1
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Ashworth E, Coughlan NJA, Hopkins WS, Bieske EJ, Bull JN. Excited-State Barrier Controls E → Z Photoisomerization in p-Hydroxycinnamate Biochromophores. J Phys Chem Lett 2022; 13:9028-9034. [PMID: 36149746 PMCID: PMC9549896 DOI: 10.1021/acs.jpclett.2c02613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Molecules based on the deprotonated p-hydroxycinnamate moiety are widespread in nature, including serving as UV filters in the leaves of plants and as the biochromophore in photoactive yellow protein. The photophysical behavior of these chromophores is centered around a rapid E → Z photoisomerization by passage through a conical intersection seam. Here, we use photoisomerization and photodissociation action spectroscopies with deprotonated 4-hydroxybenzal acetone (pCK-) to characterize a wavelength-dependent bifurcation between electron autodetachment (spontaneous ejection of an electron from the S1 state because it is situated in the detachment continuum) and E → Z photoisomerization. While autodetachment occurs across the entire S1(ππ*) band (370-480 nm), E → Z photoisomerization occurs only over a blue portion of the band (370-430 nm). No E → Z photoisomerization is observed when the ketone functional group in pCK- is replaced with an ester or carboxylic acid. The wavelength-dependent bifurcation is consistent with potential energy surface calculations showing that a barrier separates the Franck-Condon region from the E → Z isomerizing conical intersection. The barrier height, which is substantially higher in the gas phase than in solution, depends on the functional group and governs whether E → Z photoisomerization occurs more rapidly than autodetachment.
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Affiliation(s)
- Eleanor
K. Ashworth
- School
of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Neville J. A. Coughlan
- Department
of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- WaterMine
Innovation, Inc., Waterloo, Ontario N0B 2T0, Canada
| | - W. Scott Hopkins
- Department
of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- WaterMine
Innovation, Inc., Waterloo, Ontario N0B 2T0, Canada
| | - Evan J. Bieske
- School
of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - James N. Bull
- School
of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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2
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van Wilderen LJGW, Blankenburg L, Bredenbeck J. Femtosecond-to-millisecond mid-IR spectroscopy of Photoactive Yellow Protein uncovers structural micro-transitions of the chromophore's protonation mechanism. J Chem Phys 2022; 156:205103. [DOI: 10.1063/5.0091918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Protein structural dynamics can span many orders of magnitude in time. Photoactive Yellow Protein's (PYP) reversible photocycle encompasses picosecond isomerization of the light-absorbing chromophore as well as large scale protein backbone motions occurring on a millisecond timescale. Femtosecond-to-millisecond time-resolved mid-Infrared (IR) spectroscopy is employed here to uncover structural details of photocycle intermediates up to chromophore protonation and the first structural changes leading to formation of the partially-unfolded signalling state pB. The data show that a commonly thought stable transient photocycle intermediate is actually formed after a sequence of several smaller structural changes. We provide residue-specific spectroscopic evidence that protonation of the chromophore on a hundreds of microseconds timescale is delayed with respect to deprotonation of the nearby E46 residue. That implies that the direct proton donor is not E46 but most likely a water molecule. Such details may assist ongoing photocycle and protein folding simulation efforts on the complex and wide time-spanning photocycle of the model system PYP.
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3
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Time-resolved infrared absorption spectroscopy applied to photoinduced reactions: how and why. Photochem Photobiol Sci 2022; 21:557-584. [DOI: 10.1007/s43630-022-00180-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/28/2022] [Indexed: 10/19/2022]
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4
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Effect of Hydrated Ionic Liquid on Photocycle and Dynamics of Photoactive Yellow Protein. Molecules 2021; 26:molecules26154554. [PMID: 34361707 PMCID: PMC8348629 DOI: 10.3390/molecules26154554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 12/03/2022] Open
Abstract
The mechanism by which proteins are solvated in hydrated ionic liquids remains an open question. Herein, the photoexcitation dynamics of photoactive yellow protein dissolved in hydrated choline dihydrogen phosphate (Hy[ch][dhp]) were studied by transient absorption and transient grating spectroscopy. The photocyclic reaction of the protein in Hy[ch][dhp] was similar to that observed in the buffer solution, as confirmed by transient absorption spectroscopy. However, the structural change of the protein during the photocycle in Hy[ch][dhp] was found to be different from that observed in the buffer solution. The known change in the diffusion coefficient of the protein was apparently suppressed in high concentrations of [ch][dhp], plausibly due to stabilization of the secondary structure.
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5
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Kuramochi H, Takeuchi S, Kamikubo H, Kataoka M, Tahara T. Skeletal Structure of the Chromophore of Photoactive Yellow Protein in the Excited State Investigated by Ultraviolet Femtosecond Stimulated Raman Spectroscopy. J Phys Chem B 2021; 125:6154-6161. [PMID: 34102843 DOI: 10.1021/acs.jpcb.1c02828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We studied ultrafast structural dynamics of photoactive yellow protein (PYP) using ultraviolet femtosecond stimulated Raman spectroscopy. By employing the Raman pump and probe pulses in the ultraviolet region, resonantly enhanced, rich vibrational features of the excited-state chromophore were observed in the fingerprint region. In contrast to the marked spectral change reported for the excited-state chromophore in solution, in the protein, all of the observed Raman bands in the fingerprint region did not show any noticeable spectral shifts nor band shape changes during the excited-state lifetime of PYP. This indicates that the significant skeletal change does not occur on the chromophore in the excited state of PYP and that the trans conformation is retained in its lifetime. Based on the femtosecond Raman data of PYP obtained so far, we discuss a comprehensive picture of the excited-state structural dynamics of PYP.
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Affiliation(s)
- Hikaru Kuramochi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
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6
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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: 24] [Impact Index Per Article: 6.0] [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.
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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.
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7
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Anstöter CS, Curchod BFE, Verlet JRR. Geometric and electronic structure probed along the isomerisation coordinate of a photoactive yellow protein chromophore. Nat Commun 2020; 11:2827. [PMID: 32499507 PMCID: PMC7272410 DOI: 10.1038/s41467-020-16667-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/15/2020] [Indexed: 01/29/2023] Open
Abstract
Understanding the connection between the motion of the nuclei in a molecule and the rearrangement of its electrons lies at the heart of chemistry. While many experimental methods have been developed to probe either the electronic or the nuclear structure on the timescale of atomic motion, very few have been able to capture both these changes in concert. Here, we use time-resolved photoelectron imaging to probe the isomerisation coordinate on the excited state of an isolated model chromophore anion of the photoactive yellow protein. By probing both the electronic structure changes as well as nuclear dynamics, we are able to uniquely measure isomerisation about a specific bond. Our results demonstrate that the photoelectron signal dispersed in time, energy and angle combined with calculations can track the evolution of both electronic and geometric structure along the adiabatic state, which in turn defines that chemical transformation. Resolving concerted nuclear and electronic motion in real-time is a primary goal in chemistry. The authors monitor nuclear and valence electronic dynamics in the excited state single-bond isomerisation of a chromophore of photoactive yellow protein, using time-resolved photoelectron imaging and electronic structure calculations.
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Affiliation(s)
- Cate S Anstöter
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | | | - Jan R R Verlet
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK.
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8
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Zhang TS, Fang YG, Song XF, Fang WH, Cui G. Hydrogen-Bonding Interaction Regulates Photoisomerization of a Single-Bond-Rotation Locked Photoactive Yellow Protein Chromophore in Protein. J Phys Chem Lett 2020; 11:2470-2476. [PMID: 32150415 DOI: 10.1021/acs.jpclett.0c00294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We have employed the QM(CASPT2//CASSCF)/MM method to explore the excited-state isomerization and decay mechanism of a single-bond-rotation locked photoactive yellow protein (PYP) chromophore in wild-type and mutant proteins. The S1 state is a spectroscopically bright state in the Franck-Condon region. In this state, there exist two excited-state isomerization pathways separately related to the clockwise and anticlockwise rotations of the C=C bond. The clockwise path is favorable because of a small barrier of 2 kcal/mol and uses a novel bicycle-pedal unidirectional photoisomerization mechanism in which the involved two dihedral angles rotate asynchronously because of the reinforced hydrogen-bonding interaction between the chromophore and Cys69. Near the twisted S1 minimum, the chromophore hops to the S0 state via the S1/S0 conical intersection. Finally, the R52A mutation has small effects on the excited-state properties and photoisomerization of the locked PYP chromophore. The present work provides new insights for understanding the photochemistry of PYP chromophores in protein surroundings.
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Affiliation(s)
- Teng-Shuo Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
| | - Ye-Guang Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
| | - Xiu-Fang Song
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
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9
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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.
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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
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10
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Schmidt-Engler JM, Blankenburg L, Błasiak B, van Wilderen LJGW, Cho M, Bredenbeck J. Vibrational Lifetime of the SCN Protein Label in H 2O and D 2O Reports Site-Specific Solvation and Structure Changes During PYP's Photocycle. Anal Chem 2019; 92:1024-1032. [PMID: 31769286 DOI: 10.1021/acs.analchem.9b03997] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The application of vibrational labels such as thiocyanate (-S-C≡N) for studying protein structure and dynamics is thriving. Absorption spectroscopy is usually employed to obtain wavenumber and line shape of the label. An observable of great significance might be the vibrational lifetime, which can be obtained by pump probe or 2D-IR spectroscopy. Due to the insulating effect of the heavy sulfur atom in the case of the SCN label, the lifetime of the C≡N oscillator is expected to be particularly sensitive to its surrounding as it is not dominated by through-bond relaxation. We therefore investigate the vibrational lifetime of the SCN label at various positions in the blue light sensor protein Photoactive Yellow Protein (PYP) in the ground state and signaling state of the photoreceptor. We find that the vibrational lifetime of the C≡N stretching mode is strongly affected both by its protein environment and by the degree of exposure to the solvent. Even for label positions where the line shape and wavenumber observed by FTIR are barely changing upon activation of the photoreceptor, we find that the lifetime can change considerably. To obtain an unambiguous measure for the solvent exposure of the labeled site, we show that it is imperative to compare the lifetimes in H2O and D2O. Importantly, the lifetimes shorten in H2O as compared to D2O for water exposed labels, while they stay largely the same for buried labels. We quantify this effect by defining a solvent exclusion coefficient (SEC). The response of the label's vibrational lifetime to its solvent exposure renders it a suitable universal probe for protein investigations. This applies even to systems that are otherwise hard to address, such as transient or short-lived states, which could be created during a protein's working cycle (as here in PYP) or during protein folding. It is also applicable to flexible systems (intrinsically disordered proteins), protein-protein and protein-membrane interactions.
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Affiliation(s)
- Julian M Schmidt-Engler
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
| | - Larissa Blankenburg
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
| | - Bartosz Błasiak
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
| | - Luuk J G W van Wilderen
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
| | - Minhaeng Cho
- Institute of Basic Science , Center of Molecular Spectroscopy and Dynamics , 145 Anam-ro , Seongbuk-gu , Seoul 02841 , Republic of Korea.,Korea University , Department of Chemistry , 145 Anam-ro , Seongbuk-gu , Seoul 02841 , Republic of Korea
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University , Institute of Biophysics , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
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11
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Fang C, Tang L, Chen C. Unveiling coupled electronic and vibrational motions of chromophores in condensed phases. J Chem Phys 2019; 151:200901. [PMID: 31779327 DOI: 10.1063/1.5128388] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The quest for capturing molecular movies of functional systems has motivated scientists and engineers for decades. A fundamental understanding of electronic and nuclear motions, two principal components of the molecular Schrödinger equation, has the potential to enable the de novo rational design for targeted functionalities of molecular machines. We discuss the development and application of a relatively new structural dynamics technique, femtosecond stimulated Raman spectroscopy with broadly tunable laser pulses from the UV to near-IR region, in tracking the coupled electronic and vibrational motions of organic chromophores in solution and protein environments. Such light-sensitive moieties hold broad interest and significance in gaining fundamental knowledge about the intramolecular and intermolecular Hamiltonian and developing effective strategies to control macroscopic properties. Inspired by recent experimental and theoretical advances, we focus on the in situ characterization and spectroscopy-guided tuning of photoacidity, excited state proton transfer pathways, emission color, and internal conversion via a conical intersection.
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Affiliation(s)
- Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Longteng Tang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Cheng Chen
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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12
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Bull JN, Silva GD, Scholz MS, Carrascosa E, Bieske EJ. Photoinitiated Intramolecular Proton Transfer in Deprotonated para-Coumaric Acid. J Phys Chem A 2019; 123:4419-4430. [DOI: 10.1021/acs.jpca.9b02023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James N. Bull
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Gabriel da Silva
- Department of Chemical Engineering, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael S. Scholz
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Eduardo Carrascosa
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Evan J. Bieske
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
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13
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Blankenburg L, Schroeder L, Habenstein F, Błasiak B, Kottke T, Bredenbeck J. Following local light-induced structure changes and dynamics of the photoreceptor PYP with the thiocyanate IR label. Phys Chem Chem Phys 2019; 21:6622-6634. [PMID: 30855039 DOI: 10.1039/c8cp05399e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoactive Yellow Protein (PYP) is a bacterial blue light receptor that enters a photocycle after excitation. The intermediate states are formed on time scales ranging from femtoseconds up to hundreds of milliseconds, after which the signaling state with a lifetime of about 1 s is reached. To investigate structural changes and dynamics, we incorporated the SCN IR label at distinct positions of the photoreceptor via cysteine mutation and cyanylation. FT-IR measurements of the SCN label at different sites of the well-established dark state structure of PYP characterized the spectral response of the label to differences in the environment. Under constant blue light irradiation, we observed the formation of the signaling state with significant changes of wavenumber and lineshape of the SCN bands. Thereby we deduced light-induced structural changes in the local environment of the labels. These results were supported by molecular dynamics simulations on PYP providing the solvent accessible surface area (SASA) at the different positions. To follow protein dynamics via the SCN label during the photocycle, we performed step-scan FT-IR measurements with a time resolution of 10 μs. Global analysis yielded similar time constants of τ1 = 70 μs, τ2 = 640 μs, and τ3 > 20 ms for the wild type and τ1 = 36 μs, τ2 = 530 μs, and τ3 > 20 ms for the SCN-labeled mutant PYP-A44C*, a mutant which provided a sufficiently large SCN difference signal to measure step-scan FT-IR spectra. In comparison to the protein (amide, E46) and chromophore bands the dynamics of the SCN label show a different behavior. This result indicates that the local kinetics sensed by the label are different from the global protein kinetics.
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Affiliation(s)
- Larissa Blankenburg
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
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14
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Affiliation(s)
- Alice Henley
- Department of Chemistry, University College London, London, UK
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15
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Direct evidence for hula twist and single-bond rotation photoproducts. Nat Commun 2018; 9:2510. [PMID: 29955041 PMCID: PMC6023863 DOI: 10.1038/s41467-018-04928-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/03/2018] [Indexed: 12/03/2022] Open
Abstract
Photoisomerization reactions are quintessential processes driving molecular machines and motors, govern smart materials, catalytic processes, and photopharmacology, and lie at the heart of vision, phototaxis, or vitamin production. Despite this plethora of applications fundamental photoisomerization mechanisms are not well understood at present. The famous hula-twist motion—a coupled single and double-bond rotation—was proposed to explain proficient photoswitching in restricted environments but fast thermal follow-up reactions hamper identification of primary photo products. Herein we describe an asymmetric chromophore possessing four geometrically distinct diastereomeric states that do not interconvert thermally and can be crystallized separately. Employing this molecular setup direct and unequivocal evidence for the hula-twist photoreaction and for photoinduced single-bond rotation is obtained. The influences of the surrounding medium and temperature are quantified and used to favor unusual photoreactions. Based on our findings molecular engineers will be able to implement photo control of complex molecular motions more consciously. Photoisomerization mechanisms govern important (bio)catalytic reactions and lie at the core of many functional materials. Here, the authors report a molecular setup that allows for the direct and separate observation of three fundamental photoreactions, namely the hula twist, single-bond rotation, as well as double-bond isomerization.
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16
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Mix LT, Carroll EC, Morozov D, Pan J, Gordon WR, Philip A, Fuzell J, Kumauchi M, van Stokkum I, Groenhof G, Hoff WD, Larsen DS. Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila. Biochemistry 2018; 57:1733-1747. [PMID: 29465990 DOI: 10.1021/acs.biochem.7b01114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump-probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elizabeth C Carroll
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Dmitry Morozov
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Jie Pan
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | | | | | - Jack Fuzell
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Ivo van Stokkum
- Faculty of Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1081 , 1081 HV Amsterdam , The Netherlands
| | - Gerrit Groenhof
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Delmar S Larsen
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
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17
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Di Donato M, Lerch MM, Lapini A, Laurent AD, Iagatti A, Bussotti L, Ihrig SP, Medved’ M, Jacquemin D, Szymański W, Buma WJ, Foggi P, Feringa BL. Shedding Light on the Photoisomerization Pathway of Donor-Acceptor Stenhouse Adducts. J Am Chem Soc 2017; 139:15596-15599. [PMID: 29039920 PMCID: PMC5680540 DOI: 10.1021/jacs.7b09081] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Indexed: 12/20/2022]
Abstract
Donor-acceptor Stenhouse adducts (DASAs) are negative photochromes that hold great promise for a variety of applications. Key to optimizing their switching properties is a detailed understanding of the photoswitching mechanism, which, as yet, is absent. Here we characterize the actinic step of DASA-photoswitching and its key intermediate, which was studied using a combination of ultrafast visible and IR pump-probe spectroscopies and TD-DFT calculations. Comparison of the time-resolved IR spectra with DFT computations allowed to unambiguously identify the structure of the intermediate, confirming that light absorption induces a sequential reaction path in which a Z-E photoisomerization of C2-C3 is followed by a rotation around C3-C4 and a subsequent thermal cyclization step. First and second-generation DASAs share a common photoisomerization mechanism in chlorinated solvents with notable differences in kinetics and lifetimes of the excited states. The photogenerated intermediate of the second-generation DASA was photo-accumulated at low temperature and probed with time-resolved spectroscopy, demonstrating the photoreversibility of the isomerization process. Taken together, these results provide a detailed picture of the DASA isomerization pathway on a molecular level.
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Affiliation(s)
- Mariangela Di Donato
- European
Laboratory for Non Linear Spectroscopy (LENS), via N. Carrara 1, 50019 Sesto Fiorentino, Italy
- Istituto
Nazionale di Ottica, Largo Fermi 6, 50125 Firenze, Italy
- Dipartimento
di Chimica “Ugo Schiff”, Università
di Firenze, via della
Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Michael M. Lerch
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
| | - Andrea Lapini
- European
Laboratory for Non Linear Spectroscopy (LENS), via N. Carrara 1, 50019 Sesto Fiorentino, Italy
- Dipartimento
di Chimica “Ugo Schiff”, Università
di Firenze, via della
Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Adèle D. Laurent
- CEISAM, UMR CNRS 6230,
BP 92208, 2 Rue de
la Houssinière, 44322 Nantes Cedex 3, France
| | - Alessandro Iagatti
- European
Laboratory for Non Linear Spectroscopy (LENS), via N. Carrara 1, 50019 Sesto Fiorentino, Italy
- Istituto
Nazionale di Ottica, Largo Fermi 6, 50125 Firenze, Italy
| | - Laura Bussotti
- European
Laboratory for Non Linear Spectroscopy (LENS), via N. Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Svante P. Ihrig
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
| | - Miroslav Medved’
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University in Olomouc, 17. listopadu 1192/12, CZ-771 46 Olomouc, Czech Republic
- Department
of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, SK-97400 Banská Bystrica, Slovak Republic
| | - Denis Jacquemin
- CEISAM, UMR CNRS 6230,
BP 92208, 2 Rue de
la Houssinière, 44322 Nantes Cedex 3, France
- Institut Universitaire de France, 103 bd St Michael, 75005 Paris Cedex 5, France
| | - Wiktor Szymański
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
- Department
of Radiology, University of Groningen, University
Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Wybren Jan Buma
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science
Park 904, 1098XH Amsterdam, The Netherlands
| | - Paolo Foggi
- European
Laboratory for Non Linear Spectroscopy (LENS), via N. Carrara 1, 50019 Sesto Fiorentino, Italy
- Istituto
Nazionale di Ottica, Largo Fermi 6, 50125 Firenze, Italy
- Dipartimento
di Chimica, Università di Perugia, via Elce di Sotto 8, 06100 Perugia, Italy
| | - Ben L. Feringa
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
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18
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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]
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19
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Hutchison CD, van Thor JJ. Populations and coherence in femtosecond time resolved X-ray crystallography of the photoactive yellow protein. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1276726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Jasper J. van Thor
- Molecular Biophysics, Imperial College London, South Kensington Campus, London, UK
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20
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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.
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21
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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.
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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
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22
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Mix LT, Kirpich J, Kumauchi M, Ren J, Vengris M, Hoff WD, Larsen DS. Bifurcation in the Ultrafast Dynamics of the Photoactive Yellow Proteins from Leptospira biflexa and Halorhodospira halophila. Biochemistry 2016; 55:6138-6149. [DOI: 10.1021/acs.biochem.6b00547] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- L. Tyler Mix
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Julia Kirpich
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Masato Kumauchi
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Jie Ren
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Mikas Vengris
- Faculty
of Physics, Laser Research Centre, Vilnius University, Sauletekio
10, LT-10233 Vilnius, Lithuania
| | - Wouter D. Hoff
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Delmar S. Larsen
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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23
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Hutchison CD, Kaucikas M, Tenboer J, Kupitz C, Moffat K, Schmidt M, van Thor JJ. Photocycle populations with femtosecond excitation of crystalline photoactive yellow protein. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.04.087] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Pande K, Hutchison CDM, Groenhof G, Aquila A, Robinson JS, Tenboer J, Basu S, Boutet S, DePonte DP, Liang M, White TA, Zatsepin NA, Yefanov O, Morozov D, Oberthuer D, Gati C, Subramanian G, James D, Zhao Y, Koralek J, Brayshaw J, Kupitz C, Conrad C, Roy-Chowdhury S, Coe JD, Metz M, Xavier PL, Grant TD, Koglin JE, Ketawala G, Fromme R, Šrajer V, Henning R, Spence JCH, Ourmazd A, Schwander P, Weierstall U, Frank M, Fromme P, Barty A, Chapman HN, Moffat K, van Thor JJ, Schmidt M. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Science 2016; 352:725-9. [PMID: 27151871 DOI: 10.1126/science.aad5081] [Citation(s) in RCA: 286] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 04/05/2016] [Indexed: 11/02/2022]
Abstract
A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.
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Affiliation(s)
- Kanupriya Pande
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA. Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Post Office Box 35, 40014 Jyväskylä, Finland
| | - Andy Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Josef S Robinson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason Tenboer
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Shibom Basu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Thomas A White
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Oleksandr Yefanov
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Post Office Box 35, 40014 Jyväskylä, Finland
| | - Dominik Oberthuer
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Cornelius Gati
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Daniel James
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Yun Zhao
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Jake Koralek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jennifer Brayshaw
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Christopher Kupitz
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Chelsie Conrad
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Jesse D Coe
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Markus Metz
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Paulraj Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. IMPRS-UFAST, Max Planck Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Thomas D Grant
- Hauptman-Woodward Institute, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gihan Ketawala
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Raimund Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Vukica Šrajer
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Anton Barty
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N Chapman
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. Center for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Keith Moffat
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA. Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Jasper J van Thor
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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25
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Ritter E, Puskar L, Bartl FJ, Aziz EF, Hegemann P, Schade U. Time-resolved infrared spectroscopic techniques as applied to channelrhodopsin. Front Mol Biosci 2015. [PMID: 26217670 PMCID: PMC4493399 DOI: 10.3389/fmolb.2015.00038] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Among optogenetic tools, channelrhodopsins, the light gated ion channels of the plasma membrane from green algae, play the most important role. Properties like channel selectivity, timing parameters or color can be influenced by the exchange of selected amino acids. Although widely used, in the field of neurosciences for example, there is still little known about their photocycles and the mechanism of ion channel gating and conductance. One of the preferred methods for these studies is infrared spectroscopy since it allows observation of proteins and their function at a molecular level and in near-native environment. The absorption of a photon in channelrhodopsin leads to retinal isomerization within femtoseconds, the conductive states are reached in the microsecond time scale and the return into the fully dark-adapted state may take more than minutes. To be able to cover all these time regimes, a range of different spectroscopical approaches are necessary. This mini-review focuses on time-resolved applications of the infrared technique to study channelrhodopsins and other light triggered proteins. We will discuss the approaches with respect to their suitability to the investigation of channelrhodopsin and related proteins.
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Affiliation(s)
- Eglof Ritter
- Experimentelle Biophysik, Institut für Biologie, Humboldt-Universität zu Berlin Berlin, Germany
| | - Ljiljana Puskar
- Methods for Material Development, Helmholtz-Zentrum für Materialien und Energie GmbH Berlin, Germany
| | - Franz J Bartl
- Institut für medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Emad F Aziz
- Methods for Material Development, Helmholtz-Zentrum für Materialien und Energie GmbH Berlin, Germany ; Fachbereich Physik, Freie Universität Berlin Berlin, Germany
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt-Universität zu Berlin Berlin, Germany
| | - Ulrich Schade
- Methods for Material Development, Helmholtz-Zentrum für Materialien und Energie GmbH Berlin, Germany
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26
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Nakamura R, Hamada N. Vibrational Energy Flow in Photoactive Yellow Protein Revealed by Infrared Pump–Visible Probe Spectroscopy. J Phys Chem B 2015; 119:5957-61. [DOI: 10.1021/jp512994q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryosuke Nakamura
- Science
and Technology Entrepreneurship
Laboratory, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Norio Hamada
- Science
and Technology Entrepreneurship
Laboratory, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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27
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Tenboer J, Basu S, Zatsepin N, Pande K, Milathianaki D, Frank M, Hunter M, Boutet S, Williams GJ, Koglin JE, Oberthuer D, Heymann M, Kupitz C, Conrad C, Coe J, Roy-Chowdhury S, Weierstall U, James D, Wang D, Grant T, Barty A, Yefanov O, Scales J, Gati C, Seuring C, Srajer V, Henning R, Schwander P, Fromme R, Ourmazd A, Moffat K, Van Thor JJ, Spence JCH, Fromme P, Chapman HN, Schmidt M. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Science 2014; 346:1242-6. [PMID: 25477465 DOI: 10.1126/science.1259357] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal.
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Affiliation(s)
- Jason Tenboer
- Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Shibom Basu
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Kanupriya Pande
- Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Despina Milathianaki
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Mark Hunter
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Dominik Oberthuer
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Michael Heymann
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christopher Kupitz
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Chelsie Conrad
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Jesse Coe
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Shatabdi Roy-Chowdhury
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Daniel James
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Dingjie Wang
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Thomas Grant
- Hauptman-Woodward Institute, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Anton Barty
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jennifer Scales
- Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Cornelius Gati
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany.,Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Carolin Seuring
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Vukica Srajer
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - Peter Schwander
- Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Abbas Ourmazd
- Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Keith Moffat
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA.,Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Jasper J Van Thor
- Faculty of Natural Sciences, Life Sciences, Imperial College, London SW7 2AZ, UK
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Henry N Chapman
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany.,Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Marius Schmidt
- Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA.,Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA.
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28
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Gromov EV. Unveiling the mechanism of photoinduced isomerization of the photoactive yellow protein (PYP) chromophore. J Chem Phys 2014; 141:224308. [DOI: 10.1063/1.4903174] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Evgeniy V. Gromov
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg, Germany
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29
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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
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30
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Nakashima S, Ogura T, Kitagawa T. Infrared and Raman spectroscopic investigation of the reaction mechanism of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:86-97. [PMID: 25135480 DOI: 10.1016/j.bbabio.2014.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/07/2014] [Accepted: 08/11/2014] [Indexed: 10/24/2022]
Abstract
Recent progress in studies on the proton-pumping and O₂reduction mechanisms of cytochrome c oxidase (CcO) elucidated by infrared (IR) and resonance Raman (rR) spectroscopy, is reviewed. CcO is the terminal enzyme of the respiratory chain and its O₂reduction reaction is coupled with H⁺ pumping activity across the inner mitochondrial membrane. The former is catalyzed by heme a3 and its mechanism has been determined using a rR technique, while the latter used the protein moiety and has been investigated with an IR technique. The number of H⁺ relative to e⁻ transferred in the reaction is 1:1, and their coupling is presumably performed by heme a and nearby residues. To perform this function, different parts of the protein need to cooperate with each other spontaneously and sequentially. It is the purpose of this article to describe the structural details on the coupling on the basis of the vibrational spectra of certain specified residues and chromophores involved in the reaction. Recent developments in time-resolved IR and Raman technology concomitant with protein manipulation methods have yielded profound insights into such structural changes. In particular, the new IR techniques that yielded the breakthrough are reviewed and assessed in detail. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Satoru Nakashima
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Department of Life Science, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Teizo Kitagawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
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31
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van Thor JJ, Warren MM, Lincoln CN, Chollet M, Lemke HT, Fritz DM, Schmidt M, Tenboer J, Ren Z, Srajer V, Moffat K, Graber T. Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein. Faraday Discuss 2014; 171:439-55. [PMID: 25415305 DOI: 10.1039/c4fd00011k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Femtosecond time resolved pump-probe protein X-ray crystallography requires highly accurate measurements of the photoinduced structure factor amplitude differences. In the case of femtosecond photolysis of single P63 crystals of the Photoactive Yellow Protein, it is shown that photochemical dynamics place a considerable restraint on the achievable time resolution due to the requirement to stretch and add second order dispersion in order to generate threshold concentration levels in the interaction region. Here, we report on using a 'quasi-cw' approach to use the rotation method with monochromatic radiation and 2 eV bandwidth at 9.465 keV at the Linac Coherent Light Source operated in SASE mode. A source of significant Bragg reflection intensity noise is identified from the combination of mode structure and jitter with very small mosaic spread of the crystals and very low convergence of the XFEL source. The accuracy with which the three dimensional reflection is approximated by the 'quasi-cw' rotation method with the pulsed source is modelled from the experimentally collected X-ray pulse intensities together with the measured rocking curves. This model is extended to predict merging statistics for recently demonstrated self seeded mode generated pulse train with improved stability, in addition to extrapolating to single crystal experiments with increased mosaic spread. The results show that the noise level can be adequately modelled in this manner, indicating that the large intensity fluctuations dominate the merged signal-to-noise (I/σI) value. Furthermore, these results predict that using the self seeded mode together with more mosaic crystals, sufficient accuracy may be obtained in order to resolve typical photoinduced structure factor amplitude differences, as taken from representative synchrotron results.
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Affiliation(s)
- Jasper J van Thor
- Imperial College London, Division of Molecular Biosciences, South Kensington Campus, London SW7 2AZ, UK.
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32
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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
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33
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Wei L, Wang H, Chen X, Fang W, Wang H. A comprehensive study of isomerization and protonation reactions in the photocycle of the photoactive yellow protein. Phys Chem Chem Phys 2014; 16:25263-72. [DOI: 10.1039/c4cp03495c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A comprehensive picture of the overall photocycle was obtained to reveal a wide range of structural signals in the photoactive yellow protein.
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Affiliation(s)
- Lili Wei
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing, China
| | - Hongjuan Wang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing, China
| | - Xuebo Chen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing, China
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing, China
| | - Haobin Wang
- Department of Chemistry and Biochemistry
- New Mexico State University
- Las Cruces, USA
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34
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Cho HS, Schotte F, Dashdorj N, Kyndt J, Anfinrud PA. Probing anisotropic structure changes in proteins with picosecond time-resolved small-angle X-ray scattering. J Phys Chem B 2013; 117:15825-32. [PMID: 24125473 DOI: 10.1021/jp407593j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We have exploited the principle of photoselection and the method of time-resolved small-angle X-ray scattering (SAXS) to investigate protein size and shape changes following photoactivation of photoactive yellow protein (PYP) in solution with ∼150 ps time resolution. This study partially overcomes the orientational average intrinsic to solution scattering methods and provides structural information at a higher level of detail. Photoactivation of the p-coumaric acid (pCA) chromophore in PYP produces a highly contorted, short-lived, red-shifted intermediate (pR0), and triggers prompt, protein compaction of approximately 0.3% along the direction defined by the electronic transition dipole moment of the chromophore. Contraction along this dimension is accompanied by expansion along the orthogonal directions, with the net protein volume change being approximately -0.25%. More than half the strain arising from formation of pR0 is relieved by the pR0 to pR1 structure transition (1.8 ± 0.2 ns), with the persistent strain presumably contributing to the driving force needed to generate the spectroscopically blue-shifted pB signaling state. The results reported here are consistent with the near-atomic resolution structural dynamics reported in a recent time-resolved Laue crystallography study of PYP crystals and suggest that the early time structural dynamics in the crystalline state carry over to proteins in solution.
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Affiliation(s)
- Hyun Sun Cho
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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35
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Dynamic structural science: recent developments in time-resolved spectroscopy and X-ray crystallography. Biochem Soc Trans 2013; 41:1260-4. [DOI: 10.1042/bst20130125] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To understand the mechanism of biological processes, time-resolved methodologies are required to investigate how functionality is linked to changes in molecular structure. A number of spectroscopic techniques are available that probe local structural rearrangements with high temporal resolution. However, for macromolecules, these techniques do not yield an overall high-resolution description of the structure. Time-resolved X-ray crystallographic methods exist, but, due to both instrument availability and stringent sample requirements, they have not been widely applied to macromolecular systems, especially for time resolutions below 1 s. Recently, there has been a resurgent interest in time-resolved structural science, fuelled by the recognition that both chemical and life scientists face many of the same challenges. In the present article, we review the current state-of-the-art in dynamic structural science, highlighting applications to enzymes. We also look to the future and discuss current method developments with the potential to widen access to time-resolved studies across discipline boundaries.
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36
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Mendonça L, Hache F, Changenet-Barret P, Plaza P, Chosrowjan H, Taniguchi S, Imamoto Y. Ultrafast Carbonyl Motion of the Photoactive Yellow Protein Chromophore Probed by Femtosecond Circular Dichroism. J Am Chem Soc 2013; 135:14637-43. [DOI: 10.1021/ja404503q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Lucille Mendonça
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique/CNRS/INSERM, 91128 Palaiseau cedex, France
| | - François Hache
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique/CNRS/INSERM, 91128 Palaiseau cedex, France
| | | | - Pascal Plaza
- Ecole Normale Supérieure,
Département de Chimie, UMR 8640 CNRS-ENS-UPMC, 24 rue Lhomond,
75005 Paris, France
| | - Haik Chosrowjan
- Institute for Laser Technology, 2-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Seiji Taniguchi
- Institute for Laser Technology, 2-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasushi Imamoto
- Department
of Biophysics, Graduate School of Sciences, Kyoto University, Kyoto 6068502, Japan
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37
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Kubo M, Nakashima S, Yamaguchi S, Ogura T, Mochizuki M, Kang J, Tateno M, Shinzawa-Itoh K, Kato K, Yoshikawa S. Effective pumping proton collection facilitated by a copper site (CuB) of bovine heart cytochrome c oxidase, revealed by a newly developed time-resolved infrared system. J Biol Chem 2013; 288:30259-30269. [PMID: 23996000 DOI: 10.1074/jbc.m113.473983] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
X-ray structural and mutational analyses have shown that bovine heart cytochrome c oxidase (CcO) pumps protons electrostatically through a hydrogen bond network using net positive charges created upon oxidation of a heme iron (located near the hydrogen bond network) for O2 reduction. Pumping protons are transferred by mobile water molecules from the negative side of the mitochondrial inner membrane through a water channel into the hydrogen bond network. For blockage of spontaneous proton back-leak, the water channel is closed upon O2 binding to the second heme (heme a3) after complete collection of the pumping protons in the hydrogen bond network. For elucidation of the structural bases for the mechanism of the proton collection and timely closure of the water channel, conformational dynamics after photolysis of CO (an O2 analog)-bound CcO was examined using a newly developed time-resolved infrared system feasible for accurate detection of a single C=O stretch band of α-helices of CcO in H2O medium. The present results indicate that migration of CO from heme a3 to CuB in the O2 reduction site induces an intermediate state in which a bulge conformation at Ser-382 in a transmembrane helix is eliminated to open the water channel. The structural changes suggest that, using a conformational relay system, including CuB, O2, heme a3, and two helix turns extending to Ser-382, CuB induces the conformational changes of the water channel that stimulate the proton collection, and senses complete proton loading into the hydrogen bond network to trigger the timely channel closure by O2 transfer from CuB to heme a3.
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Affiliation(s)
| | | | - Satoru Yamaguchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo 678-1297 and
| | - Takashi Ogura
- From the Picobiology Institute,; Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo 678-1297 and; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | | | - Masaru Tateno
- From the Picobiology Institute,; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | | | - Shinya Yoshikawa
- From the Picobiology Institute,; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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38
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Thellamurege NM, Cui F, Li H. Quantum mechanical/molecular mechanical/continuum style solvation model: Time-dependent density functional theory. J Chem Phys 2013; 139:084106. [DOI: 10.1063/1.4819139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Zhu J, Paparelli L, Hospes M, Arents J, Kennis JTM, van Stokkum IHM, Hellingwerf KJ, Groot ML. Photoionization and Electron Radical Recombination Dynamics in Photoactive Yellow Protein Investigated by Ultrafast Spectroscopy in the Visible and Near-Infrared Spectral Region. J Phys Chem B 2013; 117:11042-8. [DOI: 10.1021/jp311906f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [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, VU University, De
Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Laura Paparelli
- Department
of Physics and Astronomy,
Faculty of Sciences, VU University, De
Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Marijke Hospes
- Laboratory for Microbiology,
Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The
Netherlands
| | - Jos Arents
- Laboratory for Microbiology,
Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The
Netherlands
| | - John T. M. Kennis
- Department
of Physics and Astronomy,
Faculty of Sciences, VU University, De
Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Ivo H. M. van Stokkum
- Department
of Physics and Astronomy,
Faculty of Sciences, VU University, De
Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Klaas J. Hellingwerf
- Laboratory for Microbiology,
Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The
Netherlands
| | - Marie Louise Groot
- Department
of Physics and Astronomy,
Faculty of Sciences, VU University, De
Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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40
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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: 139] [Impact Index Per Article: 12.6] [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.
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Affiliation(s)
- Yang Ouk Jung
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, Republic of Korea
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41
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Hospes M, Hendriks J, Hellingwerf KJ. Tryptophan fluorescence as a reporter for structural changes in photoactive yellow protein elicited by photo-activation. Photochem Photobiol Sci 2013. [DOI: 10.1039/c2pp25222h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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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.
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Affiliation(s)
- Ryosuke Nakamura
- Science and Technology Entrepreneurship Laboratory, Osaka University, Suita, Osaka, Japan.
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43
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Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography. Proc Natl Acad Sci U S A 2012; 109:19256-61. [PMID: 23132943 DOI: 10.1073/pnas.1210938109] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To understand how signaling proteins function, it is crucial to know the time-ordered sequence of events that lead to the signaling state. We recently developed on the BioCARS 14-IDB beamline at the Advanced Photon Source the infrastructure required to characterize structural changes in protein crystals with near-atomic spatial resolution and 150-ps time resolution, and have used this capability to track the reversible photocycle of photoactive yellow protein (PYP) following trans-to-cis photoisomerization of its p-coumaric acid (pCA) chromophore over 10 decades of time. The first of four major intermediates characterized in this study is highly contorted, with the pCA carbonyl rotated nearly 90° out of the plane of the phenolate. A hydrogen bond between the pCA carbonyl and the Cys69 backbone constrains the chromophore in this unusual twisted conformation. Density functional theory calculations confirm that this structure is chemically plausible and corresponds to a strained cis intermediate. This unique structure is short-lived (∼600 ps), has not been observed in prior cryocrystallography experiments, and is the progenitor of intermediates characterized in previous nanosecond time-resolved Laue crystallography studies. The structural transitions unveiled during the PYP photocycle include trans/cis isomerization, the breaking and making of hydrogen bonds, formation/relaxation of strain, and gated water penetration into the interior of the protein. This mechanistically detailed, near-atomic resolution description of the complete PYP photocycle provides a framework for understanding signal transduction in proteins, and for assessing and validating theoretical/computational approaches in protein biophysics.
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44
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Lincoln CN, Fitzpatrick AE, van Thor JJ. Photoisomerisation quantum yield and non-linear cross-sections with femtosecond excitation of the photoactive yellow protein. Phys Chem Chem Phys 2012; 14:15752-64. [PMID: 23090503 DOI: 10.1039/c2cp41718a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The quantum yield of photoisomerisation of the photoactive yellow protein (PYP) strongly depends on peak power and wavelength with femtosecond optical excitation. Using systematic power titrations and addition of second order dispersion resulting in 140, 300 and 600 fs pulse durations, the one and multi-photon cross-sections at 400, 450 and 490 nm have been assessed from transient absorption spectroscopy and additionally the Z-scan technique. Applying a target model that incorporates photoselection theory, estimates for the cross-sections for stimulated emission and absorption of the first excited state, the amount of ultrafast internal conversion and the underlying species associated dynamics have been determined. The final quantum yields for photoisomerisation were found to be 0.06, 0.14-0.19 and 0.02 for excitation wavelengths 400, 450 and 490 nm and found to increase with increasing pulse durations. Transient absorption measurements and Z-scan measurements at 450 nm, coinciding with the maximum wavelength of the ground state absorption, indicate that the photochemical quantum yield is intrinsically limited by an ultrafast internal conversion reaction as well as by stimulated emission cross-section. With excitation at 400 nm photoisomerisation quantum yield is further significantly limited by competing multi-photon excitation into excited state absorption at 385 nm previously proposed to result in photoionisation. With excitation at 490 nm the photoisomerisation quantum yield is predominantly limited further by the significantly higher stimulated emission cross-section compared to ground state cross-section as well as multi-photon processes. In addition to photoionisation, a second product of multi-photon excitation is identified and characterised by an induced absorption at 500 nm and a time constant of 2 ps for relaxation. With power densities up to 138 GW cm(-2) the measurements have not provided indication for coherent multi-photon absorption of PYP. In the saturation regime with 450 nm excitation, the limit for the photoisomerisation quantum yield was found to be 0.14-0.19 and the excited state absorption cross-section 6.1 × 10(-17) cm(2) or 0.36 times the ground state cross-section of 1.68 × 10(-16) cm(2) per molecule. This places a fundamental restriction on the maximum populations and sample penetration that may be achieved for instance in femtosecond pump-probe experiments with molecular crystals of PYP.
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Affiliation(s)
- Craig N Lincoln
- Imperial College London, Division of Molecular Biosciences, South Kensington campus, SW7 2AZ, London, UK
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White JR, Patel J, Ottesen A, Arce G, Blackwelder P, Lopez JV. Pyrosequencing of bacterial symbionts within Axinella corrugata sponges: diversity and seasonal variability. PLoS One 2012; 7:e38204. [PMID: 22701613 PMCID: PMC3373494 DOI: 10.1371/journal.pone.0038204] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 05/03/2012] [Indexed: 11/18/2022] Open
Abstract
Background Marine sponge species are of significant interest to many scientific fields including marine ecology, conservation biology, genetics, host-microbe symbiosis and pharmacology. One of the most intriguing aspects of the sponge “holobiont” system is the unique physiology, interaction with microbes from the marine environment and the development of a complex commensal microbial community. However, intraspecific variability and temporal stability of sponge-associated bacterial symbionts remain relatively unknown. Methodology/Principal Findings We have characterized the bacterial symbiont community biodiversity of seven different individuals of the Caribbean reef sponge Axinella corrugata, from two different Florida reef locations during variable seasons using multiplex 454 pyrosequencing of 16 S rRNA amplicons. Over 265,512 high-quality 16 S rRNA sequences were generated and analyzed. Utilizing versatile bioinformatics methods and analytical software such as the QIIME and CloVR packages, we have identified 9,444 distinct bacterial operational taxonomic units (OTUs). Approximately 65,550 rRNA sequences (24%) could not be matched to bacteria at the class level, and may therefore represent novel taxa. Differentially abundant classes between seasonal Axinella communities included Gammaproteobacteria, Flavobacteria, Alphaproteobacteria, Cyanobacteria, Acidobacter and Nitrospira. Comparisons with a proximal outgroup sponge species (Amphimedon compressa), and the growing sponge symbiont literature, indicate that this study has identified approximately 330 A. corrugata-specific symbiotic OTUs, many of which are related to the sulfur-oxidizing Ectothiorhodospiraceae. This family appeared exclusively within A. corrugata, comprising >34.5% of all sequenced amplicons. Other A. corrugata symbionts such as Deltaproteobacteria, Bdellovibrio, and Thiocystis among many others are described. Conclusions/Significance Slight shifts in several bacterial taxa were observed between communities sampled during spring and fall seasons. New 16 S rDNA sequences and concomitant identifications greatly expand the microbial community profile for this model reef sponge, and will likely be useful as a baseline for any future comparisons regarding sponge microbial community dynamics.
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Affiliation(s)
- James R. White
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
| | - Jignasa Patel
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
| | - Andrea Ottesen
- Food and Drug Administration Office of Regulatory Science, Division of Microbiology, College Park, Maryland, United States of America
| | - Gabriela Arce
- Food and Drug Administration Office of Regulatory Science, Division of Microbiology, College Park, Maryland, United States of America
| | - Patricia Blackwelder
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
- University of Miami Center for Advanced Microscopy and Marine Geology and Geophysics, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida, United States of America
| | - Jose V. Lopez
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
- * E-mail:
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pH dependence of the photoactive yellow protein photocycle investigated by time-resolved crystallography. Biophys J 2012; 102:325-32. [PMID: 22339869 DOI: 10.1016/j.bpj.2011.11.4021] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 11/21/2011] [Accepted: 11/29/2011] [Indexed: 11/21/2022] Open
Abstract
Visualizing the three-dimensional structures of a protein during its biological activity is key to understanding its mechanism. In general, protein structure and function are pH-dependent. Changing the pH provides new insights into the mechanisms that are involved in protein activity. Photoactive yellow protein (PYP) is a signaling protein that serves as an ideal model for time-dependent studies on light-activated proteins. Its photocycle is studied extensively under different pH conditions. However, the structures of the intermediates remain unknown until time-resolved crystallography is employed. With the newest beamline developments, a comprehensive time series of Laue data can now be collected from a single protein crystal. This allows us to vary the pH. Here we present the first structure, to our knowledge, of a short-lived protein-inhibitor complex formed in the pB state of the PYP photocycle at pH 4. A water molecule that is transiently stabilized in the chromophore active site prevents the relaxation of the chromophore back to the trans configuration. As a result, the dark-state recovery is slowed down dramatically. At pH 9, PYP stops cycling through the pB state altogether. The electrostatic environment in the chromophore-binding site is the likely reason for this altered kinetics at different pH values.
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Zhu J, Mathes T, Stahl AD, Kennis JTM, Groot ML. Ultrafast mid-infrared spectroscopy by chirped pulse upconversion in 1800-1000cm(-1) region. OPTICS EXPRESS 2012; 20:10562-10571. [PMID: 22565682 DOI: 10.1364/oe.20.010562] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Broadband femtosecond mid-infrared pulses can be converted into the visible spectral region by chirped pulse upconversion. We report here the upconversion of pump probe transient signals in the frequency region below 1800cm(-1), using the nonlinear optical crystal AgGaGeS4, realizing an important expansion of the application range of this method. Experiments were demonstrated with a slab of GaAs, in which the upconverted signals cover a window of 120cm(-1), with 1.5cm(-1) resolution. In experiments on the BLUF photoreceptor Slr1694, signals below 1 milliOD were well resolved after baseline correction. Possibilities for further optimization of the method are discussed. We conclude that this method is an attractive alternative for the traditional MCT arrays used in most mid-infrared pump probe experiments.
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Affiliation(s)
- Jingyi Zhu
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
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Changenet-Barret P, Lacombat F, Plaza P. Reaction-coordinate tracking in the excited-state deactivation of the photoactive yellow protein chromophore in solution. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Gromov EV, Burghardt I, Köppel H, Cederbaum LS. Native hydrogen bonding network of the photoactive yellow protein (PYP) chromophore: Impact on the electronic structure and photoinduced isomerization. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Schmidt M, Šrajer V, Purwar N, Tripathi S. The kinetic dose limit in room-temperature time-resolved macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:264-73. [PMID: 22338689 PMCID: PMC3284346 DOI: 10.1107/s090904951105549x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 12/23/2011] [Indexed: 05/16/2023]
Abstract
Protein X-ray structures are determined with ionizing radiation that damages the protein at high X-ray doses. As a result, diffraction patterns deteriorate with the increased absorbed dose. Several strategies such as sample freezing or scavenging of X-ray-generated free radicals are currently employed to minimize this damage. However, little is known about how the absorbed X-ray dose affects time-resolved Laue data collected at physiological temperatures where the protein is fully functional in the crystal, and how the kinetic analysis of such data depends on the absorbed dose. Here, direct evidence for the impact of radiation damage on the function of a protein is presented using time-resolved macromolecular crystallography. The effect of radiation damage on the kinetic analysis of time-resolved X-ray data is also explored.
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Affiliation(s)
- M Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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