1
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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: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 07/31/2020] [Indexed: 11/27/2022] Open
Abstract
Femtosecond time-resolved crystallography (TRC) on proteins enables resolving the spatial structure of short-lived photocycle intermediates. An open question is whether confinement and lower hydration of the proteins in the crystalline state affect the light-induced structural transformations. Here, we measured the full photocycle dynamics of a signal transduction protein often used as model system in TRC, Photoactive Yellow Protein (PYP), in the crystalline state and compared those to the dynamics in solution, utilizing electronic and vibrational transient absorption measurements from 100 fs over 12 decades in time. We find that the photocycle kinetics and structural dynamics of PYP in the crystalline form deviate from those in solution from the very first steps following photon absorption. This illustrates that ultrafast TRC results cannot be uncritically extrapolated to in vivo function, and that comparative spectroscopic experiments on proteins in crystalline and solution states can help identify structural intermediates under native conditions. Protein structural dynamics can be studied by time-resolved crystallography (TRC) and ultrafast transient spectroscopic methods. Here, the authors perform electronic and vibrational transient absorption measurements to characterise the full photocycle of Photoactive Yellow Protein (PYP) both in the crystalline and solution state and find that the photocycle kinetics and structural intermediates of PYP deviate in the crystalline state, which must be taken into consideration when planning TRC experiments.
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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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2
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Schmidt-Engler JM, Blankenburg L, Zangl R, Hoffmann J, Morgner N, Bredenbeck J. Local dynamics of the photo-switchable protein PYP in ground and signalling state probed by 2D-IR spectroscopy of –SCN labels. Phys Chem Chem Phys 2020; 22:22963-22972. [DOI: 10.1039/d0cp04307a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employ 2D-IR spectroscopy of the protein label –SCN to describe the local dynamics in the photo-switchable protein PYP in its dark state (pG) and after photoactivation, concomitant with vast structural rearrangements, in its signalling state (pB).
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Affiliation(s)
| | - Larissa Blankenburg
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
| | - Rene Zangl
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Jan Hoffmann
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Nina Morgner
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
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3
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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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4
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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: 33] [Impact Index Per Article: 6.6] [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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5
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Wang J. Visualization of H atoms in the X-ray crystal structure of photoactive yellow protein: Does it contain low-barrier hydrogen bonds? Protein Sci 2019; 28:1966-1972. [PMID: 31441173 DOI: 10.1002/pro.3716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 11/07/2022]
Abstract
The hydrogen bond (HB) between 4-hydroxycinnamic acid (HC4) and glutamic acid E46 of photoactive yellow protein is exceptionally strong. In the 0.82-å resolution X-ray structure for this protein (PDB ID: 1NWZ), the OH…O distance is only 2.57 å. The position of the H atom between these two O atoms has not been determined in that structure, and in the absence of that information, it is impossible to determine whether or not this HB is a low-barrier HB (LBHB), as was proposed recently based on neutron structures of this protein (Yamaguchi et al., Proceedings of the National Academy of Sciences of the United States of America, 2009, 106: 440-444). Residual electron density maps computed using the 1NWZ data reveal that this H atom is 0.92 å from the Oε2 atom of E46 and 1.67 å from the O4 ' of HC4, and that the OH…O bond angle is 167°. These observations indicate that E46 is protonated, and HC4 is deprotonated, as was originally suggested, and that the HB in question is not an LBHB.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
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6
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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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7
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Zhao L, Liu J, Zhou P. Does the wavelength dependent photoisomerization process of the p‑coumaric acid come out from the electronic state dependent pathways? SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 211:203-211. [PMID: 30544011 DOI: 10.1016/j.saa.2018.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Similar to the anion photoactive yellow protein (PYP) chromophore, the neutral form of the PYP chromophore was also found to exhibit a the wavelength-dependent photoisomerization quantum yield. The isomerization quantum yield increases with the increasing excitation energy on the S1 state, while decreases when being excited to the S2 state. Does this wavelength dependent product yield come out from the specific reaction pathways of the S1 and S2 states? This would mean that, the relaxation pathway of the S2 state is distinct from that of the S1 state and does not involve twisting motion. Does it break Kasha's rule by exhibiting a direct transition from the S2 state to the ground state? The underlying mechanism needs further in. In this article, we employed the on-the-fly dynamics simulations and static electronic structure calculations to reveal the deactivation mechanism of the neutral form of the PYP chromophore. Our results indicated that the CC twisting motion dominates the S1 state decay process. In contrast, for the decay process of the S2 state, an ultrafast transition from the S2 to the S1 state through a planar conical intersection is observed, and the excess energy activates a new reaction channel to the ground state characterized by a puckering distortion of the ring. This pathway competes with the photoisomerization channel. No direct transition from S2 to S0 is observed, hence Kasha's rule is valid for this process. Our calcualtions can provide a reasonable explanation of the wavelength-dependent isomerization quantum yield of neutral PYP chromophore, and we hope it can provide theoretical foundations for comparing the effect of protonation state on the dynamcal behaviors of PYP chromophore.
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Affiliation(s)
- Li Zhao
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Jianyong Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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8
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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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9
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Schmidt M. A short history of structure based research on the photocycle of photoactive yellow protein. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:032201. [PMID: 28191482 PMCID: PMC5291790 DOI: 10.1063/1.4974172] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/04/2017] [Indexed: 05/07/2023]
Abstract
The goals of time-resolved macromolecular crystallography are to extract the molecular structures of the reaction intermediates and the reaction dynamics from time-resolved X-ray data alone. To develop the techniques of time-resolved crystallography, biomolecules with special properties are required. The Photoactive Yellow Protein is the most sparkling of these.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee , 3135 N. Maryland Ave, Milwaukee, Wisconsin 53211, USA
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10
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García-Prieto FF, Muñoz-Losa A, Fdez Galván I, Sánchez ML, Aguilar MA, Martín ME. QM/MM Study of Substituent and Solvent Effects on the Excited State Dynamics of the Photoactive Yellow Protein Chromophore. J Chem Theory Comput 2017; 13:737-748. [PMID: 28072537 DOI: 10.1021/acs.jctc.6b01069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Substituent and solvent effects on the excited state dynamics of the Photoactive Yellow Protein chromophore are studied using the average solvent electrostatic potential from molecular dynamics (ASEP/MD) method. Four molecular models were considered: the ester and thioester derivatives of the p-coumaric acid anion and their methylated derivatives. We found that the solvent produces dramatic modifications on the free energy profile of the S1 state: 1) Two twisted structures that are minima in the gas phase could not be located in aqueous solution. 2) Conical intersections (CIs) associated with the rotation of the single bond adjacent to the phenyl group are found for the four derivatives in water solution but only for thio derivatives in the gas phase. 3) The relative stability of minima and CIs is reverted with respect to the gas phase values, affecting the prevalent de-excitation paths. As a consequence of these changes, three competitive de-excitation channels are open in aqueous solution: the fluorescence emission from a planar minimum on S1, the trans-cis photoisomerization through a CI that involves the rotation of the vinyl double bond, and the nonradiative, nonreactive, de-excitation through the CI associated with the rotation of the single bond adjacent to the phenyl group. In the gas phase, the minima are the structures with the lower energy, while in solution these are the conical intersections. In solution, the de-excitation prevalent path seems to be the photoisomerization for oxo compounds, while thio compounds return to the initial trans ground state without emission.
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Affiliation(s)
- Francisco F García-Prieto
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Aurora Muñoz-Losa
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Ignacio Fdez Galván
- Department of Chemistry-Ångström, The Theoretical Chemistry Programme, Uppsala University , Box 518, 751 20 Uppsala, Sweden
| | - M Luz Sánchez
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Manuel A Aguilar
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - M Elena Martín
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
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11
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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: 290] [Impact Index Per Article: 36.3] [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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12
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García-Prieto FF, Muñoz-Losa A, Luz Sánchez M, Elena Martín M, Aguilar MA. Solvent effects on de-excitation channels in the p-coumaric acid methyl ester anion, an analogue of the photoactive yellow protein (PYP) chromophore. Phys Chem Chem Phys 2016; 18:27476-27485. [DOI: 10.1039/c6cp03541h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Environmental effects on the deactivation channels of the PYP chromophore in the gas phase and water solution are compared at the CASPT2//CASSCF/cc-pVDZ level.
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Affiliation(s)
| | - Aurora Muñoz-Losa
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - M. Luz Sánchez
- Área de Química Física
- University of Extremadura
- 06006 Badajoz
- Spain
| | - M. Elena Martín
- Área de Química Física
- University of Extremadura
- 06006 Badajoz
- Spain
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13
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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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14
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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: 15] [Impact Index Per Article: 1.5] [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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15
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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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16
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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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17
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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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18
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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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19
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Liu J, Yabushita A, Taniguchi S, Chosrowjan H, Imamoto Y, Sueda K, Miyanaga N, Kobayashi T. Ultrafast Time-Resolved Pump–Probe Spectroscopy of PYP by a Sub-8 fs Pulse Laser at 400 nm. J Phys Chem B 2013; 117:4818-26. [DOI: 10.1021/jp4001016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jun Liu
- Advanced Ultrafast Laser Research
Center, University of Electro-Communications, Chofugaoka 1-5-1, Chofu, Tokyo 182-8585 Japan
- State Key Laboratory of High
Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800, China
- Core Research for Evolutional
Science and Technology (CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Atsushi Yabushita
- Department of Electrophysics, National Chiao Tung University, 1001 Ta Hsueh Road,
Hsinchu 300, Taiwan
| | - Seiji Taniguchi
- Institute
for Laser Technology, Osaka University,
Yamadaoka 2-6, Suita Osaka, 565-0871
Japan
| | - Haik Chosrowjan
- Institute
for Laser Technology, Osaka University,
Yamadaoka 2-6, Suita Osaka, 565-0871
Japan
| | - Yasushi Imamoto
- Department of Biophysics,
Graduate
School of Science, Kyoto University, Kitashirakawa-Oiwake,
Sakyo, Kyoto 606-8502 Japan
| | - Keiichi Sueda
- Institute of Laser Engineering, Osaka University, Yamadakami 2-6, Suita 565-0871, Ibaraki
567-0047, Japan
| | - Noriaki Miyanaga
- Institute of Laser Engineering, Osaka University, Yamadakami 2-6, Suita 565-0871, Ibaraki
567-0047, Japan
| | - Takayoshi Kobayashi
- Advanced Ultrafast Laser Research
Center, University of Electro-Communications, Chofugaoka 1-5-1, Chofu, Tokyo 182-8585 Japan
- Core Research for Evolutional
Science and Technology (CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Department of Electrophysics, National Chiao Tung University, 1001 Ta Hsueh Road,
Hsinchu 300, Taiwan
- Institute of Laser Engineering, Osaka University, Yamadakami 2-6, Suita 565-0871, Ibaraki
567-0047, Japan
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20
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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: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/19/2012] [Indexed: 12/23/2022]
Abstract
Trans-to-cis isomerization, the key reaction in photoactive proteins, usually cannot occur through the standard one-bond-flip mechanism. Owing to spatial constraints imposed by a protein environment, isomerization probably proceeds through a volume-conserving mechanism in which highly choreographed atomic motions are expected, the details of which have not yet been observed directly. Here we employ time-resolved X-ray crystallography to visualize structurally the isomerization of the p-coumaric acid chromophore in photoactive yellow protein with a time resolution of 100 ps and a spatial resolution of 1.6 Å. The structure of the earliest intermediate (I(T)) resembles a highly strained transition state in which the torsion angle is located halfway between the trans- and cis-isomers. The reaction trajectory of I(T) bifurcates into two structurally distinct cis intermediates via hula-twist and bicycle-pedal pathways. The bifurcating reaction pathways can be controlled by weakening the hydrogen bond between the chromophore and an adjacent residue through E46Q mutation, which switches off the bicycle-pedal pathway.
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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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21
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Hellingwerf KJ, Hendriks J, Gensch T. On the Configurational and Conformational Changes in Photoactive Yellow Protein that Leads to Signal Generation in Ectothiorhodospira halophila. J Biol Phys 2013; 28:395-412. [PMID: 23345784 DOI: 10.1023/a:1020360505111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Photoactive Yellow Protein (PYP), a phototaxis photoreceptor from Ectothiorhodospira halophila, is a small water-soluble protein that iscrystallisable and excellently photo-stable. It can be activated with light(λ(max)= 446 nm), to enter a series of transientintermediates that jointly form the photocycle of this photosensor protein.The most stable of these transient states is the signalling state forphototaxis, pB.The spatial structure of the ground state of PYP, pG and the spectralproperties of the photocycle intermediates have been very well resolved.Owing to its excellent chemical- and photochemical stability, also the spatialstructure of its photocycle intermediates has been characterised with X-raydiffraction and multinuclear NMR spectroscopy. Surprisingly, the resultsobtained showed that their structure is dependent on the molecular contextin which they are formed. Therefore, a large range of diffraction-,scattering- and spectroscopic techniques is now being employed to resolvein detail the dynamical changes of the structure of PYP while it progressesthrough its photocycle. This approach has led to considerable progress,although some techniques still result in mutually inconsistent conclusionsregarding aspects of the structure of particular intermediates.Recently, significant progress has also been made with simulations withmolecular dynamics analyses of the initial events that occur in PYP uponphoto activation. The great challenge in this field is to eventually obtainagreement between predicted dynamical alterations in PYP structure, asobtained with the MD approach and the actually measured dynamicalchanges in its structure as evolving during photocycle progression.
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22
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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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23
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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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24
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Kim PW, Freer LH, Rockwell NC, Martin SS, Lagarias JC, Larsen DS. Second-chance forward isomerization dynamics of the red/green cyanobacteriochrome NpR6012g4 from Nostoc punctiforme. J Am Chem Soc 2012; 134:130-3. [PMID: 22107125 PMCID: PMC3261522 DOI: 10.1021/ja209533x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The primary ultrafast Z-to-E isomerization photodynamics of the phytochrome-related cyanobacteriochrome NpR6012g4 from Nostoc punctiforme was studied by transient absorption pump-dump-probe spectroscopy. A 2 ps dump pulse resonant with the stimulated emission band depleted 21% of the excited-state population, while the initial photoproduct Lumi-R was depleted by only 11%. We observed a red-shifted ground-state intermediate (GSI) that we assign to a metastable state that failed to isomerize fully. Multicomponent global analysis implicates the generation of additional Lumi-R from the GSI via crossing over the ground-state thermal barrier for full isomerization, explaining the discrepancy between excited-state and Lumi-R depletion by the dump pulse. This second-chance ground-state dynamics provides a plausible explanation for the unusually high quantum yield of 40% for the primary isomerization step in the forward reaction of NpR6012g4.
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Affiliation(s)
- Peter W. Kim
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616
| | - Lucy H. Freer
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616
| | - Nathan C. Rockwell
- Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis, CA 95616
| | - Shelley S. Martin
- Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis, CA 95616
| | - J. Clark Lagarias
- Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis, CA 95616
| | - Delmar S. Larsen
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616
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25
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Rupenyan AB, Vreede J, van Stokkum IHM, Hospes M, Kennis JTM, Hellingwerf KJ, Groot ML. Proline 68 enhances photoisomerization yield in photoactive yellow protein. J Phys Chem B 2011; 115:6668-77. [PMID: 21542640 DOI: 10.1021/jp112113s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In proteins and enzymes, the local environment of an active cofactor plays an important role in controlling the outcome of a functional reaction. In photoactive yellow protein (PYP), it ensures photoisomerization of the chromophore, a prerequisite for formation of a signaling state. PYP is the prototype of a PAS domain, and the preferred model system for the studies of molecular mechanisms of biological light sensing. We investigated the effect of replacing proline-68, positioned near but not in direct contact with the chromophore, with other neutral amino acids (alanine, glycine, and valine), using ultrafast spectroscopy probing the visible and the mid-IR spectral regions, and molecular simulation to understand the interactions tuning the efficiency of light signaling. Transient absorption measurements indicate that the quantum yield of isomerization in the mutants is lower than the yield observed for the wild type. Subpicosecond mid-IR spectra and molecular dynamics simulations of the four proteins reveal that the hydrogen bond interactions around the chromophore and the access of water molecules in the active site of the protein determine the efficiency of photoisomerization. The mutants provide additional hydrogen bonds to the chromophore, directly and by allowing more water molecules access to its binding pocket. We conclude that proline-68 in the wild type protein optimizes the yield of photochemistry by maintaining a weak hydrogen bond with the chromophore, at the same time restraining the entrance of water molecules close to the alkylic part of pCa. This study provides a molecular basis for the structural optimization of biological light sensing.
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Affiliation(s)
- Alisa B Rupenyan
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands.
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26
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Carroll EC, Hospes M, Valladares C, Hellingwerf KJ, Larsen DS. Is the photoactive yellow protein a UV-B/blue light photoreceptor? Photochem Photobiol Sci 2011; 10:464-8. [DOI: 10.1039/c0pp00274g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Ma Y, Rohlfing M, Molteni C. Modeling the Excited States of Biological Chromophores within Many-Body Green's Function Theory. J Chem Theory Comput 2009; 6:257-65. [PMID: 26614336 DOI: 10.1021/ct900528h] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
First-principle many-body Green's function theory (MBGFT) has been successfully used to describe electronic excitations in many materials, from bulk crystals to nanoparticles. Here we assess its performance for the calculations of the excited states of biological chromophores. MBGFT is based on a set of Green's function equations, whose key ingredients are the electron's self-energy Σ, which is obtained by Hedin's GW approach, and the electron-hole interaction, which is described by the Bethe-Salpeter equation (BSE). The GW approach and the BSE predict orbital energies and excitation energies with high accuracy, respectively. We have calculated the low-lying excited states of a series of model biological chromophores, related to the photoactive yellow protein (PYP), rhodopsin, and the green fluorescent protein (GFP), obtaining a very good agreement with the available experimental and accurate theoretical data; the order of the excited states is also correctly predicted. MBGFT bridges the gap between time-dependent density functional theory and high-level quantum chemistry methods, combining the efficiency of the former with the accuracy of the latter: this makes MBGFT a promising method for studying excitations in complex biological systems.
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Affiliation(s)
- Yuchen Ma
- Fachbereich Physik, Universität Osnabrück, D-49069 Osnabrück, Germany, and Physics Department, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Michael Rohlfing
- Fachbereich Physik, Universität Osnabrück, D-49069 Osnabrück, Germany, and Physics Department, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Carla Molteni
- Fachbereich Physik, Universität Osnabrück, D-49069 Osnabrück, Germany, and Physics Department, King's College London, Strand, London WC2R 2LS, United Kingdom
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28
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Losi A, Gensch T, van der Horst MA, Hellingwerf KJ, Braslavsky SE. Hydrogen-bond network probed by time-resolved optoacoustic spectroscopy: photoactive yellow protein and the effect of E46Q and E46A mutations. Phys Chem Chem Phys 2009; 7:2229-36. [PMID: 19791418 DOI: 10.1039/b419079c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enthalpy and structural volume changes (delta Hi and delta Vi) produced upon photoinduced formation and decay of the red-shifted intermediate (pR = I1) in the photoactive yellow protein (WT-PYP) from Halorhodospira halophila and the mutated E46Q-PYP and E46A-PYP, were determined by laser-induced optoacoustic spectroscopy (LIOAS) using the two-temperatures method, at pH 8.5. These mutations alter the hydrogen bond between the phenolate oxygen of the chromophore and the residue at position 46. Hydrogen bonding is still possible in E46Q-PYP via the delta-NH2 group of glutamine, whereas it is no longer possible with the methyl group of alanine in E46A-PYP. In all three proteins, pR decays within hundreds of ns to micros into the next intermediate, pR'. The delta H values for the formation of pR (delta H pR) and for its decay into pR'(delta H pR-->pR') are negligibly affected by the E46Q and the E46A substitution. In all three proteins the large delta H pR value drives the photocycle. Whereas delta V pR is a similar contraction of ca. 15 ml mol(-1) for E46Q-PYP and WT-PYP, attributed to strengthening the hydrogen bond network (between 4 and 5 hydrogen bonds) inside the protein chromophore cavity, an expansion is observed for E46A-PYP, indicating just an enlargement of the chromophore cavity upon chromophore isomerization. The results are discussed in the light of the recent time-resolved room temperature, crystallographic studies with WT-PYP and E46Q-PYP. Formation of pR' is somewhat slower for E46Q-PYP and much slower for E46A-PYP. The structural volume change for this transition, delta V pR-->pR', is relatively small and positive for WT-PYP, slightly larger for E46Q-PYP, and definitely larger for the hydrogen-bond lacking E46A-PYP. This indicates a larger entropic change for this transition in E46A-PYP, reflected in the large pre-exponential factor for the pR to pR' decay rate constant determined in the 5-30 degrees C temperature range. This decay also shows an activation entropy that compensates the larger activation energy in E46A-PYP, as compared to the values for WT-PYP and E46Q-PYP.
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Affiliation(s)
- Aba Losi
- Max-Planck-Institut für Bioanorganische Chemie (formerly Strahlenchemie), Postfach 101365, D-45413 Mülheim an der Ruhr, Germany
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Picometer-scale conformational heterogeneity separates functional from nonfunctional states of a photoreceptor protein. Structure 2008; 16:863-72. [PMID: 18547519 DOI: 10.1016/j.str.2008.02.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 02/27/2008] [Accepted: 02/27/2008] [Indexed: 11/23/2022]
Abstract
Protein structural fluctuations occur over a wide spatial scale, ranging from minute, picometer-scale displacements, to large, interdomain motions and partial unfolding. While large-scale protein structural changes and their effects on protein function have been the focus of much recent attention, small-scale fluctuations have been less well studied, and are generally assumed to have proportionally smaller effects. Here we use the bacterial photoreceptor photoactive yellow protein (PYP) to test if subtle structural changes do, indeed, imply equally subtle functional effects. We flash froze crystals of PYP to trap the protein's conformational ensemble, and probed the molecules in this ensemble for their ability to facilitate PYP's biological function (i.e., light-driven isomerization of its chromophore). Our results indicate that the apparently homogeneous structural state observed in a 0.82 A crystal structure in fact comprises an ensemble of conformational states, in which subpopulations with nearly identical structures display dramatically different functional properties.
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Kumauchi M, Hara MT, Stalcup P, Xie A, Hoff WD. Identification of Six New Photoactive Yellow ProteinsDiversity and StructureFunction Relationships in a Bacterial Blue Light Photoreceptor. Photochem Photobiol 2008; 84:956-69. [DOI: 10.1111/j.1751-1097.2008.00335.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Gromov EV, Burghardt I, Hynes JT, Köppel H, Cederbaum LS. Electronic structure of the photoactive yellow protein chromophore: Ab initio study of the low-lying excited singlet states. J Photochem Photobiol A Chem 2007. [DOI: 10.1016/j.jphotochem.2007.04.033] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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Kühn O, Wöste L. Biological systems: Applications and perspectives. ANALYSIS AND CONTROL OF ULTRAFAST PHOTOINDUCED REACTIONS 2007. [PMCID: PMC7122019 DOI: 10.1007/978-3-540-68038-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Oliver Kühn
- Institut f. Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, D-14195 Berlin, Germany
| | - Ludger Wöste
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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Masciangioli T, Devanathan S, Cusanovich MA, Tollin G, El-Sayed MA. Probing the Primary Event in the Photocycle of Photoactive Yellow Protein Using Photochemical Hole-burning Technique¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2000)0720639ptpeit2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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34
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Nakamura R, Hamada N, Ichida H, Tokunaga F, Kanematsu Y. Ultrafast Dynamics of Photoactive Yellow Protein via the Photoexcitation and Emission Processes†. Photochem Photobiol 2007; 83:397-402. [PMID: 17576348 DOI: 10.1562/2006-06-23-ra-946] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Pump-dump fluorescence spectroscopy was performed for photoactive yellow protein (PYP) at room temperature. The effect of the dump pulse on the population of the potential energy surface of the electronic excited state was examined as depletion in the stationary fluorescence intensity. The dynamic behavior of the population in the electronic excited state was successfully probed in the various combinations of the pump-dump delay, the dump-pulse wavelength, the dump-pulse energy and the observation wavelength. The experimental results were compared with the results obtained by the femtosecond time-resolved fluorescence spectroscopy.
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Affiliation(s)
- Ryosuke Nakamura
- JST-CREST, Venture Business Laboratory, Center for Advanced Science and Innovation, Osaka University, Suita, Osaka 565-0871, Japan.
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35
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Adesokan AA, Pan D, Fredj E, Mathies RA, Gerber RB. Anharmonic Vibrational Calculations Modeling the Raman Spectra of Intermediates in the Photoactive Yellow Protein (PYP) Photocycle. J Am Chem Soc 2007; 129:4584-94. [PMID: 17378558 DOI: 10.1021/ja066903v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of anharmonic effects in the vibrational spectroscopy of the dark state and two major chromophore intermediates of the photoactive yellow protein (PYP) photocycle is examined via ab initio vibrational self-consistent field (VSCF) calculations and time-resolved resonance Raman spectroscopy. For the first time, anharmonicity is considered explicitly in calculating the vibrational spectra of an ensemble consisting of the PYP chromophore surrounded by model compounds used as mimics of the important active-site residues. Predictions of vibrational frequencies on an ab initio corrected semiempirical potential energy surface show remarkable agreement with experimental frequencies for all three states, thus shedding light on the potential along the reaction path. For example, calculated frequencies for vibrational modes of the red-shifted intermediate, PYPL, exhibit an overall average error of 0.82% from experiment. Upon analysis of anharmonicity patterns in the PYP modes we observe a decrease in anharmonicity in the C8-C9 stretching mode nu29 (trans-cis isomerization marker mode) with the onset of the cis configuration in PYPL. This can be attributed to the loss of the hydrogen-bonding character of the adjacent C9-O2 to the methylamine (Cys69 backbone). For several of the modes, the anharmonicity is mostly due to mode-mode coupling, while for others it is mostly intrinsic. This study shows the importance of the inclusion of anharmonicity in theoretical spectroscopic calculations, and the sensitivity of experiments to anharmonicity. The characterization of protein active-site residues by small molecular mimics provides an acceptable chemical structural representation for biomolecular spectroscopy calculations.
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Affiliation(s)
- Adeyemi A Adesokan
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697, USA
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36
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Changenet-Barret P, Plaza P, Martin MM, Chosrowjan H, Taniguchi S, Mataga N, Imamoto Y, Kataoka M. Role of arginine 52 on the primary photoinduced events in the PYP photocycle. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2006.12.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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37
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Brudler R, Gessner CR, Li S, Tyndall S, Getzoff ED, Woods VL. PAS domain allostery and light-induced conformational changes in photoactive yellow protein upon I2 intermediate formation, probed with enhanced hydrogen/deuterium exchange mass spectrometry. J Mol Biol 2006; 363:148-60. [PMID: 16952373 PMCID: PMC2575420 DOI: 10.1016/j.jmb.2006.07.078] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 07/24/2006] [Accepted: 07/28/2006] [Indexed: 11/21/2022]
Abstract
Photoactive yellow protein (PYP) is a small bacterial photoreceptor that undergoes a light-activated reaction cycle. PYP is also the prototypical Per-Arnt-Sim (PAS) domain. PAS domains, found in diverse multi-domain proteins from bacteria to humans, mediate protein-protein interactions and function as sensors and signal transducers. Here, we investigate conformational and dynamic changes in solution in wild-type PYP upon formation of the long-lived putative signaling intermediate I2 with enhanced hydrogen/deuterium exchange mass spectrometry (DXMS). The DXMS results showed that the central beta-sheet remains stable but specific external protein segments become strongly deprotected. Light-induced disruption of the dark-state hydrogen bonding network in I2 produces increased flexibility and opening of PAS core helices alpha3 and alpha4, releases the beta4-beta5 hairpin, and propagates conformational changes to the central beta-sheet. Surprisingly, the first approximately 10 N-terminal residues, which are essential for fast dark-state recovery from I2, become more protected. By combining the DXMS results with our crystallographic structures, which reveal detailed changes near the chromophore but limited protein conformational change, we propose a mechanism for I2 state formation. This mechanism integrates the results from diverse biophysical studies of PYP, and links an allosteric T to R-state conformational transition to three pathways for signal propagation within the PYP fold. On the basis of the observed changes in PYP plus commonalities shared among PAS domain proteins, we further propose that PAS domains share this conformational mechanism, which explains the versatile signal transduction properties of the structurally conserved PYP/PAS module by framework-encoded allostery.
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Affiliation(s)
- Ronald Brudler
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chris R. Gessner
- Department of Medicine and Biomedical Sciences Graduate Program, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Sheng Li
- Department of Medicine and Biomedical Sciences Graduate Program, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Sammy Tyndall
- Department of Medicine and Biomedical Sciences Graduate Program, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Elizabeth D. Getzoff
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Virgil L. Woods
- Department of Medicine and Biomedical Sciences Graduate Program, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
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38
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van Wilderen LJGW, van der Horst MA, van Stokkum IHM, Hellingwerf KJ, van Grondelle R, Groot ML. Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein. Proc Natl Acad Sci U S A 2006; 103:15050-5. [PMID: 17015839 PMCID: PMC1940041 DOI: 10.1073/pnas.0603476103] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photoactive proteins such as PYP (photoactive yellow protein) are generally accepted as model systems for studying protein signal state formation. PYP is a blue-light sensor from the bacterium Halorhodospira halophila. The formation of PYP's signaling state is initiated by trans-cis isomerization of the p-coumaric acid chromophore upon the absorption of light. The quantum yield of signaling state formation is approximately 0.3. Using femtosecond visible pump/mid-IR probe spectroscopy, we investigated the structure of the very short-lived ground state intermediate (GSI) that results from an unsuccessful attempt to enter the photocycle. This intermediate and the first stable GSI on pathway into the photocycle, I0, both have a mid-IR difference spectrum that is characteristic of a cis isomer, but only the I0 intermediate has a chromophore with a broken hydrogen bond with the backbone N atom of Cys-69. We suggest, therefore, that breaking this hydrogen bond is decisive for a successful entry into the photocycle. The chromophore also engages in a hydrogen-bonding network by means of its phenolate group with residues Tyr-42 and Glu-46. We have investigated the role of this hydrogen bond by exchanging the H bond-donating residue Glu-46 with the weaker H bond-donating glutamine (i.e., Gln-46). We have observed that this mutant exhibits virtually identical kinetics and product yields as WT PYP, even though during the I0-to-I1 transition, on the 800-ps time scale, the hydrogen bond of the chromophore with Gln-46 is broken, whereas this hydrogen bond remains intact with Glu-46.
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Affiliation(s)
- L J G W van Wilderen
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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39
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Espagne A, Paik DH, Changenet-Barret P, Martin MM, Zewail AH. Ultrafast Photoisomerization of Photoactive Yellow Protein Chromophore Analogues in Solution: Influence of the Protonation State. Chemphyschem 2006; 7:1717-26. [PMID: 16847839 DOI: 10.1002/cphc.200600137] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We investigate solvent viscosity and polarity effects on the photoisomerization of the protonated and deprotonated forms of two analogues of the photoactive yellow protein (PYP) chromophore. These are trans-p-hydroxybenzylidene acetone and trans-p-hydroxyphenyl cinnamate, studied in solutions of different polarity and viscosity at room temperature, by means of femtosecond fluorescence up-conversion. The fluorescence lifetimes of the protonated forms are found to be barely sensitive to solvent viscosity, and to increase with increasing solvent polarity. In contrast, the fluorescence decays of the deprotonated forms are significantly slowed down in viscous media and accelerated in polar solvents. These results elucidate the dramatic influence of the protonation state of the PYP chromophore analogues on their photoinduced dynamics. The viscosity and polarity effects are, respectively, interpreted in terms of different isomerization coordinates and charge redistribution in S(1). A trans-to-cis isomerization mechanism involving mainly the ethylenic double-bond torsion and/or solvation is proposed for the anionic forms, whereas "concerted" intramolecular motions are proposed for the neutral forms.
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Affiliation(s)
- Agathe Espagne
- UMR CNRS-ENS 8640 Pasteur, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France
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40
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Abstract
The photoactive yellow protein (PYP) is the photoreceptor protein responsible for initiating the blue-light repellent response of the Halorhodospira halophila bacterium. Optical excitation of the intrinsic chromophore in PYP, p-coumaric acid, leads to the initiation of a photocycle that comprises several distinct intermediates. The dynamical processes responsible for the initiation of the PYP photocycle have been explored with several time-resolved techniques, which include ultrafast electronic and vibrational spectroscopies. Ultrafast electronic spectroscopies, such as pump-visible probe, pump-dump-visible probe, and fluorescence upconversion, are useful in identifying the timescales and connectivity of the transient intermediates, while ultrafast vibrational spectroscopies link these intermediates to dynamic structures. Herein, we present the use of these techniques for exploring the initial dynamics of PYP, and show how these techniques provide the basis for understanding the complex relationship between protein and chromophore, which ultimately results in biological function.
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Affiliation(s)
- Delmar S Larsen
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
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41
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Heyne K, Mohammed OF, Usman A, Dreyer J, Nibbering ETJ, Cusanovich MA. Structural evolution of the chromophore in the primary stages of trans/cis isomerization in photoactive yellow protein. J Am Chem Soc 2006; 127:18100-6. [PMID: 16366562 PMCID: PMC2580759 DOI: 10.1021/ja051210k] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have studied the structural changes induced by optical excitation of the chromophore in wild-type photoactive yellow protein (PYP) in liquid solution with a combined approach of polarization-sensitive ultrafast infrared spectroscopy and density functional theory calculations. We identify the nuC8-C9 marker modes for solution phase PYP in the P and I0 states, from which we derive that the first intermediate state I0 that appears with a 3 ps time constant can be characterized to have a cis geometry. This is the first unequivocal demonstration that the formation of I0 correlates with the conversion from the trans to the cis state. For the P and I0 states we compare the experimentally measured vibrational band patterns and anisotropies with calculations and find that for both trans and cis configurations the planarity of the chromophore has a strong influence. The C7=C8-(C9=O)-S moiety of the chromophore in the dark P state has a trans geometry with the C=O group slightly tilted out-of-plane, in accordance with the earlier reported structure obtained in an X-ray diffraction study of PYP crystals. In the case of I0, experiment and theory are only in agreement when the C7=C8-(C9=O)-S moiety has a planar configuration. We find that the carboxylic side group of Glu46 that is hydrogen-bonded to the chromophore phenolate oxygen does not alter its orientation on going from the electronic ground P state, via the electronic excited P state to the intermediate I0 state, providing conclusive experimental evidence that the primary stages of PYP photoisomerization involve flipping of the enone thioester linkage without significant relocation of the phenolate moiety.
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Affiliation(s)
- Karsten Heyne
- : Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Omar F. Mohammed
- : Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Anwar Usman
- : Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - J. Dreyer
- : Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Erik T. J. Nibbering
- : Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Michael A. Cusanovich
- :Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
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42
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Espagne A, Changenet-Barret P, Plaza P, Martin MM. Solvent Effect on the Excited-State Dynamics of Analogues of the Photoactive Yellow Protein Chromophore. J Phys Chem A 2006; 110:3393-404. [PMID: 16526618 DOI: 10.1021/jp0563843] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We previously reported that two analogues of the Photoactive Yellow Protein chromophore, trans-p-hydroxycinnamic acid (pCA(2-)) and its amide derivative (pCM-) in their deprotonated forms, undergo a trans-cis photoisomerization whereas the thioester derivative, trans-p-hydroxythiophenyl cinnamate (pCT-), does not. pCT- is also the only one to exhibit a short-lived intermediate on its excited-state deactivation pathway. We here further stress the existence of two different relaxation mechanisms for these molecules and examine the reaction coordinates involved. We looked at the effect of the solvent properties (viscosity, polarity, solvation dynamics) on their excited-state relaxation dynamics, probed by ultrafast transient absorption spectroscopy. Sensitivity to the solvent properties is found to be larger for pCT- than for pCA(2-) and pCM-. This difference is considered to reveal that either the relaxation pathway or the reaction coordinate is different for these two classes of analogues. It is also found to be correlated to the electron donor-acceptor character of the molecule. We attribute the excited-state deactivation of analogues bearing a weaker acceptor group, pCA(2-) and pCM-, to a stilbene-like photoisomerization mechanism with the concerted rotation of the ethylenic bond and one adjacent single bond. For pCT-, which contains a stronger acceptor group, we consider a photoisomerization mechanism mainly involving the single torsion of the ethylenic bond. The excited-state deactivation of pCT- would lead to the formation of a ground-state intermediate at the "perp" geometry, which would return to the initial trans conformation without net isomerization.
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Affiliation(s)
- Agathe Espagne
- Département de Chimie, Ecole Normale Supérieure (UMR CNRS 8640 PASTEUR), 24 rue Lhomond, 75231 Paris Cedex 05, France
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43
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Lee IR, Lee W, Zewail AH. Primary steps of the photoactive yellow protein: isolated chromophore dynamics and protein directed function. Proc Natl Acad Sci U S A 2006; 103:258-62. [PMID: 16407155 PMCID: PMC1326191 DOI: 10.1073/pnas.0510015103] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cycle of the photoactive yellow protein (PYP) has been extensively studied, but the dynamics of the isolated chromophore responsible for transduction is unknown. Here, we present real-time observation of the dynamics of the negatively charged chromophore and detection of intermediates along the path of trans-to-cis isomerization using femtosecond mass selection/electron detachment techniques. The results show that the role of the protein environment is not in the first step of double-bond twisting (barrier crossing) but in directing efficient conversion to the cis-structure and in impeding radical formation within the protein.
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Affiliation(s)
- I-Ren Lee
- Arthur Amos Noyes Laboratory of Chemical Physics, Laboratory for Molecular Sciences, California Institute of Technology, Pasadena, CA 91125, USA
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44
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Li QS, Fang WH. Ab initio study on the structures and properties of trans-p-coumaric acid in low-lying electronic states. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2004.12.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Vengris M, van der Horst MA, Zgrablic G, van Stokkum IHM, Haacke S, Chergui M, Hellingwerf KJ, van Grondelle R, Larsen DS. Contrasting the excited-state dynamics of the photoactive yellow protein chromophore: protein versus solvent environments. Biophys J 2005; 87:1848-57. [PMID: 15345563 PMCID: PMC1304589 DOI: 10.1529/biophysj.104.043224] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Wavelength- and time-resolved fluorescence experiments have been performed on the photoactive yellow protein, the E46Q mutant, the hybrids of these proteins containing a nonisomerizing "locked" chromophore, and the native and locked chromophores in aqueous solution. The ultrafast dynamics of these six systems is compared and spectral signatures of isomerization and solvation are discussed. We find that the ultrafast red-shifting of fluorescence is associated mostly with solvation dynamics, whereas isomerization manifests itself as quenching of fluorescence. The observed multiexponential quenching of the protein samples differs from the single-exponential lifetimes of the chromophores in solution. The locked chromophore in the protein environment decays faster than in solution. This is due to additional channels of excited-state energy dissipation via the covalent and hydrogen bonds with the protein environment. The observed large dispersion of quenching timescales observed in the protein samples that contain the native pigment favors both an inhomogeneous model and an excited-state barrier for isomerization.
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Affiliation(s)
- Mikas Vengris
- Faculty of Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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46
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Larsen DS, van Stokkum IHM, Vengris M, van Der Horst MA, de Weerd FL, Hellingwerf KJ, van Grondelle R. Incoherent manipulation of the photoactive yellow protein photocycle with dispersed pump-dump-probe spectroscopy. Biophys J 2005; 87:1858-72. [PMID: 15345564 PMCID: PMC1304590 DOI: 10.1529/biophysj.104.043794] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photoactive yellow protein is the protein responsible for initiating the "blue-light vision" of Halorhodospira halophila. The dynamical processes responsible for triggering the photoactive yellow protein photocycle have been disentangled with the use of a novel application of dispersed ultrafast pump-dump-probe spectroscopy, where the photocycle can be started and interrupted with appropriately tuned and timed laser pulses. This "incoherent" manipulation of the photocycle allows for the detailed spectroscopic investigation of the underlying photocycle dynamics and the construction of a fully self-consistent dynamical model. This model requires three kinetically distinct excited-state intermediates, two (ground-state) photocycle intermediates, I(0) and pR, and a ground-state intermediate through which the protein, after unsuccessful attempts at initiating the photocycle, returns to the equilibrium ground state. Also observed is a previously unknown two-photon ionization channel that generates a radical and an ejected electron into the protein environment. This second excitation pathway evolves simultaneously with the pathway containing the one-photon photocycle intermediates.
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Affiliation(s)
- Delmar S Larsen
- Faculty of Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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47
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Kyndt JA, Fitch JC, Meyer TE, Cusanovich MA. Thermochromatium tepidumPhotoactive Yellow Protein/Bacteriophytochrome/Diguanylate Cyclase: Characterization of the PYP Domain†. Biochemistry 2005; 44:4755-64. [PMID: 15779902 DOI: 10.1021/bi047373n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The purple phototrophic bacterium, Thermochromatium tepidum, contains a gene for a chimeric photoactive yellow protein/bacteriophytochrome/diguanylate cyclase (Ppd). We produced the Tc. tepidum PYP domain (Tt PYP) in Escherichia coli, and found that it has a wavelength maximum at 358 nm due to a Leu46 substitution of the color-tuning Glu46 found in the prototypic Halorhodospira halophila PYP (Hh PYP). However, the 358 nm dark-adapted state is in a pH-dependent equilibrium with a yellow species absorbing at 465 nm (pK(a) = 10.2). Following illumination at 358 nm, photocycle kinetics are characterized at pH 7.0 by a small bleach and red shift to what appears to be a long-lived cis intermediate (comparable to the I(2) intermediate in Hh PYP). The recovery to the dark-adapted state has a lifetime of approximately 4 min, which is approximately 1500 times slower than that for Hh PYP. However, when the Tt PYP is illuminated at pH values above 7.5, the light-induced difference spectrum indicates a pH-dependent equilibrium between the I(2) intermediate and a red-shifted 440 nm intermediate. This equilibrium could be responsible for the sigmoidal pH dependence of the recovery of the dark-adapted state (pK(a) = 8.8). In addition, the light-induced difference spectrum shows that, at pH values above 9.3, there is an apparent bleach near 490 nm superimposed on the 358 and 440 nm changes, which we ascribe to the equilibrium between the protonated and ionized dark-adapted forms. The L46E mutant of Tt PYP has a wavelength maximum at 446 nm, resembling wild-type Hh PYP. The kinetics of recovery of L46E following illumination with white light are slow (lifetime of 15 min at pH 7), but are comparable to those of wild-type Tt PYP. We conclude that Tt PYP is unique among the PYPs studied to date in that it has a photocycle initiated from a dark-adapted state with a protonated chromophore at physiological pH. However, it is kinetically most similar to Rhodocista centenaria PYP (Ppr) despite the very different absorption spectra due to the lack of E46.
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Affiliation(s)
- John A Kyndt
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
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Vengris M, Larsen DS, van der Horst MA, Larsen OFA, Hellingwerf KJ, van Grondelle R. Ultrafast Dynamics of Isolated Model Photoactive Yellow Protein Chromophores: “Chemical Perturbation Theory” in the Laboratory. J Phys Chem B 2005; 109:4197-208. [PMID: 16851482 DOI: 10.1021/jp045763d] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pump-probe and pump-dump probe experiments have been performed on several isolated model chromophores of the photoactive yellow protein (PYP). The observed transient absorption spectra are discussed in terms of the spectral signatures ascribed to solvation, excited-state twisting, and vibrational relaxation. It is observed that the protonation state has a profound effect on the excited-state lifetime of p-coumaric acid. Pigments with ester groups on the coumaryl tail end and charged phenolic moieties show dynamics that are significantly different from those of other pigments. Here, an unrelaxed ground-state intermediate could be observed in pump-probe signals. A similar intermediate could be identified in the sinapinic acid and in isomerization-locked chromophores by means of pump-dump probe spectroscopy; however, in these compounds it is less pronounced and could be due to ground-state solvation and/or vibrational relaxation. Because of strong protonation-state dependencies and the effect of electron donor groups, it is argued that charge redistribution upon excitation determines the twisting reaction pathway, possibly through interaction with the environment. It is suggested that the same pathway may be responsible for the initiation of the photocycle in native PYP.
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Affiliation(s)
- Mikas Vengris
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
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Excited state dynamics of a PYP chromophore model system explored with ultrafast infrared spectroscopy. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2004.11.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Changenet-Barret P, Espagne A, Plaza P, Hellingwerf KJ, Martin MM. Investigations of the primary events in a bacterial photoreceptor for photomotility: photoactive yellow protein (PYP). NEW J CHEM 2005. [DOI: 10.1039/b418134d] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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