1
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Kim SO, Yun SR, Lee H, Jo J, Ahn DS, Kim D, Kosheleva I, Henning R, Kim J, Kim C, You S, Kim H, Lee SJ, Ihee H. Serial X-ray liquidography: multi-dimensional assay framework for exploring biomolecular structural dynamics with microgram quantities. Nat Commun 2024; 15:6287. [PMID: 39060271 PMCID: PMC11282289 DOI: 10.1038/s41467-024-50696-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Understanding protein structure and kinetics under physiological conditions is crucial for elucidating complex biological processes. While time-resolved (TR) techniques have advanced to track molecular actions, their practical application in biological reactions is often confined to reversible photoreactions within limited experimental parameters due to inefficient sample utilization and inflexibility of experimental setups. Here, we introduce serial X-ray liquidography (SXL), a technique that combines time-resolved X-ray liquidography with a fixed target of serially arranged microchambers. SXL breaks through the previously mentioned barriers, enabling microgram-scale TR studies of both irreversible and reversible reactions of even a non-photoactive protein. We demonstrate its versatility in studying a wide range of biological reactions, highlighting its potential as a flexible and multi-dimensional assay framework for kinetic and structural characterization. Leveraging X-ray free-electron lasers and micro-focused X-ray pulses promises further enhancements in both temporal resolution and minimizing sample quantity. SXL offers unprecedented insights into the structural and kinetic landscapes of molecular actions, paving the way for a deeper understanding of complex biological processes.
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Affiliation(s)
- Seong Ok Kim
- Center for Advanced Reactions Dynamics (CARD), Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - So Ri Yun
- Center for Advanced Reactions Dynamics (CARD), Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyosub Lee
- Center for Advanced Reactions Dynamics (CARD), Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Junbeom Jo
- Center for Advanced Reactions Dynamics (CARD), Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Doo-Sik Ahn
- Center for Advanced Reactions Dynamics (CARD), Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Doyeong Kim
- Center for Advanced Reactions Dynamics (CARD), Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Jungmin Kim
- Center for Advanced Reactions Dynamics (CARD), Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Changin Kim
- Center for Advanced Reactions Dynamics (CARD), Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Seyoung You
- Center for Advanced Reactions Dynamics (CARD), Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hanui Kim
- Center for Advanced Reactions Dynamics (CARD), Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sang Jin Lee
- Center for Advanced Reactions Dynamics (CARD), Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyotcherl Ihee
- Center for Advanced Reactions Dynamics (CARD), Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea.
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
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2
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Konold PE, Monrroy L, Bellisario A, Filipe D, Adams P, Alvarez R, Bean R, Bielecki J, Bódizs S, Ducrocq G, Grubmueller H, Kirian RA, Kloos M, Koliyadu JCP, Koua FHM, Larkiala T, Letrun R, Lindsten F, Maihöfer M, Martin AV, Mészáros P, Mutisya J, Nimmrich A, Okamoto K, Round A, Sato T, Valerio J, Westphal D, Wollter A, Yenupuri TV, You T, Maia F, Westenhoff S. Microsecond time-resolved X-ray scattering by utilizing MHz repetition rate at second-generation XFELs. Nat Methods 2024:10.1038/s41592-024-02344-0. [PMID: 38969722 DOI: 10.1038/s41592-024-02344-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 06/10/2024] [Indexed: 07/07/2024]
Abstract
Detecting microsecond structural perturbations in biomolecules has wide relevance in biology, chemistry and medicine. Here we show how MHz repetition rates at X-ray free-electron lasers can be used to produce microsecond time-series of protein scattering with exceptionally low noise levels of 0.001%. We demonstrate the approach by examining Jɑ helix unfolding of a light-oxygen-voltage photosensory domain. This time-resolved acquisition strategy is easy to implement and widely applicable for direct observation of structural dynamics of many biochemical processes.
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Affiliation(s)
- Patrick E Konold
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Leonardo Monrroy
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Alfredo Bellisario
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Diogo Filipe
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Patrick Adams
- School of Science, STEM College, RMIT University, Melbourne, Victoria, Australia
| | - Roberto Alvarez
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | | | | | - Szabolcs Bódizs
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Gabriel Ducrocq
- Department of Computer and Information Science (IDA), Linköping University, Linköping, Sweden
- The Division of Statistics and Machine Learning (STIMA), Linköping University, Linköping, Sweden
| | - Helmut Grubmueller
- Department of Computer and Information Science (IDA), Linköping University, Linköping, Sweden
| | | | - Marco Kloos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jayanath C P Koliyadu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Taru Larkiala
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Fredrik Lindsten
- Department of Computer and Information Science (IDA), Linköping University, Linköping, Sweden
- The Division of Statistics and Machine Learning (STIMA), Linköping University, Linköping, Sweden
| | - Michael Maihöfer
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Andrew V Martin
- School of Science, STEM College, RMIT University, Melbourne, Victoria, Australia
| | - Petra Mészáros
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jennifer Mutisya
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Kenta Okamoto
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | | | | | | | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - August Wollter
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Tej Varma Yenupuri
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Tong You
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Filipe Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
| | - Sebastian Westenhoff
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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3
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Lee Y, Oang KY, Kim D, Ihee H. A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:031301. [PMID: 38706888 PMCID: PMC11065455 DOI: 10.1063/4.0000249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
The structure of molecules, particularly the dynamic changes in structure, plays an essential role in understanding physical and chemical phenomena. Time-resolved (TR) scattering techniques serve as crucial experimental tools for studying structural dynamics, offering direct sensitivity to molecular structures through scattering signals. Over the past decade, the advent of x-ray free-electron lasers (XFELs) and mega-electron-volt ultrafast electron diffraction (MeV-UED) facilities has ushered TR scattering experiments into a new era, garnering significant attention. In this review, we delve into the basic principles of TR scattering experiments, especially focusing on those that employ x-rays and electrons. We highlight the variations in experimental conditions when employing x-rays vs electrons and discuss their complementarity. Additionally, cutting-edge XFELs and MeV-UED facilities for TR x-ray and electron scattering experiments and the experiments performed at those facilities are reviewed. As new facilities are constructed and existing ones undergo upgrades, the landscape for TR x-ray and electron scattering experiments is poised for further expansion. Through this review, we aim to facilitate the effective utilization of these emerging opportunities, assisting researchers in delving deeper into the intricate dynamics of molecular structures.
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Affiliation(s)
| | - Key Young Oang
- Radiation Center for Ultrafast Science, Korea Atomic Energy Research Institute (KAERI), Daejeon 34057, South Korea
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4
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Zha J, He J, Wu C, Zhang M, Liu X, Zhang J. Designing drugs and chemical probes with the dualsteric approach. Chem Soc Rev 2023; 52:8651-8677. [PMID: 37990599 DOI: 10.1039/d3cs00650f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Traditionally, drugs are monovalent, targeting only one site on the protein surface. This includes orthosteric and allosteric drugs, which bind the protein at orthosteric and allosteric sites, respectively. Orthosteric drugs are good in potency, whereas allosteric drugs have better selectivity and are solutions to classically undruggable targets. However, it would be difficult to simultaneously reach high potency and selectivity when targeting only one site. Also, both kinds of monovalent drugs suffer from mutation-caused drug resistance. To overcome these obstacles, dualsteric modulators have been proposed in the past twenty years. Compared to orthosteric or allosteric drugs, dualsteric modulators are bivalent (or bitopic) with two pharmacophores. Each of the two pharmacophores bind the protein at the orthosteric and an allosteric site, which could bring the modulator with special properties beyond monovalent drugs. In this study, we comprehensively review the current development of dualsteric modulators. Our main effort reason and illustrate the aims to apply the dualsteric approach, including a "double win" of potency and selectivity, overcoming mutation-caused drug resistance, developments of function-biased modulators, and design of partial agonists. Moreover, the strengths of the dualsteric technique also led to its application outside pharmacy, including the design of highly sensitive fluorescent tracers and usage as molecular rulers. Besides, we also introduced drug targets, designing strategies, and validation methods of dualsteric modulators. Finally, we detail the conclusions and perspectives.
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Affiliation(s)
- Jinyin Zha
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jixiao He
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chengwei Wu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingyang Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyi Liu
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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5
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Harder OF, Barrass SV, Drabbels M, Lorenz UJ. Fast viral dynamics revealed by microsecond time-resolved cryo-EM. Nat Commun 2023; 14:5649. [PMID: 37704664 PMCID: PMC10499870 DOI: 10.1038/s41467-023-41444-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/01/2023] [Indexed: 09/15/2023] Open
Abstract
Observing proteins as they perform their tasks has largely remained elusive, which has left our understanding of protein function fundamentally incomplete. To enable such observations, we have recently proposed a technique that improves the time resolution of cryo-electron microscopy (cryo-EM) to microseconds. Here, we demonstrate that microsecond time-resolved cryo-EM enables observations of fast protein dynamics. We use our approach to elucidate the mechanics of the capsid of cowpea chlorotic mottle virus (CCMV), whose large-amplitude motions play a crucial role in the viral life cycle. We observe that a pH jump causes the extended configuration of the capsid to contract on the microsecond timescale. While this is a concerted process, the motions of the capsid proteins involve different timescales, leading to a curved reaction path. It is difficult to conceive how such a detailed picture of the dynamics could have been obtained with any other method, which highlights the potential of our technique. Crucially, our experiments pave the way for microsecond time-resolved cryo-EM to be applied to a broad range of protein dynamics that previously could not have been observed. This promises to fundamentally advance our understanding of protein function.
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Affiliation(s)
- Oliver F Harder
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Molecular Nanodynamics, CH-1015, Lausanne, Switzerland
| | - Sarah V Barrass
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Molecular Nanodynamics, CH-1015, Lausanne, Switzerland
| | - Marcel Drabbels
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Molecular Nanodynamics, CH-1015, Lausanne, Switzerland
| | - Ulrich J Lorenz
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Molecular Nanodynamics, CH-1015, Lausanne, Switzerland.
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6
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Ki H, Gu J, Cha Y, Lee KW, Ihee H. Projection to extract the perpendicular component (PEPC) method for extracting kinetics from time-resolved data. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:034103. [PMID: 37388296 PMCID: PMC10306411 DOI: 10.1063/4.0000189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/22/2023] [Indexed: 07/01/2023]
Abstract
Time-resolved x-ray liquidography (TRXL) is a potent method for investigating the structural dynamics of chemical and biological reactions in the liquid phase. It has enabled the extraction of detailed structural aspects of various dynamic processes, the molecular structures of intermediates, and kinetics of reactions across a wide range of systems, from small molecules to proteins and nanoparticles. Proper data analysis is key to extracting the information of the kinetics and structural dynamics of the studied system encrypted in the TRXL data. In typical TRXL data, the signals from solute scattering, solvent scattering, and solute-solvent cross scattering are mixed in the q-space, and the solute kinetics and solvent hydrodynamics are mixed in the time domain, thus complicating the data analysis. Various methods developed so far generally require prior knowledge of the molecular structures of candidate species involved in the reaction. Because such information is often unavailable, a typical data analysis often involves tedious trial and error. To remedy this situation, we have developed a method named projection to extract the perpendicular component (PEPC), capable of removing the contribution of solvent kinetics from TRXL data. The resulting data then contain only the solute kinetics, and, thus, the solute kinetics can be easily determined. Once the solute kinetics is determined, the subsequent data analysis to extract the structural information can be performed with drastically improved convenience. The application of the PEPC method is demonstrated with TRXL data from the photochemistry of two molecular systems: [Au(CN)2-]3 in water and CHI3 in cyclohexane.
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Affiliation(s)
| | | | | | | | - H. Ihee
- Author to whom correspondence should be addressed:
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7
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Oang KY, Park S, Moon J, Park E, Lee HK, Sato T, Nozawa S, Adachi SI, Kim J, Kim J, Sohn JH, Ihee H. Extracting Kinetics and Thermodynamics of Molecules without Heavy Atoms via Time-Resolved Solvent Scattering Signals. J Phys Chem Lett 2023; 14:3103-3110. [PMID: 36951437 DOI: 10.1021/acs.jpclett.3c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Time-resolved X-ray liquidography (TRXL) has emerged as a powerful technique for studying the structural dynamics of small molecules and macromolecules in liquid solutions. However, TRXL has limited sensitivity for small molecules containing light atoms only, whose signal has lower contrast compared with the signal from solvent molecules. Here, we present an alternative approach to bypass this limitation by detecting the change in solvent temperature resulting from a photoinduced reaction. Specifically, we analyzed the heat dynamics of TRXL data obtained from p-hydroxyphenacyl diethyl phosphate (HPDP). This analysis enabled us to experimentally determine the number of intermediates and their respective enthalpy changes, which can be compared to theoretical enthalpies to identify the intermediates. This work demonstrates that TRXL can be used to uncover the kinetics and reaction pathways for small molecules without heavy atoms even if the scattering signal from the solute molecules is buried under the strong solvent scattering signal.
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Affiliation(s)
- Key Young Oang
- Radiation Center for Ultrafast Science, Korea Atomic Energy Research Institute (KAERI), Daejeon 34057, Republic of Korea
| | - Sungjun Park
- Department of Chemistry and KI for 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
| | - Jiwon Moon
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Eunji Park
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Hyun Kyung Lee
- Department of Chemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Tokushi Sato
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Shunsuke Nozawa
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Shin-Ichi Adachi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 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
| | - Joonghan Kim
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Jeong-Hun Sohn
- Department of Chemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for 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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8
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Wang R, Sang P, Guo Y, Jin P, Cheng Y, Yu H, Xie Y, Yao W, Qian H. Cadmium in food: Source, distribution and removal. Food Chem 2023; 405:134666. [DOI: 10.1016/j.foodchem.2022.134666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 10/10/2022] [Accepted: 10/15/2022] [Indexed: 12/07/2022]
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9
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Chiral control of spin-crossover dynamics in Fe(II) complexes. Nat Chem 2022; 14:739-745. [PMID: 35618767 DOI: 10.1038/s41557-022-00933-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/14/2022] [Indexed: 11/08/2022]
Abstract
Iron-based spin-crossover complexes hold tremendous promise as multifunctional switches in molecular devices. However, real-world technological applications require the excited high-spin state to be kinetically stable-a feature that has been achieved only at cryogenic temperatures. Here we demonstrate high-spin-state trapping by controlling the chiral configuration of the prototypical iron(II)tris(4,4'-dimethyl-2,2'-bipyridine) in solution, associated for stereocontrol with the enantiopure Δ- or Λ-enantiomer of tris(3,4,5,6-tetrachlorobenzene-1,2-diolato-κ2O1,O2)phosphorus(V) (P(O2C6Cl4)3- or TRISPHAT) anions. We characterize the high-spin-state relaxation using broadband ultrafast circular dichroism spectroscopy in the deep ultraviolet in combination with transient absorption and anisotropy measurements. We find that the high-spin-state decay is accompanied by ultrafast changes of its optical activity, reflecting the coupling to a symmetry-breaking torsional twisting mode, contrary to the commonly assumed picture. The diastereoselective ion pairing suppresses the vibrational population of the identified reaction coordinate, thereby achieving a fourfold increase of the high-spin-state lifetime. More generally, our results motivate the synthetic control of the torsional modes of iron(II) complexes as a complementary route to manipulate their spin-crossover dynamics.
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10
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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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11
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Control of the Longitudinal Compression and Transverse Focus of Ultrafast Electron Beam for Detecting the Transient Evolution of Materials. MATERIALS 2022; 15:ma15020571. [PMID: 35057289 PMCID: PMC8781741 DOI: 10.3390/ma15020571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 02/05/2023]
Abstract
Ultrafast detection is an effective method to reveal the transient evolution mechanism of materials. Compared with ultra-fast X-ray diffraction (XRD), the ultra-fast electron beam is increasingly adopted because the larger scattering cross-section is less harmful to the sample. The keV single-shot ultra-fast electron imaging system has been widely used with its compact structure and easy integration. To achieve both the single pulse imaging and the ultra-high temporal resolution, magnetic lenses are typically used for transverse focus to increase signal strength, while radio frequency (RF) cavities are generally utilized for longitudinal compression to improve temporal resolution. However, the detection signal is relatively weak due to the Coulomb force between electrons. Moreover, the effect of RF compression on the transverse focus is usually ignored. We established a particle tracking model to simulate the electron pulse propagation based on the 1-D fluid equation and the 2-D mean-field equation. Under considering the relativity effect and Coulomb force, the impact of RF compression on the transverse focus was studied by solving the fifth-order Rung–Kutta equation. The results show that the RF cavity is not only a key component of longitudinal compression but also affects the transverse focusing. While the effect of transverse focus on longitudinal duration is negligible. By adjusting the position and compression strength of the RF cavity, the beam spot radius can be reduced from 100 μm to 30 μm under the simulation conditions in this paper. When the number of single pulse electrons remains constant, the electrons density incident on the sample could be increased from 3.18×1012 m−2 to 3.54×1013 m−2, which is 11 times the original. The larger the electron density incident on the sample, the greater the signal intensity, which is more conducive to detecting the transient evolution of the material.
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12
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Ki H, Choi S, Kim J, Choi EH, Lee S, Lee Y, Yoon K, Ahn CW, Ahn DS, Lee JH, Park J, Eom I, Kim M, Chun SH, Kim J, Ihee H, Kim J. Optical Kerr Effect of Liquid Acetonitrile Probed by Femtosecond Time-Resolved X-ray Liquidography. J Am Chem Soc 2021; 143:14261-14273. [PMID: 34455778 DOI: 10.1021/jacs.1c06088] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Optical Kerr effect (OKE) spectroscopy is a method that measures the time-dependent change of the birefringence induced by an optical laser pulse using another optical laser pulse and has been used often to study the ultrafast dynamics of molecular liquids. Here we demonstrate an alternative method, femtosecond time-resolved X-ray liquidography (fs-TRXL), where the microscopic structural motions related to the OKE response can be monitored using a different type of probe, i.e., X-ray solution scattering. By applying fs-TRXL to acetonitrile and a dye solution in acetonitrile, we demonstrate that different types of molecular motions around photoaligned molecules can be resolved selectively, even without any theoretical modeling, based on the anisotropy of two-dimensional scattering patterns and extra structural information contained in the q-space scattering data. Specifically, the dynamics of reorientational (libration and orientational diffusion) and translational (interaction-induced motion) motions are captured separately by anisotropic and isotropic scattering signals, respectively. Furthermore, the two different types of reorientational motions are distinguished from each other by their own characteristic scattering patterns and time scales. The measured time-resolved scattering signals are in excellent agreement with the simulated scattering signals based on a molecular dynamics simulation for plausible molecular configurations, providing the detailed structural description of the OKE response in liquid acetonitrile.
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Affiliation(s)
- Hosung Ki
- 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
| | - Seungjoo Choi
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Jungmin 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
| | - Eun Hyuk Choi
- 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
| | - Seonggon 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
| | - Yunbeom 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
| | - Kihwan Yoon
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Chi Woo Ahn
- 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
| | - Doo-Sik Ahn
- 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
| | - Jae Hyuk Lee
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Jaeku Park
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Intae Eom
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Minseok Kim
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Sae Hwan Chun
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Joonghan Kim
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, 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
| | - Jeongho Kim
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
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13
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Suzuki T. Spiers Memorial Lecture: Introduction to ultrafast spectroscopy and imaging of photochemical reactions. Faraday Discuss 2021; 228:11-38. [PMID: 33876168 DOI: 10.1039/d1fd00015b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A brief overview is presented on ultrafast spectroscopy and imaging of photochemical reactions by highlighting several experimental studies reported in the last five years. A particular focus is placed on new experiments performed using high-order harmonic generation, X-ray free electron lasers, and relativistic electron beams. Exploration of fundamental chemical reaction dynamics using these advanced experimental methodologies is in an early stage, and exciting new research opportunities await in this rapidly expanding and advancing research field. At the same time, there is no experimental methodology that provides all aspects of the electronic and structural dynamics in a single experiment, and investigations using different methodologies with various perspectives need to be considered in a comprehensive manner.
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Affiliation(s)
- Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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14
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Hada M, Nishina Y, Kato T. Exploring Structures and Dynamics of Molecular Assemblies: Ultrafast Time-Resolved Electron Diffraction Measurements. Acc Chem Res 2021; 54:731-743. [PMID: 33319986 DOI: 10.1021/acs.accounts.0c00576] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ConspectusMolecular assemblies have been widely applied to functional soft materials in a variety of fields. Liquid crystal is one of the representative molecular soft materials in which weak intermolecular interactions induce its dynamic molecular behavior under external stimuli, such as electric and magnetic fields, photoirradiation, and thermal treatment. It is important to understand molecular behavior and motion in the liquid-crystalline (LC) states at the picosecond level for further functionalization of liquid crystals and molecular assembled materials. For investigation of assembled structures of the materials on the nanometer scale, X-ray diffraction (XRD) measurements have been a powerful tool. Despite the dynamic nature of the assembled materials, however, time resolution of XRD is limited to millisecond due to the response speed of the detector, which hampered real-time observation of the dynamics of the molecular assembly. For further understanding of the dynamic behavior of functional molecules and improvement of performance for their applications, the insights of faster dynamics on the micro-, nano-, pico-, and even femtosecond time scales are required. In this context, the interdisciplinary approaches of the emerging fields of materials chemistry and ultrafast science will open up new aspects of molecular science and technology. These approaches may lead to more effective design of new functional materials, which enables us to control molecular behaviors and motions.The development of ultrashort pulsed X-ray and electron sources has resulted in the visualization of the key structural dynamics on the femto- to picosecond time scale not only in isolated molecules but also in assembled molecules, such as in the LC, crystal, and amorphous phases. We focus on ultrafast phenomena in molecular assemblies induced by photoexcitation. Ultrafast time-resolved electron diffraction measurements are sensitive to the molecular periodicity under photoexcitation, and thus the methodologies directly provide the ultrafast photoinduced molecular dynamic arrangements.In this Account, we describe ultrafast structural dynamics of molecules in the LC phases observed by time-resolved electron diffraction measurements. Photoinduced conformational changes of LC molecules is shown as the example, which is the first observation of LC molecule using time-resolved electron diffraction. It is important to understand the correlation between the conformational or configurational changes induced in a photoirradiated single molecule and the oriented collective motions of molecular assemblies induced by intermolecular interaction. We also show observation of collective motions of azobenzene LC molecules. The collective motions are initiated from photoreaction in a single molecule and are subsequently amplified by the steric interaction with its neighboring molecules.One remaining challenge is to create the platform of materials and sample preparations for time-resolved electron diffraction experiments, which can only be achieved by the interdisciplinary fusion of the fields of materials chemistry and ultrafast science. Time-resolved electron diffraction is a powerful tool for structural investigation of molecular materials with a dynamic nature, whose adaptability goes beyond that of more complex assemblies of carbon nanomaterials. This methodology will extend the possibility to investigate motions of a variety of molecular self-assemblies on a larger scale, for example, to understand responses of biomolecular assemblies and intermolecular chemical reactions.
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Affiliation(s)
- Masaki Hada
- Tsukuba Research Center for Energy Materials Science (TREMS), Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8573, Japan
| | - Yuta Nishina
- Graduate School of Natural Science and Technology, Research Core for Interdisciplinary Sciences, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan
| | - Takashi Kato
- Department of Chemistry & Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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15
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Romei MG, Lin CY, Boxer SG. Structural and spectroscopic characterization of photoactive yellow protein and photoswitchable fluorescent protein constructs containing heavy atoms. J Photochem Photobiol A Chem 2020; 401. [PMID: 32753830 PMCID: PMC7402594 DOI: 10.1016/j.jphotochem.2020.112738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Photo-induced structural rearrangements of chromophore-containing proteins are essential for various light-dependent signaling pathways and optogenetic applications. Ultrafast structural and spectroscopic methods have offered insights into these structural rearrangements across many timescales. However, questions still remain about exact mechanistic details, especially regarding photoisomerization of the chromophore within these proteins femtoseconds to picoseconds after photoexcitation. Instrumentation advancements for time-resolved crystallography and ultrafast electron diffraction provide a promising opportunity to study these reactions, but achieving enough signal-to-noise is a constant challenge. Here we present four new photoactive yellow protein constructs and one new fluorescent protein construct that contain heavy atoms either within or around the chromophore and can be expressed with high yields. Structural characterization of these constructs, most at atomic resolution, show minimal perturbation caused by the heavy atoms compared to wild-type structures. Spectroscopic studies report the effects of the heavy atom identity and location on the chromophore's photophysical properties. None of the substitutions prevent photoisomerization, although certain rates within the photocycle may be affected. Overall, these new proteins containing heavy atoms are ideal samples for state-of-theart time-resolved crystallography and electron diffraction experiments to elucidate crucial mechanistic information of photoisomerization.
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Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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16
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Gold Nanoparticle Formation via X-ray Radiolysis Investigated with Time-Resolved X-ray Liquidography. Int J Mol Sci 2020; 21:ijms21197125. [PMID: 32992497 PMCID: PMC7582564 DOI: 10.3390/ijms21197125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 11/17/2022] Open
Abstract
We report the generation of gold nanoparticles (AuNPs) from the aqueous solution of chloro(2,2',2″-terpyridine)gold(III) ion ([Au(tpy)Cl]2+) through X-ray radiolysis and optical excitation at a synchrotron. The original purpose of the experiment was to investigate the photoinduced structural changes of [Au(tpy)Cl]2+ upon 400 nm excitation using time-resolved X-ray liquidography (TRXL). Initially, the TRXL data did not show any signal that would suggest structural changes of the solute molecule, but after an induction time, the TRXL data started to show sharp peaks and valleys. In the early phase, AuNPs with two types of morphology, dendrites, and spheres, were formed by the reducing action of hydrated electrons generated by the X-ray radiolysis of water, thereby allowing the detection of TRXL data due to the laser-induced lattice expansion and relaxation of AuNPs. Along with the lattice expansion, the dendritic and spherical AuNPs were transformed into smaller, raspberry-shaped AuNPs of a relatively uniform size via ablation by the optical femtosecond laser pulse used for the TRXL experiment. Density functional theory calculations confirm that the reduction potential of the metal complex relative to the hydration potential of X-ray-generated electrons determines the facile AuNP formation observed for [Au(tpy)Cl]2+.
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17
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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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18
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Zhang J, Bradford SD, Kong W, Zhang C, Xue L. Electron diffraction of CS 2 nanoclusters embedded in superfluid helium droplets. J Chem Phys 2020; 152:224306. [PMID: 32534524 PMCID: PMC7292678 DOI: 10.1063/5.0011340] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/25/2020] [Indexed: 11/14/2022] Open
Abstract
We report experimental results from electron diffraction of CS2 nanoclusters embedded in superfluid helium droplets. From detailed measurements of the sizes of doped droplets, we can model the doping statistics under different experimental conditions, thereby obtaining the range of cluster sizes of CS2. Using a least squares fitting procedure, we can then determine the structures and contributions of dimers, trimers, and tetramers embedded in small droplets. While dimers prefer a stable gas phase structure, trimers and tetramers seem to forgo the highly symmetric gas phase structures and prefer compact cuts from the crystalline structure of CS2. In larger droplets containing more than 12 CS2 monomers, the diffraction profile is consistent with a three-dimensional nanostructure of bulk CS2. This work demonstrates the feasibility of electron diffraction for in situ monitoring of nanocluster formation in superfluid helium droplets.
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Affiliation(s)
- Jie Zhang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Stephen D. Bradford
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Wei Kong
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Chengzhu Zhang
- Department of Statistics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Lan Xue
- Department of Statistics, Oregon State University, Corvallis, Oregon 97331, USA
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19
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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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20
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Smolentsev G, Milne CJ, Guda A, Haldrup K, Szlachetko J, Azzaroli N, Cirelli C, Knopp G, Bohinc R, Menzi S, Pamfilidis G, Gashi D, Beck M, Mozzanica A, James D, Bacellar C, Mancini GF, Tereshchenko A, Shapovalov V, Kwiatek WM, Czapla-Masztafiak J, Cannizzo A, Gazzetto M, Sander M, Levantino M, Kabanova V, Rychagova E, Ketkov S, Olaru M, Beckmann J, Vogt M. Taking a snapshot of the triplet excited state of an OLED organometallic luminophore using X-rays. Nat Commun 2020; 11:2131. [PMID: 32358505 PMCID: PMC7195477 DOI: 10.1038/s41467-020-15998-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/07/2020] [Indexed: 12/21/2022] Open
Abstract
OLED technology beyond small or expensive devices requires light-emitters, luminophores, based on earth-abundant elements. Understanding and experimental verification of charge transfer in luminophores are needed for this development. An organometallic multicore Cu complex comprising Cu–C and Cu–P bonds represents an underexplored type of luminophore. To investigate the charge transfer and structural rearrangements in this material, we apply complementary pump-probe X-ray techniques: absorption, emission, and scattering including pump-probe measurements at the X-ray free-electron laser SwissFEL. We find that the excitation leads to charge movement from C- and P- coordinated Cu sites and from the phosphorus atoms to phenyl rings; the Cu core slightly rearranges with 0.05 Å increase of the shortest Cu–Cu distance. The use of a Cu cluster bonded to the ligands through C and P atoms is an efficient way to keep structural rigidity of luminophores. Obtained data can be used to verify computational methods for the development of luminophores. OLED materials based on thermally activated delayed fluorescence have promising efficiency. Here, the authors investigate an organometallic multicore Cu complex as luminophore, by pump-probe X-ray techniques at three different facilities deriving a complete picture of the charge transfer in the triplet excited state.
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Affiliation(s)
| | | | - Alexander Guda
- The Smart Materials Research Institute, Southern Federal University, 344090, Rostov-on-Don, Russia
| | - Kristoffer Haldrup
- Physics Department, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Jakub Szlachetko
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342, Kraków, Poland
| | | | | | - Gregor Knopp
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Rok Bohinc
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Samuel Menzi
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | | | - Dardan Gashi
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Martin Beck
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | | | - Daniel James
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Camila Bacellar
- Paul Scherrer Institute, 5232, Villigen, Switzerland.,Laboratory for Ultrafast Spectroscopy, Lausanne Center for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Giulia F Mancini
- Paul Scherrer Institute, 5232, Villigen, Switzerland.,Laboratory for Ultrafast Spectroscopy, Lausanne Center for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Andrei Tereshchenko
- The Smart Materials Research Institute, Southern Federal University, 344090, Rostov-on-Don, Russia
| | - Victor Shapovalov
- The Smart Materials Research Institute, Southern Federal University, 344090, Rostov-on-Don, Russia
| | - Wojciech M Kwiatek
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342, Kraków, Poland
| | | | - Andrea Cannizzo
- Institute of Applied Physics, University of Bern, 3012, Bern, Switzerland
| | - Michela Gazzetto
- Institute of Applied Physics, University of Bern, 3012, Bern, Switzerland
| | - Mathias Sander
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Matteo Levantino
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Victoria Kabanova
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Elena Rychagova
- G. A. Razuvaev Institute of Organometallic Chemistry, Russian Academy of Sciences, Tropinina, 49, Nizhny Novgorod, 603950, Russia
| | - Sergey Ketkov
- G. A. Razuvaev Institute of Organometallic Chemistry, Russian Academy of Sciences, Tropinina, 49, Nizhny Novgorod, 603950, Russia
| | - Marian Olaru
- Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobenerstr. 7, 28359, Bremen, Germany
| | - Jens Beckmann
- Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobenerstr. 7, 28359, Bremen, Germany
| | - Matthias Vogt
- Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobenerstr. 7, 28359, Bremen, Germany. .,Martin-Luther-Universität Halle-Wittenberg Naturwissenschaftliche Fakultät II, Institut für Chemie, Anorganische Chemie, D-06120, Halle, Germany.
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21
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Miller NA, Michocki LB, Konar A, Alonso-Mori R, Deb A, Glownia JM, Sofferman DL, Song S, Kozlowski PM, Kubarych KJ, Penner-Hahn JE, Sension RJ. Ultrafast XANES Monitors Femtosecond Sequential Structural Evolution in Photoexcited Coenzyme B 12. J Phys Chem B 2020; 124:199-209. [PMID: 31850761 DOI: 10.1021/acs.jpcb.9b09286] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Polarized X-ray absorption near-edge structure (XANES) at the Co K-edge and broadband UV-vis transient absorption are used to monitor the sequential evolution of the excited-state structure of coenzyme B12 (adenosylcobalamin) over the first picosecond following excitation. The initial state is characterized by sub-100 fs sequential changes around the central cobalt. These are polarized first in the y-direction orthogonal to the transition dipole and 50 fs later in the x-direction along the transition dipole. Expansion of the axial bonds follows on a ca. 200 fs time scale as the molecule moves out of the Franck-Condon active region of the potential energy surface. On the same 200 fs time scale there are electronic changes that result in the loss of stimulated emission and the appearance of a strong absorption at 340 nm. These measurements provide a cobalt-centered movie of the excited molecule as it evolves to the local excited-state minimum.
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Affiliation(s)
- Nicholas A Miller
- Department of Chemistry , University of Michigan , 930 N. University Ave. , Ann Arbor , Michigan 48109-1055 , United States
| | - Lindsay B Michocki
- Department of Chemistry , University of Michigan , 930 N. University Ave. , Ann Arbor , Michigan 48109-1055 , United States
| | - Arkaprabha Konar
- Department of Physics , University of Michigan , 450 Church Street , Ann Arbor , Michigan 48109-1040 , United States
| | - Roberto Alonso-Mori
- Linac Coherent Light Source , SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Aniruddha Deb
- Department of Chemistry , University of Michigan , 930 N. University Ave. , Ann Arbor , Michigan 48109-1055 , United States.,Department of Biophysics , University of Michigan , 930 N. University Ave. , Ann Arbor , Michigan 48109-1055 , United States
| | - James M Glownia
- Linac Coherent Light Source , SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Danielle L Sofferman
- Program in Applied Physics , University of Michigan , 450 Church Street , Ann Arbor , Michigan 48109-1040 , United States
| | - Sanghoon Song
- Linac Coherent Light Source , SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Pawel M Kozlowski
- Department of Chemistry , University of Louisville , 2320 South Brook Street , Louisville , Kentucky 40292 , United States
| | - Kevin J Kubarych
- Department of Chemistry , University of Michigan , 930 N. University Ave. , Ann Arbor , Michigan 48109-1055 , United States.,Department of Biophysics , University of Michigan , 930 N. University Ave. , Ann Arbor , Michigan 48109-1055 , United States
| | - James E Penner-Hahn
- Department of Chemistry , University of Michigan , 930 N. University Ave. , Ann Arbor , Michigan 48109-1055 , United States.,Department of Biophysics , University of Michigan , 930 N. University Ave. , Ann Arbor , Michigan 48109-1055 , United States
| | - Roseanne J Sension
- Department of Chemistry , University of Michigan , 930 N. University Ave. , Ann Arbor , Michigan 48109-1055 , United States.,Department of Physics , University of Michigan , 450 Church Street , Ann Arbor , Michigan 48109-1040 , United States.,Department of Biophysics , University of Michigan , 930 N. University Ave. , Ann Arbor , Michigan 48109-1055 , United States
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22
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Abstract
A review that summarizes the most recent technological developments in the field of ultrafast structural dynamics with focus on the use of ultrashort X-ray and electron pulses follows. Atomistic views of chemical processes and phase transformations have long been the exclusive domain of computer simulators. The advent of femtosecond (fs) hard X-ray and fs-electron diffraction techniques made it possible to bring such a level of scrutiny to the experimental area. The following review article provides a summary of the main ultrafast techniques that enabled the generation of atomically resolved movies utilizing ultrashort X-ray and electron pulses. Recent advances are discussed with emphasis on synchrotron-based methods, tabletop fs-X-ray plasma sources, ultrabright fs-electron diffractometers, and timing techniques developed to further improve the temporal resolution and fully exploit the use of intense and ultrashort X-ray free electron laser (XFEL) pulses.
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23
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Choi EH, Ahn DS, Park S, Kim C, Ahn CW, Kim S, Choi M, Yang C, Kim TW, Ki H, Choi J, Pedersen MN, Wulff M, Kim J, Ihee H. Structural Dynamics of Bismuth Triiodide in Solution Triggered by Photoinduced Ligand-to-Metal Charge Transfer. J Phys Chem Lett 2019; 10:1279-1285. [PMID: 30835478 DOI: 10.1021/acs.jpclett.9b00365] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bismuth triiodide, BiI3, is one of the simplest bismuth halides, which have recently attracted considerable attention because of their promising properties. Here, we investigate the structural dynamics of a photoinduced reaction of BiI3 in solution phase using time-resolved X-ray liquidography (TRXL) and density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. The photoreaction was initiated by excitation at 400 nm, which corresponds to the ligand-to-metal charge-transfer transition. The detailed structures and kinetic profiles of all relevant intermediate species from the TRXL data show that the trigonal planar structure of BiI3, which is predicted to be the most stable structure of the lowest excited state by TDDFT calculation, was not observed, and the photoreaction proceeds via two parallel pathways within the time resolution of 100 ps: (i) isomer formation to produce iso-BiI2-I, which relaxes back to the ground-state structure, and (ii) dissociation into BiI2· and I· radicals, which nongeminately recombine to generate ground-state BiI3 and I2.
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Affiliation(s)
- Eun Hyuk Choi
- 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
| | - Doo-Sik Ahn
- 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
| | - Sungjun Park
- 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
| | - Changwon 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
| | - Chi Woo Ahn
- 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
| | - Siin 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
| | - Minseo Choi
- 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
- Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
| | - Tae Wu Kim
- Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
| | - Hosung Ki
- Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
| | - Jungkweon Choi
- 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
| | | | - Michael Wulff
- European Synchrotron Radiation Facility (ESRF) , 38000 Grenoble Cedex 9, France
| | - Jeongho Kim
- Department of Chemistry , Inha University , 100 Inha-ro, Nam-gu , Incheon 22212 , 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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24
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Ki H, Lee Y, Choi EH, Lee S, Ihee H. SVD-aided non-orthogonal decomposition (SANOD) method to exploit prior knowledge of spectral components in the analysis of time-resolved data. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:024303. [PMID: 30931347 PMCID: PMC6435371 DOI: 10.1063/1.5085864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
Analysis of time-resolved data typically involves discriminating noise against the signal and extracting time-independent components and their time-dependent contributions. Singular value decomposition (SVD) serves this purpose well, but the extracted time-independent components are not necessarily the physically meaningful spectra directly representing the actual dynamic or kinetic processes but rather a mathematically orthogonal set necessary for constituting the physically meaningful spectra. Converting the orthogonal components into physically meaningful spectra requires subsequent posterior analyses such as linear combination fitting (LCF) and global fitting (GF), which takes advantage of prior knowledge about the data but requires that all components are known or satisfactory components are guessed. Since in general not all components are known, they have to be guessed and tested via trial and error. In this work, we introduce a method, which is termed SVD-aided Non-Orthogonal Decomposition (SANOD), to circumvent trial and error. The key concept of SANOD is to combine the orthogonal components from SVD with the known prior knowledge to fill in the gap of the unknown signal components and to use them for LCF. We demonstrate the usefulness of SANOD via applications to a variety of cases.
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Affiliation(s)
- H. Ki
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, South Korea
| | | | | | | | - H. Ihee
- Author to whom correspondence should be addressed:
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25
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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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26
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Multiscale wavelet decomposition of time-resolved X-ray diffraction signals in cyclohexadiene. Proc Natl Acad Sci U S A 2018; 115:10269-10274. [PMID: 30254170 DOI: 10.1073/pnas.1811983115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We demonstrate how the wavelet transform, which is a powerful tool for compression, filtering, and scaling analysis of signals, may be used to separate large- and short-scale electron density features in X-ray diffraction patterns. Wavelets can isolate the electron density associated with delocalized bonds from the much stronger background of highly localized core electrons. The wavelet-processed signals clearly reveal the bond formation and breaking in the early steps of the photoinduced pericyclic ring opening reaction of 1,3-cyclohexadiene, which are not resolved in the bare signal.
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27
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Zhang W, Walton T, Li L, Szostak JW. Crystallographic observation of nonenzymatic RNA primer extension. eLife 2018; 7:36422. [PMID: 29851379 PMCID: PMC5980232 DOI: 10.7554/elife.36422] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/26/2018] [Indexed: 12/31/2022] Open
Abstract
The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5′-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process. Enzymes speed up chemical reactions that are essential to life. Most enzymes are proteins, but some are molecules of ribonucleic acid or RNA. Like DNA, RNA is made from a chain of building blocks called nucleotides. In modern organisms, protein-based enzymes build RNAs by linking nucleotides together, while the building blocks of proteins are linked by an RNA-based enzyme at the heart of a structure called a ribosome. The earliest life on Earth most likely relied only on RNA-based enzymes, but during the emergence of life, scientists believe that RNA molecules must have replicated spontaneously before dedicated RNA-based enzymes had evolved. How RNA could replicate without enzymes has been a puzzle for decades. Recently, scientists discovered a previously unsuspected chemical intermediate that forms during the process, and hypothesized that this molecule’s special structure is what enables the chemical reaction that adds new nucleotides to a growing strand of RNA. To test this hypothesis, Zhang et al. diffused free RNA nucleotides into a crystalized complex containing template strands of RNA attached to short pieces of RNA called primers, which kick-start replication. Then, the crystals were frozen at various intervals and viewed using X-rays. This allowed Zhang et al. to observe the structural changes that occurred over time as the compounds reacted. The approach first revealed that the free nucleotides had paired with complementary nucleotides on the RNA template strands. Then, pairs of free nucleotides reacted with each other to form the intermediate. Finally, the intermediate reacted with the primer, forming a new bond that connects the RNA primer to one of the nucleotides of the intermediate, while the other nucleotide of the intermediate was released as a free nucleotide. This experiment confirms that the specific structure of the intermediate molecule promotes RNA replication without help from enzymes. These findings will benefit chemists and biologists who study how RNA evolves and replicates. Future research building upon this work will deepen scientific understanding of the environmental conditions that were required for life to appear on Earth.
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Affiliation(s)
- Wen Zhang
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
| | - Travis Walton
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
| | - Li Li
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
| | - Jack W Szostak
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
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28
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Capturing dynamic conformational shifts in protein–ligand recognition using integrative structural biology in solution. Emerg Top Life Sci 2018; 2:107-119. [DOI: 10.1042/etls20170090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 03/18/2018] [Accepted: 03/20/2018] [Indexed: 11/17/2022]
Abstract
In recent years, a dynamic view of the structure and function of biological macromolecules is emerging, highlighting an essential role of dynamic conformational equilibria to understand molecular mechanisms of biological functions. The structure of a biomolecule, i.e. protein or nucleic acid in solution, is often best described as a dynamic ensemble of conformations, rather than a single structural state. Strikingly, the molecular interactions and functions of the biological macromolecule can then involve a shift between conformations that pre-exist in such an ensemble. Upon external cues, such population shifts of pre-existing conformations allow gradually relaying the signal to the downstream biological events. An inherent feature of this principle is conformational dynamics, where intrinsically disordered regions often play important roles to modulate the conformational ensemble. Unequivocally, solution-state NMR spectroscopy is a powerful technique to study the structure and dynamics of such biomolecules in solution. NMR is increasingly combined with complementary techniques, including fluorescence spectroscopy and small angle scattering. The combination of these techniques provides complementary information about the conformation and dynamics in solution and thus affords a comprehensive description of biomolecular functions and regulations. Here, we illustrate how an integrated approach combining complementary techniques can assess the structure and dynamics of proteins and protein complexes in solution.
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29
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Plech A, Ibrahimkutty S, Reich S, Newby G. Thermal dynamics of pulsed-laser excited gold nanorods in suspension. NANOSCALE 2017; 9:17284-17292. [PMID: 29090293 DOI: 10.1039/c7nr06125k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Photothermal reactions of metallic nanostructures, such as gold nanorods show appealing structural relaxations, such as bubble formation or particle modification. We have employed a pump-probe method to record the structural relaxations of a suspension of gold nanorods upon femtosecond laser excitation by pulsed X-ray scattering both with wide-angle and small-angle sensitivity. Single-pulse reactions include transient bubble formation at 20 J m-2 and irreversible nanorod reshaping at 30 J m-2. Thus the window for reversible excitation is very narrow. Additionally we could map the time-domain and fluence behaviour in a wide range to characterize the relaxations comprehensively. The polarized laser pulse first selectively excites nanorods aligned with the laser electric field, but at higher fluence non-aligned rods are also transformed. At low fluence this transformation happens in the solid state, while at higher fluence the rods melt.
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Affiliation(s)
- Anton Plech
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany.
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