching reaction that leads directly to the ground state. Significantly, with these altered characteristics, the spectroscopic data on PYP are fully consistent with the structural data obtained for this photoreceptor protein with time-resolved x-ray diffraction analysis, particularly for wild-type PYP.
Collapse
Affiliation(s)
- Sergey Yeremenko
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, NL-1018 WV Amsterdam, The Netherlands
| | | | | | | |
Collapse
|
15
|
Shimizu N, Imamoto Y, Harigai M, Kamikubo H, Yamazaki Y, Kataoka M. pH-dependent Equilibrium between Long Lived Near-UV Intermediates of Photoactive Yellow Protein. J Biol Chem 2006; 281:4318-25. [PMID: 16368695 DOI: 10.1074/jbc.m506403200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The long lived intermediate (signaling state) of photoactive yellow protein (PYP(M)), which is formed in the photocycle, was characterized at various pHs. PYP(M) at neutral pH was in equilibrium between two spectroscopically distinct states. Absorption maxima of the acidic form (PYP(M)(acid)) and alkaline form (PYP(M)(alkali)) were located at 367 and 356 nm, respectively. Equilibrium was represented by the Henderson-Hasselbalch equation, in which apparent pK(a) was 6.4. Content of alpha- and/or beta-structure of PYP(M)(acid) was significantly greater than PYP(M)(alkali) as demonstrated by the molar ellipticity at 222 nm. In addition, changes in amide I and II modes of beta-structure in the difference Fourier transform infrared spectra for formation of PYP(M)(acid) was smaller than that of PYP(M)(alkali). The vibrational mode at 1747 cm(-1) of protonated Glu-46 was found as a small band for PYP(M)(acid) but not for PYP(M)(alkali), suggesting that Glu-46 remains partially protonated in PYP(M)(acid), whereas it is fully deprotonated in PYP(M)(alkali). Small angle x-ray scattering measurements demonstrated that the radius of gyration of PYP(M)(acid) was 15.7 Angstroms, whereas for PYP(M)(alkali) it was 16.2 Angstroms. These results indicate that PYP(M)(acid) assumes a more ordered and compact structure than PYP(M)(alkali). Binding of citrate shifts this equilibrium toward PYP(M)(alkali). UV-visible absorption spectra and difference infrared spectra of the long lived intermediate formed from E46Q mutant was consistent with those of PYP(M)(acid), indicating that the mutation shifts this equilibrium toward PYP(M)(acid). Alterations in the nature of PYP(M) by pH, citrate, and mutation of Glu-46 are consistently explained by the shift of the equilibrium between PYP(M)(acid) and PYP(M)(alkali).
Collapse
Affiliation(s)
- Nobutaka Shimizu
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Japan
| | | | | | | | | | | |
Collapse
|
16
|
Nibbering ETJ, Fidder H, Pines E. ULTRAFAST CHEMISTRY: Using Time-Resolved Vibrational Spectroscopy for Interrogation of Structural Dynamics. Annu Rev Phys Chem 2005; 56:337-67. [PMID: 15796704 DOI: 10.1146/annurev.physchem.56.092503.141314] [Citation(s) in RCA: 257] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Time-resolved infrared (IR) and Raman spectroscopy elucidates molecular structure evolution during ultrafast chemical reactions. Following vibrational marker modes in real time provides direct insight into the structural dynamics, as is evidenced in studies on intramolecular hydrogen transfer, bimolecular proton transfer, electron transfer, hydrogen bonding during solvation dynamics, bond fission in organometallic compounds and heme proteins, cis-trans isomerization in retinal proteins, and transformations in photochromic switch pairs. Femtosecond IR spectroscopy monitors the site-specific interactions in hydrogen bonds. Conversion between excited electronic states can be followed for intramolecular electron transfer by inspection of the fingerprint IR- or Raman-active vibrations in conjunction with quantum chemical calculations. Excess internal vibrational energy, generated either by optical excitation or by internal conversion from the electronic excited state to the ground state, is observable through transient frequency shifts of IR-active vibrations and through nonequilibrium populations as deduced by Raman resonances.
Collapse
Affiliation(s)
- Erik T J Nibbering
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany.
| | | | | |
Collapse
|
17
|
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
|
18
|
Excited state dynamics of a PYP chromophore model system explored with ultrafast infrared spectroscopy. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2004.11.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
19
|
Changenet-Barret P, Espagne A, Plaza P, Hellingwerf KJ, Martin MM. Investigations of the primary events in a bacterial photoreceptor for photomotility: photoactive yellow protein (PYP). NEW J CHEM 2005. [DOI: 10.1039/b418134d] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
20
|
Larsen DS, Vengris M, van Stokkum IHM, van der Horst MA, de Weerd FL, Hellingwerf KJ, van Grondelle R. Photoisomerization and photoionization of the photoactive yellow protein chromophore in solution. Biophys J 2004; 86:2538-50. [PMID: 15041690 PMCID: PMC1304101 DOI: 10.1016/s0006-3495(04)74309-x] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Dispersed pump-dump-probe spectroscopy has the ability to characterize and identify the underlying ultrafast dynamical processes in complicated chemical and biological systems. This technique builds on traditional pump-probe techniques by exploring both ground- and excited-state dynamics and characterizing the connectivity between constituent transient states. We have used the dispersed pump-dump-probe technique to investigate the ground-state dynamics and competing excited-state processes in the excitation-induced ultrafast dynamics of thiomethyl p-coumaric acid, a model chromophore for the photoreceptor photoactive yellow protein. Our results demonstrate the parallel formation of two relaxation pathways (with multiple transient states) that jointly lead to two different types of photochemistry: cis-trans isomerization and detachment of a hydrated electron. The relative transition rates and quantum yields of both pathways have been determined. We find that the relaxation of the photoexcited chromophores involves multiple, transient ground-state intermediates and the chromophore in solution does not generate persistent photoisomerized products, but instead undergoes photoionization resulting in the generation of detached electrons and radicals. These results are of great value in interpreting the more complex dynamical changes in the optical properties of the photoactive yellow protein.
Collapse
Affiliation(s)
- Delmar S Larsen
- Faculty of Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
21
|
Anderson S, Srajer V, Pahl R, Rajagopal S, Schotte F, Anfinrud P, Wulff M, Moffat K. Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein. Structure 2004; 12:1039-45. [PMID: 15274923 DOI: 10.1016/j.str.2004.04.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Revised: 04/01/2004] [Accepted: 04/05/2004] [Indexed: 11/29/2022]
Abstract
We use time-resolved crystallography to observe the structural progression of a bacterial blue light photoreceptor throughout its photocycle. Data were collected from 10 ns to 100 ms after photoactivation of the E46Q mutant of photoactive yellow protein. Refinement of transient chromophore conformations shows that the spectroscopically distinct intermediates are formed via progressive disruption of the hydrogen bond network to the chromophore. Although structural change occurs within a few nanoseconds on and around the chromophore, it takes milliseconds for a distinct pattern of tertiary structural change to fully progress through the entire molecule, thus generating the putative signaling state. Remarkably, the coupling between the chromophore conformation and the tertiary structure of this small protein is not tight: there are leads and lags between changes in the conformation of the chromophore and the protein tertiary structure.
Collapse
Affiliation(s)
- Spencer Anderson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Chosrowjan H, Taniguchi S, Mataga N, Unno M, Yamauchi S, Hamada N, Kumauchi M, Tokunaga F. Low-Frequency Vibrations and Their Role in Ultrafast Photoisomerization Reaction Dynamics of Photoactive Yellow Protein. J Phys Chem B 2004. [DOI: 10.1021/jp031126w] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haik Chosrowjan
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Seiji Taniguchi
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Noboru Mataga
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Masashi Unno
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Seigo Yamauchi
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Norio Hamada
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Masato Kumauchi
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Fumio Tokunaga
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| |
Collapse
|
23
|
Premvardhan LL, van der Horst MA, Hellingwerf KJ, van Grondelle R. Stark spectroscopy on photoactive yellow protein, E46Q, and a nonisomerizing derivative, probes photo-induced charge motion. Biophys J 2003; 84:3226-39. [PMID: 12719252 PMCID: PMC1302883 DOI: 10.1016/s0006-3495(03)70047-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The change in the electrostatic properties on excitation of the cofactor of wild-type photoactive yellow protein (WT-PYP) have been directly determined using Stark-effect spectroscopy. We find that, instantaneously on photon absorption, there is a large change in the permanent dipole moment, /Delta(-->)mu/, (26 Debye) and in the polarizability, (-)Deltaalpha, (1000 A(3)). We expect such a large degree of charge motion to have a significant impact on the photocycle that is associated with the important blue-light negative phototactic response of Halorhodospira halophila. Furthermore, changing E46 to Q in WT-PYP does not significantly alter its electrostatic properties, whereas, altering the chromophore to prevent it from undergoing trans-cis isomerization results in a significant diminution of /Delta(-->)mu/ and (-)Deltaalpha. We propose that the enormous charge motion that occurs on excitation of 4-hydroxycinnamyl thioester, the chromophore in WT-PYP, plays a crucial role in initiating the photocycle by translocation of the negative charge, localized on the phenolate oxygen in the ground state, across the chromophore. We hypothesize that this charge motion would consequently increase the flexibility of the thioester tail thereby decreasing the activation barrier for the rotation of this moiety in the excited state.
Collapse
Affiliation(s)
- L 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.
| | | | | | | |
Collapse
|
24
|
Hellingwerf KJ, Hendriks J, Gensch T. Photoactive Yellow Protein, A New Type of Photoreceptor Protein: Will This “Yellow Lab” Bring Us Where We Want to Go? J Phys Chem A 2003. [DOI: 10.1021/jp027005y] [Citation(s) in RCA: 248] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Klaas J. Hellingwerf
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences (SILS), BioCentrum, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Biological Information Processing 1, Research Centre Jülich, D-52425 Jülich, Germany
| | - Johnny Hendriks
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences (SILS), BioCentrum, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Biological Information Processing 1, Research Centre Jülich, D-52425 Jülich, Germany
| | - Thomas Gensch
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences (SILS), BioCentrum, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Biological Information Processing 1, Research Centre Jülich, D-52425 Jülich, Germany
| |
Collapse
|
25
|
Devanathan S, Lin S, Cusanovich MA, Woodbury N, Tollin G. Early photocycle kinetic behavior of the E46A and Y42F mutants of photoactive yellow protein: femtosecond spectroscopy. Biophys J 2001; 81:2314-9. [PMID: 11566800 PMCID: PMC1301701 DOI: 10.1016/s0006-3495(01)75877-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In the photoactive yellow protein, PYP, both Glu46 and Tyr42 form hydrogen bonds to the phenolic OH group of the p-hydroxycinnamoyl chromophore. Previous work on replacement of the carboxyl group of Glu46 by an amide group (Glu46Gln) has shown that changing the nature of this hydrogen bond has a minimal effect on the rate constant for the formation of the first intermediate (I(0)) and on the excited state lifetime, whereas the rate constants for the formation of the second (I(0)( not equal)) and third (I(1)) intermediates were increased by factors of approximately 30 and 5, respectively. In the present experiments, two additional mutants (Glu46Ala and Tyr42Phe) have been studied. These two mutants are shown to behave kinetically very similarly to one another. In both cases, the rate constant for I(0) formation is decreased by a factor of approximately 2, with little or no effect on the photochemical yield as a consequence of a compensating increase in the excited state lifetime. Although we are unable to resolve the rate constant for the formation of the second intermediate from that of the first intermediate, the rate constant for the formation of the third intermediate is increased by a factor of approximately 100. The structural implications of these results are discussed.
Collapse
Affiliation(s)
- S Devanathan
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
| | | | | | | | | |
Collapse
|