1
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Sarabi D, Ostojić L, Bosman R, Vallejos A, Linse JB, Wulff M, Levantino M, Neutze R. Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:054102. [PMID: 36329868 PMCID: PMC9625836 DOI: 10.1063/4.0000157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Time-resolved x-ray solution scattering (TR-XSS) is a sub-field of structural biology, which observes secondary structural changes in proteins as they evolve along their functional pathways. While the number of distinct conformational states and their rise and decay can be extracted directly from TR-XSS experimental data recorded from light-sensitive systems, structural modeling is more challenging. This step often builds from complementary structural information, including secondary structural changes extracted from crystallographic studies or molecular dynamics simulations. When working with integral membrane proteins, another challenge arises because x-ray scattering from the protein and the surrounding detergent micelle interfere and these effects should be considered during structural modeling. Here, we utilize molecular dynamics simulations to explicitly incorporate the x-ray scattering cross term between a membrane protein and its surrounding detergent micelle when modeling TR-XSS data from photoactivated samples of detergent solubilized bacteriorhodopsin. This analysis provides theoretical foundations in support of our earlier approach to structural modeling that did not explicitly incorporate this cross term and improves agreement between experimental data and theoretical predictions at lower x-ray scattering angles.
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Affiliation(s)
- Daniel Sarabi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Lucija Ostojić
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Johanna-Barbara Linse
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Michael Wulff
- European Synchrotron Radiation Facility, 38043 Grenoble Cedex 9, France
| | - Matteo Levantino
- European Synchrotron Radiation Facility, 38043 Grenoble Cedex 9, France
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
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2
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Lee SJ, Kim TW, Kim JG, Yang C, Yun SR, Kim C, Ren Z, Kumarapperuma I, Kuk J, Moffat K, Yang X, Ihee H. Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering. SCIENCE ADVANCES 2022; 8:eabm6278. [PMID: 35622911 PMCID: PMC9140987 DOI: 10.1126/sciadv.abm6278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/13/2022] [Indexed: 05/25/2023]
Abstract
Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light-absorbing (Pr)-to-far-red light-absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of Pseudomonas aeruginosa. Kinetic analysis of the TRXSS data identifies three distinct structural species, which are attributed to lumi-F, meta-F, and Pr, connected by time constants of 95 μs and 21 ms. Structural analysis based on molecular dynamics simulations shows that the light activation of PaBphP accompanies quaternary structural rearrangements from an "II"-framed close form of the Pfr state to an "O"-framed open form of the Pr state in terms of the helical backbones. This study provides mechanistic insights into how modular signaling proteins such as BphPs transmit structural signals over long distances and regulate their downstream biological responses.
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Affiliation(s)
- Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry, Mokpo National University, Muan-gun, Jeollanam-do, 58554, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - So Ri Yun
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Changin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Indika Kumarapperuma
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jane Kuk
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Keith Moffat
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
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3
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van Wilderen LJGW, Blankenburg L, Bredenbeck J. Femtosecond-to-millisecond mid-IR spectroscopy of Photoactive Yellow Protein uncovers structural micro-transitions of the chromophore's protonation mechanism. J Chem Phys 2022; 156:205103. [DOI: 10.1063/5.0091918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Protein structural dynamics can span many orders of magnitude in time. Photoactive Yellow Protein's (PYP) reversible photocycle encompasses picosecond isomerization of the light-absorbing chromophore as well as large scale protein backbone motions occurring on a millisecond timescale. Femtosecond-to-millisecond time-resolved mid-Infrared (IR) spectroscopy is employed here to uncover structural details of photocycle intermediates up to chromophore protonation and the first structural changes leading to formation of the partially-unfolded signalling state pB. The data show that a commonly thought stable transient photocycle intermediate is actually formed after a sequence of several smaller structural changes. We provide residue-specific spectroscopic evidence that protonation of the chromophore on a hundreds of microseconds timescale is delayed with respect to deprotonation of the nearby E46 residue. That implies that the direct proton donor is not E46 but most likely a water molecule. Such details may assist ongoing photocycle and protein folding simulation efforts on the complex and wide time-spanning photocycle of the model system PYP.
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4
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Jeong H, Ki H, Kim JG, Kim J, Lee Y, Ihee H. Sensitivity of
time‐resolved
diffraction data to changes in internuclear distances and atomic positions. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Haeyun Jeong
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Jungmin Kim
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
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5
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Brändén G, Neutze R. Advances and challenges in time-resolved macromolecular crystallography. Science 2021; 373:373/6558/eaba0954. [PMID: 34446579 DOI: 10.1126/science.aba0954] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Conformational changes within biological macromolecules control a vast array of chemical reactions in living cells. Time-resolved crystallography can reveal time-dependent structural changes that occur within protein crystals, yielding chemical insights in unparalleled detail. Serial crystallography approaches developed at x-ray free-electron lasers are now routinely used for time-resolved diffraction studies of macromolecules. These techniques are increasingly being applied at synchrotron radiation sources and to a growing diversity of macromolecules. Here, we review recent progress in the field, including visualizing ultrafast structural changes that guide the initial trajectories of light-driven reactions as well as capturing biologically important conformational changes on slower time scales, for which bacteriorhodopsin and photosystem II are presented as illustrative case studies.
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Affiliation(s)
- Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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6
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Lee SJ, Kim Y, Kim TW, Yang C, Thamilselvan K, Jeong H, Hyun J, Ihee H. Reversible molecular motional switch based on circular photoactive protein oligomers exhibits unexpected photo-induced contraction. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100512. [PMID: 35509376 PMCID: PMC9062587 DOI: 10.1016/j.xcrp.2021.100512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Molecular switches alterable between two stable states by environmental stimuli, such as light and temperature, offer the potential for controlling biological functions. Here, we report a circular photoswitchable protein complex made of multiple protein molecules that can rapidly and reversibly switch with significant conformational changes. The structural and photochromic properties of photoactive yellow protein (PYP) are harnessed to construct circular oligomer PYPs (coPYPs) of desired sizes. Considering the light-induced N-terminal protrusion of monomer PYP, we expected coPYPs would expand upon irradiation, but time-resolved X-ray scattering data reveal that the late intermediate has a pronounced light-induced contraction motion. This work not only provides an approach to engineering a novel protein-based molecular switch based on circular oligomers of well-known protein units but also demonstrates the importance of characterizing the structural dynamics of designed molecular switches.
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Affiliation(s)
- Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Youngmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Tae Wu Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Kamatchi Thamilselvan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Hyeongseop Jeong
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
| | - Jaekyung Hyun
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology (OIST), Okinawa 904-0495, Japan
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Lead contact
- Correspondence:
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7
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Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering. Proc Natl Acad Sci U S A 2020; 117:14996-15005. [PMID: 32541047 PMCID: PMC7334511 DOI: 10.1073/pnas.1913442117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.
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8
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Kim J, Kim JG, Ki H, Ahn CW, Ihee H. Estimating signal and noise of time-resolved X-ray solution scattering data at synchrotrons and XFELs. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:633-645. [PMID: 32381763 PMCID: PMC7206544 DOI: 10.1107/s1600577520002738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
Elucidating the structural dynamics of small molecules and proteins in the liquid solution phase is essential to ensure a fundamental understanding of their reaction mechanisms. In this regard, time-resolved X-ray solution scattering (TRXSS), also known as time-resolved X-ray liquidography (TRXL), has been established as a powerful technique for obtaining the structural information of reaction intermediates and products in the liquid solution phase and is expected to be applied to a wider range of molecules in the future. A TRXL experiment is generally performed at the beamline of a synchrotron or an X-ray free-electron laser (XFEL) to provide intense and short X-ray pulses. Considering the limited opportunities to use these facilities, it is necessary to verify the plausibility of a target experiment prior to the actual experiment. For this purpose, a program has been developed, referred to as S-cube, which is short for a Solution Scattering Simulator. This code allows the routine estimation of the shape and signal-to-noise ratio (SNR) of TRXL data from known experimental parameters. Specifically, S-cube calculates the difference scattering curve and the associated quantum noise on the basis of the molecular structure of the target reactant and product, the target solvent, the energy of the pump laser pulse and the specifications of the beamline to be used. Employing a simplified form for the pair-distribution function required to calculate the solute-solvent cross term greatly increases the calculation speed as compared with a typical TRXL data analysis. Demonstrative applications of S-cube are presented, including the estimation of the expected TRXL data and SNR level for the future LCLS-II HE beamlines.
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Affiliation(s)
- Jungmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Chi Woo Ahn
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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9
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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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10
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Kong Q, Khakhulin D, Shkrob IA, Lee JH, Zhang X, Kim J, Kim KH, Jo J, Kim J, Kang J, Pham VT, Jennings G, Kurtz C, Spence R, Chen LX, Wulff M, Ihee H. Solvent-dependent complex reaction pathways of bromoform revealed by time-resolved X-ray solution scattering and X-ray transient absorption spectroscopy. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:064902. [PMID: 31893214 PMCID: PMC6930140 DOI: 10.1063/1.5132968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
The photochemical reaction pathways of CHBr3 in solution were unveiled using two complementary X-ray techniques, time-resolved X-ray solution scattering (TRXSS) and X-ray transient absorption spectroscopy, in a wide temporal range from 100 ps to tens of microseconds. By performing comparative measurements in protic (methanol) and aprotic (methylcyclohexane) solvents, we found that the reaction pathways depend significantly on the solvent properties. In methanol, the major photoproducts are CH3OCHBr2 and HBr generated by rapid solvolysis of iso-CHBr2-Br, an isomer of CHBr3. In contrast, in methylcyclohexane, iso-CHBr2-Br returns to CHBr3 without solvolysis. In both solvents, the formation of CHBr2 and Br is a competing reaction channel. From the structural analysis of TRXSS data, we determined the structures of key intermediate species, CH3OCHBr2 and iso-CHBr2-Br in methanol and methylcyclohexane, respectively, which are consistent with the structures from density functional theory calculations.
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Affiliation(s)
- Qingyu Kong
- Authors to whom correspondence should be addressed: and
| | | | - Ilya A. Shkrob
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, Illinois 60349, USA
| | - Jae Hyuk Lee
- Pohang Accelerator Laboratory, Pohang 37673, South Korea
| | - Xiaoyi Zhang
- X-ray Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, Illinois 60349, USA
| | - Jeongho Kim
- Department of Chemistry, Inha University, Incheon 22212, South Korea
| | - Kyung Hwan Kim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | | | | | | | - Van-Thai Pham
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin, 91192 Gif-sur-Yvette, France
| | - Guy Jennings
- X-ray Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, Illinois 60349, USA
| | - Charles Kurtz
- X-ray Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, Illinois 60349, USA
| | - Rick Spence
- X-ray Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, Illinois 60349, USA
| | | | - Michael Wulff
- European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble Cedex, France
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11
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Yang C, Choi M, Kim JG, Kim H, Muniyappan S, Nozawa S, Adachi SI, Henning R, Kosheleva I, Ihee H. Protein Structural Dynamics of Wild-Type and Mutant Homodimeric Hemoglobin Studied by Time-Resolved X-Ray Solution Scattering. Int J Mol Sci 2018; 19:ijms19113633. [PMID: 30453670 PMCID: PMC6274816 DOI: 10.3390/ijms19113633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 01/30/2023] Open
Abstract
The quaternary transition between the relaxed (R) and tense (T) states of heme-binding proteins is a textbook example for the allosteric structural transition. Homodimeric hemoglobin (HbI) from Scapharca inaequivalvis is a useful model system for investigating the allosteric behavior because of the relatively simple quaternary structure. To understand the cooperative transition of HbI, wild-type and mutants of HbI have been studied by using time-resolved X-ray solution scattering (TRXSS), which is sensitive to the conformational changes. Herein, we review the structural dynamics of HbI investigated by TRXSS and compare the results of TRXSS with those of other techniques.
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Affiliation(s)
- Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Minseo Choi
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Hanui Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Srinivasan Muniyappan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Shunsuke Nozawa
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
| | - Shin-Ichi Adachi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA.
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA.
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
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12
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Leitner T, Josefsson I, Mazza T, Miedema PS, Schröder H, Beye M, Kunnus K, Schreck S, Düsterer S, Föhlisch A, Meyer M, Odelius M, Wernet P. Time-resolved electron spectroscopy for chemical analysis of photodissociation: Photoelectron spectra of Fe(CO)5, Fe(CO)4, and Fe(CO)3. J Chem Phys 2018; 149:044307. [DOI: 10.1063/1.5035149] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- T. Leitner
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - I. Josefsson
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - T. Mazza
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - P. S. Miedema
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - H. Schröder
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24/25, 14476 Potsdam, Germany
| | - M. Beye
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - K. Kunnus
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24/25, 14476 Potsdam, Germany
| | - S. Schreck
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24/25, 14476 Potsdam, Germany
| | - S. Düsterer
- Deutsches Elektronen-Synchrotron DESY, FS-FLASH, Notkestrasse 85, 22607 Hamburg, Germany
| | - A. Föhlisch
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24/25, 14476 Potsdam, Germany
| | - M. Meyer
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Odelius
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Ph. Wernet
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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13
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Kim Y, Ganesan P, Jo J, Kim SO, Thamilselvan K, Ihee H. Chromophore-Removal-Induced Conformational Change in Photoactive Yellow Protein Determined through Spectroscopic and X-ray Solution Scattering Studies. J Phys Chem B 2018; 122:4513-4520. [PMID: 29648836 DOI: 10.1021/acs.jpcb.8b01768] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photoactive yellow protein (PYP) induces negative phototaxis in Halorhodospira halophila via photoactivation triggered by light-mediated chromophore isomerization. Chromophore isomerization proceeds via a volume-conserving isomerization mechanism due to the hydrogen-bond network and steric constraints inside the protein, and causes significant conformational changes accompanied by N-terminal protrusion. However, it is unclear how the structural change of the chromophore affects the remote N-terminal domain. To understand photocycle-related structural changes, we investigated the structural aspect of chromophore removal in PYP because it possesses a disrupted hydrogen-bond network similar to that in photocycle intermediates. A comparison of the structural aspects with those observed in the photocycle would give a clue related to the structural change mechanism in the photocycle. Chromophore removal effects were assessed via UV-vis spectroscopy, circular dichroism, and X-ray solution scattering. Molecular shape reconstruction and an experiment-restrained rigid-body molecular dynamics simulation based on the scattering data were performed to determine protein shape, size, and conformational changes upon PYP bleaching. Data show that chromophore removal disrupted the holo-PYP structure, resulting in a small N-terminal protrusion, but the extent of conformational changes was markedly less than those in the photocycle. This indicates that disruption of the hydrogen-bond network alone in bleached PYP does not induce the large conformational change observed in the photocycle, which thus must result from the organized structural transition around the chromophore triggered by chromophore photoisomerization along with disruption of the hydrogen-bond network between the chromophore and the PYP core.
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Affiliation(s)
- Youngmin Kim
- Department of Chemistry and KI for the BioCentury , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
| | - Prabhakar Ganesan
- Department of Chemistry and KI for the BioCentury , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Republic of Korea
| | - Junbeom Jo
- Department of Chemistry and KI for the BioCentury , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
| | - Seong Ok Kim
- Department of Chemistry and KI for the BioCentury , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
| | - Kamatchi Thamilselvan
- Department of Chemistry and KI for the BioCentury , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
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14
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Lee K, Kim Y, Jung J, Ihee H, Park Y. Measurements of complex refractive index change of photoactive yellow protein over a wide wavelength range using hyperspectral quantitative phase imaging. Sci Rep 2018; 8:3064. [PMID: 29449627 PMCID: PMC5814402 DOI: 10.1038/s41598-018-21403-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/31/2018] [Indexed: 12/25/2022] Open
Abstract
A novel optical holographic technique is presented to simultaneously measure both the real and imaginary components of the complex refractive index (CRI) of a protein solution over a wide visible wavelength range. Quantitative phase imaging was employed to precisely measure the optical field transmitted from a protein solution, from which the CRIs of the protein solution were retrieved using the Fourier light scattering technique. Using this method, we characterized the CRIs of the two dominant structural states of a photoactive yellow protein solution over a broad wavelength range (461-582 nm). The significant CRI deviation between the two structural states was quantified and analysed. The results of both states show the similar overall shape of the expected rRI obtained from the Kramers-Kronig relations.
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Affiliation(s)
- KyeoReh Lee
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Youngmin Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - JaeHwang Jung
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Hyotcherl Ihee
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea.
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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15
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Yang C, Kim TW, Kim Y, Choi J, Lee SJ, Ihee H. Kinetics of the E46Q mutant of photoactive yellow protein investigated by transient grating spectroscopy. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Oang KY, Yang C, Muniyappan S, Kim J, Ihee H. SVD-aided pseudo principal-component analysis: A new method to speed up and improve determination of the optimum kinetic model from time-resolved data. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044013. [PMID: 28405591 PMCID: PMC5382018 DOI: 10.1063/1.4979854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/24/2017] [Indexed: 05/22/2023]
Abstract
Determination of the optimum kinetic model is an essential prerequisite for characterizing dynamics and mechanism of a reaction. Here, we propose a simple method, termed as singular value decomposition-aided pseudo principal-component analysis (SAPPA), to facilitate determination of the optimum kinetic model from time-resolved data by bypassing any need to examine candidate kinetic models. We demonstrate the wide applicability of SAPPA by examining three different sets of experimental time-resolved data and show that SAPPA can efficiently determine the optimum kinetic model. In addition, the results of SAPPA for both time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) data of the same protein reveal that global structural changes of protein, which is probed by TRXSS, may occur more slowly than local structural changes around the chromophore, which is probed by TA spectroscopy.
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Affiliation(s)
| | | | | | - Jeongho Kim
- Department of Chemistry, Inha University , Incheon 22212, South Korea
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17
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Xu J, Van Doren SR. Tracking Equilibrium and Nonequilibrium Shifts in Data with TREND. Biophys J 2017; 112:224-233. [PMID: 28122211 DOI: 10.1016/j.bpj.2016.12.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 11/21/2016] [Accepted: 12/09/2016] [Indexed: 11/16/2022] Open
Abstract
Principal component analysis (PCA) discovers patterns in multivariate data that include spectra, microscopy, and other biophysical measurements. Direct application of PCA to crowded spectra, images, and movies (without selecting peaks or features) was shown recently to identify their equilibrium or temporal changes. To enable the community to utilize these capabilities with a wide range of measurements, we have developed multiplatform software named TREND to Track Equilibrium and Nonequilibrium population shifts among two-dimensional Data frames. TREND can also carry this out by independent component analysis. We highlight a few examples of finding concurrent processes. TREND extracts dual phases of binding to two sites directly from the NMR spectra of the titrations. In a cardiac movie from magnetic resonance imaging, TREND resolves principal components (PCs) representing breathing and the cardiac cycle. TREND can also reconstruct the series of measurements from selected PCs, as illustrated for a biphasic, NMR-detected titration and the cardiac MRI movie. Fidelity of reconstruction of series of NMR spectra or images requires more PCs than needed to plot the largest population shifts. TREND reads spectra from many spectroscopies in the most common formats (JCAMP-DX and NMR) and multiple movie formats. The TREND package thus provides convenient tools to resolve the processes recorded by diverse biophysical methods.
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Affiliation(s)
- Jia Xu
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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18
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Wernet P, Leitner T, Josefsson I, Mazza T, Miedema PS, Schröder H, Beye M, Kunnus K, Schreck S, Radcliffe P, Düsterer S, Meyer M, Odelius M, Föhlisch A. Communication: Direct evidence for sequential dissociation of gas-phase Fe(CO) 5 via a singlet pathway upon excitation at 266 nm. J Chem Phys 2017; 146:211103. [PMID: 28595420 PMCID: PMC5457291 DOI: 10.1063/1.4984774] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 05/18/2017] [Indexed: 11/14/2022] Open
Abstract
We prove the hitherto hypothesized sequential dissociation of Fe(CO)5 in the gas phase upon photoexcitation at 266 nm via a singlet pathway with time-resolved valence and core-level photoelectron spectroscopy with an x-ray free-electron laser. Valence photoelectron spectra are used to identify free CO molecules and to determine the time constants of stepwise dissociation to Fe(CO)4 within the temporal resolution of the experiment and further to Fe(CO)3 within 3 ps. Fe 3p core-level photoelectron spectra directly reflect the singlet spin state of the Fe center in Fe(CO)5, Fe(CO)4, and Fe(CO)3 showing that the dissociation exclusively occurs along a singlet pathway without triplet-state contribution. Our results are important for assessing intra- and intermolecular relaxation processes in the photodissociation dynamics of the prototypical Fe(CO)5 complex in the gas phase and in solution, and they establish time-resolved core-level photoelectron spectroscopy as a powerful tool for determining the multiplicity of transition metals in photochemical reactions of coordination complexes.
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Affiliation(s)
- Ph Wernet
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - T Leitner
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - I Josefsson
- Department of Physics, Stockholm University, AlbaNova University Center, 106 91 Stockholm, Sweden
| | - T Mazza
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - P S Miedema
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - H Schröder
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - M Beye
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - K Kunnus
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - S Schreck
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - P Radcliffe
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - S Düsterer
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - M Meyer
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M Odelius
- Department of Physics, Stockholm University, AlbaNova University Center, 106 91 Stockholm, Sweden
| | - A Föhlisch
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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19
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Abstract
Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers.
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Affiliation(s)
- Hosung Ki
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea; , , .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea
| | - Key Young Oang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea; , , .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, Incheon 402-751, South Korea;
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea; , , .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea
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20
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Cho HS, Schotte F, Dashdorj N, Kyndt J, Henning R, Anfinrud PA. Picosecond Photobiology: Watching a Signaling Protein Function in Real Time via Time-Resolved Small- and Wide-Angle X-ray Scattering. J Am Chem Soc 2016; 138:8815-23. [PMID: 27305463 DOI: 10.1021/jacs.6b03565] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The capacity to respond to environmental changes is crucial to an organism's survival. Halorhodospira halophila is a photosynthetic bacterium that swims away from blue light, presumably in an effort to evade photons energetic enough to be genetically harmful. The protein responsible for this response is believed to be photoactive yellow protein (PYP), whose chromophore photoisomerizes from trans to cis in the presence of blue light. We investigated the complete PYP photocycle by acquiring time-resolved small and wide-angle X-ray scattering patterns (SAXS/WAXS) over 10 decades of time spanning from 100 ps to 1 s. Using a sequential model, global analysis of the time-dependent scattering differences recovered four intermediates (pR0/pR1, pR2, pB0, pB1), the first three of which can be assigned to prior time-resolved crystal structures. The 1.8 ms pB0 to pB1 transition produces the PYP signaling state, whose radius of gyration (Rg = 16.6 Å) is significantly larger than that for the ground state (Rg = 14.7 Å) and is therefore inaccessible to time-resolved protein crystallography. The shape of the signaling state, reconstructed using GASBOR, is highly anisotropic and entails significant elongation of the long axis of the protein. This structural change is consistent with unfolding of the 25 residue N-terminal domain, which exposes the β-scaffold of this sensory protein to a potential binding partner. This mechanistically detailed description of the complete PYP photocycle, made possible by time-resolved crystal and solution studies, provides a framework for understanding signal transduction in proteins and for assessing and validating theoretical/computational approaches in protein biophysics.
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Affiliation(s)
- Hyun Sun Cho
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Friedrich Schotte
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Naranbaatar Dashdorj
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - John Kyndt
- College of Science and Technology, Bellevue University , Bellevue, Nebraska 68005, United States
| | - Robert Henning
- Center for Advanced Radiation Sources, University of Chicago , Chicago, Illinois 60637, United States
| | - Philip A Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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