1
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Gao X, Ishikawa H, Mizuno M, Mizutani Y. Cooperative Protein Dynamics of Heterotetrameric Hemoglobin from Scapharca inaequivalvis. J Phys Chem B 2024; 128:7558-7567. [PMID: 39072557 DOI: 10.1021/acs.jpcb.4c03917] [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: 07/30/2024]
Abstract
Hemoglobins achieve cooperative oxygen binding by diverse strategies based on different assemblies of globin subunits. Heterotetrameric hemoglobin from Scapharca inaequivalvis (HbII) consists of two AB-dimers, whose structure closely resembles that of homodimeric hemoglobin from the same organism (HbI). Herein, we investigated the structural dynamics of HbII following carbon monoxide (CO) dissociation using time-resolved resonance Raman (RR) spectroscopy. The observed spectra showed that the heme structure of the transient dissociated form of HbII was similar to that of HbI; however, the transition from the transient dissociated form to the equilibrium unligated form was faster for HbII than for HbI. Furthermore, the dependence of the time-resolved spectra on the yield of CO dissociation revealed that the transition became faster as the number of dissociated ligands increased from one to four. The positive correlation between the rate constants and number of dissociated ligands indicates that the structural transition of HbII following CO dissociation is cooperative.
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Affiliation(s)
- Xiang Gao
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Haruto Ishikawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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2
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Khusainov G, Standfuss J, Weinert T. The time revolution in macromolecular crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:020901. [PMID: 38616866 PMCID: PMC11015943 DOI: 10.1063/4.0000247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Macromolecular crystallography has historically provided the atomic structures of proteins fundamental to cellular functions. However, the advent of cryo-electron microscopy for structure determination of large and increasingly smaller and flexible proteins signaled a paradigm shift in structural biology. The extensive structural and sequence data from crystallography and advanced sequencing techniques have been pivotal for training computational models for accurate structure prediction, unveiling the general fold of most proteins. Here, we present a perspective on the rise of time-resolved crystallography as the new frontier of macromolecular structure determination. We trace the evolution from the pioneering time-resolved crystallography methods to modern serial crystallography, highlighting the synergy between rapid detection technologies and state-of-the-art x-ray sources. These innovations are redefining our exploration of protein dynamics, with high-resolution crystallography uniquely positioned to elucidate rapid dynamic processes at ambient temperatures, thus deepening our understanding of protein functionality. We propose that the integration of dynamic structural data with machine learning advancements will unlock predictive capabilities for protein kinetics, revolutionizing dynamics like macromolecular crystallography revolutionized structural biology.
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Affiliation(s)
- Georgii Khusainov
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
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3
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Broz M, Jukič M, Bren U. Naive Prediction of Protein Backbone Phi and Psi Dihedral Angles Using Deep Learning. Molecules 2023; 28:7046. [PMID: 37894526 PMCID: PMC10609058 DOI: 10.3390/molecules28207046] [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: 09/01/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Protein structure prediction represents a significant challenge in the field of bioinformatics, with the prediction of protein structures using backbone dihedral angles recently achieving significant progress due to the rise of deep neural network research. However, there is a trend in protein structure prediction research to employ increasingly complex neural networks and contributions from multiple models. This study, on the other hand, explores how a single model transparently behaves using sequence data only and what can be expected from the predicted angles. To this end, the current paper presents data acquisition, deep learning model definition, and training toward the final protein backbone angle prediction. The method applies a simple fully connected neural network (FCNN) model that takes only the primary structure of the protein with a sliding window of size 21 as input to predict protein backbone ϕ and ψ dihedral angles. Despite its simplicity, the model shows surprising accuracy for the ϕ angle prediction and somewhat lower accuracy for the ψ angle prediction. Moreover, this study demonstrates that protein secondary structure prediction is also possible with simple neural networks that take in only the protein amino-acid residue sequence, but more complex models are required for higher accuracies.
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Affiliation(s)
- Matic Broz
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
| | - Marko Jukič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, SI-6000 Koper, Slovenia
- Institute of Environmental Protection and Sensors, Beloruska ulica 7, SI-2000 Maribor, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, SI-6000 Koper, Slovenia
- Institute of Environmental Protection and Sensors, Beloruska ulica 7, SI-2000 Maribor, Slovenia
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4
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Guan F, Li T, Dong W, Guo R, Chai H, Chen Z, Ren Z, Li Y, Ye S. Novel insights into the allosteric gating mechanism of MthK channel. Natl Sci Rev 2022; 9:nwac072. [PMID: 36072506 PMCID: PMC9440719 DOI: 10.1093/nsr/nwac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 02/28/2022] [Accepted: 03/29/2022] [Indexed: 11/29/2022] Open
Abstract
Allostery is a fundamental element during channel gating in response to an appropriate stimulus by which events occurring at one site are transmitted to distal sites to regulate activity. To address how binding of the first Ca2+ ion at one of the eight chemically identical subunits facilitates the other Ca2+-binding events in MthK, a Ca2+-gated K+ channel containing a conserved ligand-binding RCK domain, we analysed a large collection of MthK structures and performed the corresponding thermodynamic and electrophysiological measurements. These structural and functional studies led us to conclude that the conformations of the Ca2+-binding sites alternate between two quaternary states and exhibit significant differences in Ca2+ affinity. We further propose an allosteric model of the MthK-gating mechanism by which a cascade of structural events connect the initial Ca2+-binding to the final changes of the ring structure that open the ion-conduction pore. This mechanical model reveals the exquisite design that achieves the allosteric gating and could be of general relevance for the action of other ligand-gated ion channels containing the RCK domain.
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Affiliation(s)
- Fenghui Guan
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin300072, China
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Tianyu Li
- State Key Laboratory of Drug Research and Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing100049, China
| | - Wei Dong
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058Zhejiang, China
| | - Rui Guo
- Department of Logistics, Tianjin University, 92 Weijin Road, Nankai District, Tianjin300072, China
| | - Hao Chai
- State Key Laboratory of Drug Research and Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing100049, China
| | - Zhiqiu Chen
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing100049, China
| | - Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL60607, USA
- Renz Research Inc., Westmont, IL60559, USA
| | - Yang Li
- State Key Laboratory of Drug Research and Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing100049, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, China
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin300072, China
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058Zhejiang, China
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5
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Lee Y, Kim JG, Lee SJ, Muniyappan S, Kim TW, Ki H, Kim H, Jo J, Yun SR, Lee H, Lee KW, Kim SO, Cammarata M, Ihee H. Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering. Nat Commun 2021; 12:3677. [PMID: 34135339 PMCID: PMC8209046 DOI: 10.1038/s41467-021-23947-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022] Open
Abstract
Ultrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion. Femtosecond time-resolved X-ray solution scattering (fs-TRXSS) measurements provide information on the structural dynamics of proteins in solution. Here, the authors present a structure refinement method for the analysis of fs-TRXSS data and use it to characterise the ultrafast structural changes of homodimeric haemoglobin.
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Affiliation(s)
- Yunbeom Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, 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 Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Srinivasan Muniyappan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), 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 Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hanui Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Junbeom Jo
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - So Ri Yun
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hyosub Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Kyung Won Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Seong Ok Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, 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 Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea.
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6
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Protein Dynamics and Time Resolved Protein Crystallography at Synchrotron Radiation Sources: Past, Present and Future. CRYSTALS 2021. [DOI: 10.3390/cryst11050521] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The ultrabright and ultrashort pulses produced at X-ray free electron lasers (XFELs) has enabled studies of crystallized molecular machines at work under ‘native’ conditions at room temperature by the so-called time-resolved serial femtosecond crystallography (TR-SFX) technique. Since early TR-SFX experiments were conducted at XFELs, it has been largely reported in the literature that time-resolved X-ray experiments at synchrotrons are no longer feasible or are impractical due to the severe technical limitations of these radiation sources. The transfer of the serial crystallography approach to newest synchrotrons upgraded for higher flux density and with beamlines using sophisticated focusing optics, submicron beam diameters and fast low-noise photon-counting detectors offers a way to overcome these difficulties opening new and exciting possibilities. In fact, there is an increasing amount of publications reporting new findings in structural dynamics of protein macromolecules by using time resolved crystallography from microcrystals at synchrotron sources. This review gathers information to provide an overview of the recent work and the advances made in this filed in the past years, as well as outlines future perspectives at the next generation of synchrotron sources and the upcoming compact pulsed X-ray sources.
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7
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Leitner DM, Hyeon C, Reid KM. Water-mediated biomolecular dynamics and allostery. J Chem Phys 2020; 152:240901. [DOI: 10.1063/5.0011392] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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8
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Reid KM, Yamato T, Leitner DM. Variation of Energy Transfer Rates across Protein–Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin. J Phys Chem B 2020; 124:1148-1159. [DOI: 10.1021/acs.jpcb.9b11413] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557, United States
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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9
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Abstract
Direct visualization of electronic and molecular events during biochemical reactions is essential to mechanistic insights. This Letter presents an in-depth analysis of the serial crystallographic data sets collected by Barends and Schlichting et al. ( Science 2015 , 350 , 445 ) that probe the ligand photodissociation in carbonmonoxy myoglobin. This analysis reveals electron density changes caused by the formation of high-spin 3d atomic orbitals of the heme iron upon photolysis and their dynamic behaviors within the first few picoseconds. The heme iron is found popping out of and recoiling back into the heme plane in succession. These findings provide long-awaited visual validations for previous works using ultrafast spectroscopy and molecular dynamics simulations. Electron density variations are also found largely in the solvent during the first period of a low-frequency oscillation. This work demonstrates the importance of the analytical methods in detecting and isolating weak, transient signals of electronic changes arising from chemical reactions.
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10
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Structural basis of molecular logic OR in a dual-sensor histidine kinase. Proc Natl Acad Sci U S A 2019; 116:19973-19982. [PMID: 31527275 DOI: 10.1073/pnas.1910855116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Signal detection and integration by sensory proteins constitute the critical molecular events as living organisms respond to changes in a complex environment. Many sensory proteins adopt a modular architecture that integrates the perception of distinct chemical or physical signals and the generation of a biological response in the same protein molecule. Currently, how signal perception and integration are achieved in such a modular, often dimeric, framework remains elusive. Here, we report a dynamic crystallography study on the tandem sensor domains of a dual-sensor histidine kinase PPHK (phosphorylation-responsive photosensitive histidine kinase) that operates a molecular logic OR, by which the output kinase activity is modulated by a phosphorylation signal and a light signal. A joint analysis of ∼170 crystallographic datasets probing different signaling states shows remarkable dimer asymmetry as PPHK responds to the input signals and transitions from one state to the other. Supported by mutational data and structural analysis, these direct observations reveal the working mechanics of the molecular logic OR in PPHK, where the light-induced bending of a long signaling helix at the dimer interface is counteracted by the ligand-induced structural changes from a different sensor domain. We propose that the logic OR of PPHK, together with an upstream photoreceptor, implements a "long-pass" red light response distinct from those accomplished by classical phytochromes.
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11
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Leitner DM, Pandey HD, Reid KM. Energy Transport across Interfaces in Biomolecular Systems. J Phys Chem B 2019; 123:9507-9524. [DOI: 10.1021/acs.jpcb.9b07086] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Hari Datt Pandey
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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12
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Martin-Garcia JM, Zhu L, Mendez D, Lee MY, Chun E, Li C, Hu H, Subramanian G, Kissick D, Ogata C, Henning R, Ishchenko A, Dobson Z, Zhang S, Weierstall U, Spence JCH, Fromme P, Zatsepin NA, Fischetti RF, Cherezov V, Liu W. High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source. IUCRJ 2019; 6:412-425. [PMID: 31098022 PMCID: PMC6503920 DOI: 10.1107/s205225251900263x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/20/2019] [Indexed: 05/29/2023]
Abstract
Since the first successful serial crystallography (SX) experiment at a synchrotron radiation source, the popularity of this approach has continued to grow showing that third-generation synchrotrons can be viable alternatives to scarce X-ray free-electron laser sources. Synchrotron radiation flux may be increased ∼100 times by a moderate increase in the bandwidth ('pink beam' conditions) at some cost to data analysis complexity. Here, we report the first high-viscosity injector-based pink-beam SX experiments. The structures of proteinase K (PK) and A2A adenosine receptor (A2AAR) were determined to resolutions of 1.8 and 4.2 Å using 4 and 24 consecutive 100 ps X-ray pulse exposures, respectively. Strong PK data were processed using existing Laue approaches, while weaker A2AAR data required an alternative data-processing strategy. This demonstration of the feasibility presents new opportunities for time-resolved experiments with microcrystals to study structural changes in real time at pink-beam synchrotron beamlines worldwide.
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Affiliation(s)
- Jose M. Martin-Garcia
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Derek Mendez
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Ming-Yue Lee
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Eugene Chun
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Chufeng Li
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Hao Hu
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Ganesh Subramanian
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - David Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Craig Ogata
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, 1002 Childs Way, Los Angeles, CA 90089, USA
| | - Zachary Dobson
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Shangji Zhang
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Uwe Weierstall
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - John C. H. Spence
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Nadia A. Zatsepin
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Robert F. Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, 1002 Childs Way, Los Angeles, CA 90089, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
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13
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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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14
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Leitner DM, Yamato T. MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for C-type inactivation. Proc Natl Acad Sci U S A 2017; 114:11145-11150. [PMID: 28973956 DOI: 10.1073/pnas.1706983114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In many K+ channels, prolonged activating stimuli lead to a time-dependent reduction in ion conduction, a phenomenon known as C-type inactivation. X-ray structures of the KcsA channel suggest that this inactivated state corresponds to a "constricted" conformation of the selectivity filter. However, the functional significance of the constricted conformation has become a matter of debate. Functional and structural studies based on chemically modified semisynthetic KcsA channels along the selectivity filter led to the conclusion that the constricted conformation does not correspond to the C-type inactivated state. The main results supporting this view include the observation that C-type inactivation is not suppressed by a substitution of D-alanine at Gly77, even though this modification is believed to lock the selectivity filter into its conductive conformation, whereas it is suppressed following amide-to-ester backbone substitutions at Gly77 and Tyr78, even though these structure-conserving modifications are not believed to prevent the selectivity filter from adopting the constricted conformation. However, several untested assumptions about the structural and functional impact of these chemical modifications underlie these arguments. To make progress, molecular dynamics simulations based on atomic models of the KcsA channel were performed. The computational results support the notion that the constricted conformation of the selectivity filter corresponds to the functional C-type inactivated state of the KcsA. Importantly, MD simulations reveal that the semisynthetic KcsAD-ala77 channel can adopt an asymmetrical constricted-like nonconductive conformation and that the amide-to-ester backbone substitutions at Gly77 and Tyr78 perturb the hydrogen bonding involving the buried water molecules stabilizing the constricted conformation.
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16
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Šrajer V, Schmidt M. Watching Proteins Function with Time-resolved X-ray Crystallography. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2017; 50:373001. [PMID: 29353938 PMCID: PMC5771432 DOI: 10.1088/1361-6463/aa7d32] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron X-ray sources. An expansive database of more than 100,000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al., 2005a; Schmidt 2008; Neutze and Moffat, 2012; Šrajer 2014). In this approach, short and intense X-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron X-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard X-rays (XFELs; 5-20 keV), which provide exceptionally intense, femtosecond X-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al., 2014; Barends et al., 2015; Pande et al., 2016). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline challenges and further developments necessary to broaden the application of these methods to many important proteins and enzymes of biomedical relevance.
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Affiliation(s)
- Vukica Šrajer
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, IL, USA
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17
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Glossoscolex paulistus hemoglobin with fluorescein isothiocyanate: Steady-state and time-resolved fluorescence. Int J Biol Macromol 2017; 98:777-785. [DOI: 10.1016/j.ijbiomac.2017.02.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 11/20/2022]
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18
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Sheu SY, Liu YC, Yang DY. Interfacial water effect on cooperativity and signal communication in Scapharca dimeric hemoglobin. Phys Chem Chem Phys 2017; 19:7380-7389. [DOI: 10.1039/c7cp00280g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cooperativity is important in controlling the biological functions of allosteric proteins.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences
- National Yang-Ming University
- Taipei 112
- Taiwan
- Institute of Biomedical Informatics
| | - Yu-Cheng Liu
- Institute of Biomedical Informatics
- National Yang-Ming University
- Taipei 112
- Taiwan
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 106
- Taiwan
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19
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Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin. Proc Natl Acad Sci U S A 2016; 113:10565-70. [PMID: 27601659 DOI: 10.1073/pnas.1603539113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
"Protein quake" denotes the dissipation of excess energy across a protein, in response to a local perturbation such as the breaking of a chemical bond or the absorption of a photon. Femtosecond time-resolved small- and wide-angle X-ray scattering (TR-SWAXS) is capable of tracking such ultrafast protein dynamics. However, because the structural interpretation of the experiments is complicated, a molecular picture of protein quakes has remained elusive. In addition, new questions arose from recent TR-SWAXS data that were interpreted as underdamped oscillations of an entire protein, thus challenging the long-standing concept of overdamped global protein dynamics. Based on molecular-dynamics simulations, we present a detailed molecular movie of the protein quake after carbon monoxide (CO) photodissociation in myoglobin. The simulations suggest that the protein quake is characterized by a single pressure peak that propagates anisotropically within 500 fs across the protein and further into the solvent. By computing TR-SWAXS patterns from the simulations, we could interpret features in the reciprocal-space SWAXS signals as specific real-space dynamics, such as CO displacement and pressure wave propagation. Remarkably, we found that the small-angle data primarily detect modulations of the solvent density but not oscillations of the bare protein, thereby reconciling recent TR-SWAXS experiments with the notion of overdamped global protein dynamics.
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20
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Ren Z, Yang X. Angular-split/temporal-delay approach to ultrafast protein dynamics at XFELs. Acta Crystallogr D Struct Biol 2016; 72:871-82. [PMID: 27377384 PMCID: PMC6688658 DOI: 10.1107/s2059798316008573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 05/27/2016] [Indexed: 11/10/2022] Open
Abstract
X-ray crystallography promises direct insights into electron-density changes that lead to and arise from structural changes such as electron and proton transfer and the formation, rupture and isomerization of chemical bonds. The ultrashort pulses of hard X-rays produced by free-electron lasers present an exciting opportunity for capturing ultrafast structural events in biological macromolecules within femtoseconds after photoexcitation. However, shot-to-shot fluctuations, which are inherent to the very process of self-amplified spontaneous emission (SASE) that generates the ultrashort X-ray pulses, are a major source of noise that may conceal signals from structural changes. Here, a new approach is proposed to angularly split a single SASE pulse and to produce a temporal delay of picoseconds between the split pulses. These split pulses will allow the probing of two distinct states before and after photoexcitation triggered by a laser pulse between the split X-ray pulses. The split pulses originate from a single SASE pulse and share many common properties; thus, noise arising from shot-to-shot fluctuations is self-canceling. The unambiguous interpretation of ultrafast structural changes would require diffraction data at atomic resolution, as these changes may or may not involve any atomic displacement. This approach, in combination with the strategy of serial crystallography, offers a solution to study ultrafast dynamics of light-initiated biochemical reactions or biological processes at atomic resolution.
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Affiliation(s)
- Zhong Ren
- Renz Research Inc., Westmont, IL 60559, USA
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, 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
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21
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Ren Z. Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase. Nucleic Acids Res 2016; 44:7457-74. [PMID: 27325739 PMCID: PMC5009745 DOI: 10.1093/nar/gkw555] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/07/2016] [Indexed: 01/26/2023] Open
Abstract
DNA polymerases in family B are workhorses of DNA replication that carry out the bulk of the job at a high speed with high accuracy. A polymerase in this family relies on a built-in exonuclease for proofreading. It has not been observed at the atomic resolution how the polymerase advances one nucleotide space on the DNA template strand after a correct nucleotide is incorporated, that is, a process known as translocation. It is even more puzzling how translocation is avoided after the primer strand is excised by the exonuclease and returned back to the polymerase active site once an error occurs. The structural events along the bifurcate pathways of translocation and proofreading have been unwittingly captured by hundreds of structures in Protein Data Bank. This study analyzes all available structures of a representative member in family B and reveals the orchestrated event sequence during translocation and proofreading.
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Affiliation(s)
- Zhong Ren
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA Renz Research, Inc., Westmont, IL 60559, USA
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22
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Application of advanced X-ray methods in life sciences. Biochim Biophys Acta Gen Subj 2016; 1861:3671-3685. [PMID: 27156488 DOI: 10.1016/j.bbagen.2016.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Synchrotron radiation (SR) sources provide diverse X-ray methods for the investigation of structure-function relationships in biological macromolecules. SCOPE OF REVIEW Recent developments in SR sources and in the X-ray tools they offer for life sciences are reviewed. Specifically, advances in macromolecular crystallography, small angle X-ray solution scattering, X-ray absorption and fluorescence spectroscopy, and imaging are discussed with examples. MAJOR CONCLUSIONS SR sources offer a range of X-ray techniques that can be used in a complementary fashion in studies of biological systems at a wide range of resolutions from atomic to cellular scale. Emerging applications of X-ray techniques include the characterization of disordered proteins, noncrystalline and nonequilibrium systems, elemental imaging of tissues, cells and organs, and detection of time-resolved changes in molecular structures. GENERAL SIGNIFICANCE X-ray techniques are in the center of hybrid approaches that are used to gain insight into complex problems relating to biomolecular mechanisms, disease and possible therapeutic solutions. This article is part of a Special Issue entitled "Science for Life". Guest Editors: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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23
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Abstract
We examine energy dynamics in the unliganded and liganded states of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI), which exhibits cooperativity mediated by the cluster of water molecules at the interface upon ligand binding and dissociation. We construct and analyze a dynamic network in which nodes representing the residues, hemes, and water cluster are connected by edges that represent energy transport times, as well as a nonbonded network (NBN) indicating regions that respond rapidly to local strain within the protein via nonbonded interactions. One of the two largest NBNs includes the Lys30-Asp89 salt bridge critical for stabilizing the dimer. The other includes the hemes and surrounding residues, as well as, in the unliganded state, the cluster of water molecules between the globules. Energy transport in the protein appears to be controlled by the Lys30-Asp89 salt bridge critical for stabilizing the dimer, as well as the interface water cluster in the unliganded state. Possible connections between energy transport dynamics in response to local strain identified here and allosteric transitions in HbI are discussed.
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Affiliation(s)
- David M Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada , Reno, Nevada 89557, United States
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24
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Kim JG, Muniyappan S, Oang KY, Kim TW, Yang C, Kim KH, Kim J, Ihee H. Cooperative protein structural dynamics of homodimeric hemoglobin linked to water cluster at subunit interface revealed by time-resolved X-ray solution scattering. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:023610. [PMID: 27158635 PMCID: PMC4833754 DOI: 10.1063/1.4947071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 04/06/2016] [Indexed: 05/30/2023]
Abstract
Homodimeric hemoglobin (HbI) consisting of two subunits is a good model system for investigating the allosteric structural transition as it exhibits cooperativity in ligand binding. In this work, as an effort to extend our previous study on wild-type and F97Y mutant HbI, we investigate structural dynamics of a mutant HbI in solution to examine the role of well-organized interfacial water cluster, which has been known to mediate intersubunit communication in HbI. In the T72V mutant of HbI, the interfacial water cluster in the T state is perturbed due to the lack of Thr72, resulting in two less interfacial water molecules than in wild-type HbI. By performing picosecond time-resolved X-ray solution scattering experiment and kinetic analysis on the T72V mutant, we identify three structurally distinct intermediates (I1, I2, and I3) and show that the kinetics of the T72V mutant are well described by the same kinetic model used for wild-type and F97Y HbI, which involves biphasic kinetics, geminate recombination, and bimolecular CO recombination. The optimized kinetic model shows that the R-T transition and bimolecular CO recombination are faster in the T72V mutant than in the wild type. From structural analysis using species-associated difference scattering curves for the intermediates, we find that the T-like deoxy I3 intermediate in solution has a different structure from deoxy HbI in crystal. In addition, we extract detailed structural parameters of the intermediates such as E-F distance, intersubunit rotation angle, and heme-heme distance. By comparing the structures of protein intermediates in wild-type HbI and the T72V mutant, we reveal how the perturbation in the interfacial water cluster affects the kinetics and structures of reaction intermediates of HbI.
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Affiliation(s)
| | | | | | | | | | | | - Jeongho Kim
- Department of Chemistry, Inha University , Incheon 402-751, South Korea
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25
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Pawate AS, Šrajer V, Schieferstein J, Guha S, Henning R, Kosheleva I, Schmidt M, Ren Z, Kenis PJA, Perry SL. Towards time-resolved serial crystallography in a microfluidic device. Acta Crystallogr F Struct Biol Commun 2015; 71:823-30. [PMID: 26144226 PMCID: PMC4498702 DOI: 10.1107/s2053230x15009061] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/11/2015] [Indexed: 11/10/2022] Open
Abstract
Serial methods for crystallography have the potential to enable dynamic structural studies of protein targets that have been resistant to single-crystal strategies. The use of serial data-collection strategies can circumvent challenges associated with radiation damage and repeated reaction initiation. This work utilizes a microfluidic crystallization platform for the serial time-resolved Laue diffraction analysis of macroscopic crystals of photoactive yellow protein (PYP). Reaction initiation was achieved via pulsed laser illumination, and the resultant electron-density difference maps clearly depict the expected pR(1)/pR(E46Q) and pR(2)/pR(CW) states at 10 µs and the pB1 intermediate at 1 ms. The strategies presented here have tremendous potential for extension to chemical triggering methods for reaction initiation and for extension to dynamic, multivariable analyses.
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Affiliation(s)
- Ashtamurthy S. Pawate
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Vukica Šrajer
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
| | - Jeremy Schieferstein
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sudipto Guha
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
| | - Marius Schmidt
- Department of Physics, The University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA
| | - Zhong Ren
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
- Renz Research Inc., Westmont, Illinois, USA
| | - Paul J. A. Kenis
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sarah L. Perry
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, Massachusetts, USA
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26
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Trujillo K, Papagiannopoulos T, Olsen KW. Effects of mutations on the molecular dynamics of oxygen escape from the dimeric hemoglobin of Scapharca inaequivalvis. F1000Res 2015; 4:65. [PMID: 25866622 PMCID: PMC4376171 DOI: 10.12688/f1000research.6127.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/23/2015] [Indexed: 12/15/2022] Open
Abstract
Like many hemoglobins, the structure of the dimeric hemoglobin from the clam
Scapharca inaequivalvis is a “closed bottle” since there is no direct tunnel from the oxygen binding site on the heme to the solvent. The proximal histidine faces the dimer interface, which consists of the E and F helicies. This is significantly different from tetrameric vertebrate hemoglobins and brings the heme groups near the subunit interface. The subunit interface is also characterized by an immobile, hydrogen-bonded network of water molecules. Although there is data which is consistent with the histidine gate pathway for ligand escape, these aspects of the structure would seem to make that pathway less likely. Locally enhanced sampling molecular dynamics are used here to suggest alternative pathways in the wild-type and six mutant proteins. In most cases the point mutations change the selection of exit routes observed in the simulations. Exit via the histidine gate is rarely seem although oxygen molecules do occasionally cross over the interface from one subunit to the other. The results suggest that changes in flexibility and, in some cases, creation of new cavities can explain the effects of the mutations on ligand exit paths.
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Affiliation(s)
- Kevin Trujillo
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Tasso Papagiannopoulos
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Kenneth W Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60660, USA
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27
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Perry SL, Guha S, Pawate AS, Henning R, Kosheleva I, Srajer V, Kenis PJA, Ren Z. In situ serial Laue diffraction on a microfluidic crystallization device. J Appl Crystallogr 2014; 47:1975-1982. [PMID: 25484843 PMCID: PMC4248567 DOI: 10.1107/s1600576714023322] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/22/2014] [Indexed: 11/10/2022] Open
Abstract
Renewed interest in room-temperature diffraction has been prompted by the desire to observe structural dynamics of proteins as they function. Serial crystallography, an experimental strategy that aggregates small pieces of data from a large uniform pool of crystals, has been demonstrated at synchrotrons and X-ray free-electron lasers. This work utilizes a microfluidic crystallization platform for serial Laue diffraction from macroscopic crystals and proposes that a collection of small slices of Laue data from many individual crystals is a realistic solution to the difficulties in dynamic studies of irreversible biochemical reactions.
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Affiliation(s)
- Sarah L. Perry
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA, USA
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Sudipto Guha
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Ashtamurthy S. Pawate
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
| | - Vukica Srajer
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
| | - Paul J. A. Kenis
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Zhong Ren
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
- Renz Research Inc., Westmont, IL, USA
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28
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Agbo JK, Gnanasekaran R, Leitner DM. Communication Maps: Exploring Energy Transport through Proteins and Water. Isr J Chem 2014. [DOI: 10.1002/ijch.201300139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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29
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Ren Z. Reverse engineering the cooperative machinery of human hemoglobin. PLoS One 2013; 8:e77363. [PMID: 24312167 PMCID: PMC3842276 DOI: 10.1371/journal.pone.0077363] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/30/2013] [Indexed: 11/25/2022] Open
Abstract
Hemoglobin transports molecular oxygen from the lungs to all human tissues for cellular respiration. Its α2β2 tetrameric assembly undergoes cooperative binding and releasing of oxygen for superior efficiency and responsiveness. Over past decades, hundreds of hemoglobin structures were determined under a wide range of conditions for investigation of molecular mechanism of cooperativity. Based on a joint analysis of hemoglobin structures in the Protein Data Bank (Ren, companion article), here I present a reverse engineering approach to elucidate how two subunits within each dimer reciprocate identical motions that achieves intradimer cooperativity, how ligand-induced structural signals from two subunits are integrated to drive quaternary rotation, and how the structural environment at the oxygen binding sites alter their binding affinity. This mechanical model reveals the intricate design that achieves the cooperative mechanism and has previously been masked by inconsistent structural fluctuations. A number of competing theories on hemoglobin cooperativity and broader protein allostery are reconciled and unified.
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Affiliation(s)
- Zhong Ren
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, United States of America
- Renz Research, Inc., Westmont, Illinois, United States of America
- * E-mail:
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30
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Reaction trajectory revealed by a joint analysis of protein data bank. PLoS One 2013; 8:e77141. [PMID: 24244274 PMCID: PMC3823880 DOI: 10.1371/journal.pone.0077141] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/29/2013] [Indexed: 11/19/2022] Open
Abstract
Structural motions along a reaction pathway hold the secret about how a biological macromolecule functions. If each static structure were considered as a snapshot of the protein molecule in action, a large collection of structures would constitute a multidimensional conformational space of an enormous size. Here I present a joint analysis of hundreds of known structures of human hemoglobin in the Protein Data Bank. By applying singular value decomposition to distance matrices of these structures, I demonstrate that this large collection of structural snapshots, derived under a wide range of experimental conditions, arrange orderly along a reaction pathway. The structural motions along this extensive trajectory, including several helical transformations, arrive at a reverse engineered mechanism of the cooperative machinery (Ren, companion article), and shed light on pathological properties of the abnormal homotetrameric hemoglobins from α-thalassemia. This method of meta-analysis provides a general approach to structural dynamics based on static protein structures in this post genomics era.
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31
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Wu CT, Wang WC, Chen MF, Su HY, Chen WY, Wu CH, Chang YJ, Liu HH. Glucose-regulated protein 78 mediates hormone-independent prostate cancer progression and metastasis through maspin and COX-2 expression. Tumour Biol 2013; 35:195-204. [PMID: 23922175 DOI: 10.1007/s13277-013-1024-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 07/12/2013] [Indexed: 12/22/2022] Open
Abstract
Glucose-regulated protein 78 (GRP78) plays an essential role in embryonic development and in the progression and therapeutic resistance of many cancers. However, little is known about the function of GRP78 in hormone-independent prostate cancer. Here, we found that the expression levels of GRP78 were higher in PC-3 cells than in DU-145 cells. When the expression of GRP78 was silenced using a GRP78-specific small interfering RNA in PC-3 cells, the growth rate and adhesive ability were reduced. Cell migration was dramatically decreased in GRP78-depleted cells. Dissection of the involved signal pathways revealed that maspin expression was upregulated after silencing GRP78 expression. The upregulation of maspin and downregulation of COX-2 may cause the decrease in cell proliferation and migration observed after silencing GRP78 expression. Silencing GRP78 expression may suppress the proliferation, adhesion, and migration of prostate cancer cells via maspin and COX-2 regulation.
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Affiliation(s)
- Chun-Te Wu
- Chang Gung University College of Medicine and Chang Gung Institute of Technology, Taipei, Taiwan
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32
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Ren Z, Chan PWY, Moffat K, Pai EF, Royer WE, Šrajer V, Yang X. Resolution of structural heterogeneity in dynamic crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:946-59. [PMID: 23695239 PMCID: PMC3663119 DOI: 10.1107/s0907444913003454] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 02/04/2013] [Indexed: 05/15/2024]
Abstract
Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.
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Affiliation(s)
- Zhong Ren
- Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Avenue, Building 434B, Argonne, IL 60439, USA.
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Chakraborty S. A quantitative measure of electrostatic perturbation in holo and apo enzymes induced by structural changes. PLoS One 2013; 8:e59352. [PMID: 23516628 PMCID: PMC3597595 DOI: 10.1371/journal.pone.0059352] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 02/13/2013] [Indexed: 11/19/2022] Open
Abstract
Biological pathways are subject to subtle manipulations that achieve a wide range of functional variation in differing physiological niches. In many instances, changes in the structure of an enzyme on ligand binding germinate electrostatic perturbations that form the basis of its changed catalytic or transcriptional efficiency. Computational methods that seek to gain insights into the electrostatic changes in enzymes require expertise to setup and computing prowess. In the current work, we present a fast, easy and reliable methodology to compute electrostatic perturbations induced by ligand binding (MEPP). The theoretical foundation of MEPP is the conserved electrostatic potential difference (EPD) in cognate pairs of active site residues in proteins with the same functionality. Previously, this invariance has been used to unravel promiscuous serine protease and metallo-β-lactamase scaffolds in alkaline phosphatases. Given that a similarity in EPD is significant, we expect differences in the EPD to be significant too. MEPP identifies residues or domains that undergo significant electrostatic perturbations, and also enumerates residue pairs that undergo significant polarity change. The gain in a certain polarity of a residue with respect to neighboring residues, or the reversal of polarity between two residues might indicate a change in the preferred ligand. The methodology of MEPP has been demonstrated on several enzymes that employ varying mechanisms to perform their roles. For example, we have attributed the change in polarity in residue pairs to be responsible for the loss of metal ion binding in fructose 1,6-bisphosphatases, and corroborated the pre-organized state of the active site of the enzyme with respect to functionally relevant changes in electric fields in ketosteroid isomerases.
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Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.
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Tertiary and quaternary effects in the allosteric regulation of animal hemoglobins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1860-72. [PMID: 23523886 DOI: 10.1016/j.bbapap.2013.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/07/2013] [Accepted: 03/08/2013] [Indexed: 12/16/2022]
Abstract
In the last decade, protein allostery has experienced a major resurgence, boosted by the extension of the concept to systems of increasing complexity and by its exploitation for the development of drugs. Expansion of the field into new directions has not diminished the key role of hemoglobin as a test molecule for theory and experimental validation of allosteric models. Indeed, the diffusion of hemoglobins in all kingdoms of life and the variety of functions and of quaternary assemblies based on a common tertiary fold indicate that this superfamily of proteins is ideally suited for investigating the physical and molecular basis of allostery and firmly maintains its role as a main player in the field. This review is an attempt to briefly recollect common and different strategies adopted by metazoan hemoglobins, from monomeric molecules to giant complexes, exploiting homotropic and heterotropic allostery to increase their functional dynamic range. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Ronda L, Bettati S, Henry ER, Kashav T, Sanders JM, Royer WE, Mozzarelli A. Tertiary and quaternary allostery in tetrameric hemoglobin from Scapharca inaequivalvis. Biochemistry 2013; 52:2108-17. [PMID: 23458680 DOI: 10.1021/bi301620x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The clam Scapharca inaequivalvis possesses two cooperative oxygen binding hemoglobins in its red cells: a homodimeric HbI and a heterotetrameric A2B2 HbII. Each AB dimeric half of HbII is assembled in a manner very similar to that of the well-studied HbI. This study presents crystal structures of HbII along with oxygen binding data both in the crystalline state and in wet nanoporous silica gels. Despite very similar ligand-linked structural transitions observed in HbI and HbII crystals, HbII in the crystal or encapsulated in silica gels apparently exhibits minimal cooperativity in oxygen binding, in contrast with the full cooperativity exhibited by HbI crystals. However, oxygen binding curves in the crystal indicate the presence of a significant functional inequivalence of A and B chains. When this inequivalence is taken into account, both crystal and R state gel functional data are consistent with the conservation of a tertiary contribution to cooperative oxygen binding, quantitatively similar to that measured for HbI, and are in keeping with the structural information. Furthermore, our results indicate that to fully express cooperative ligand binding, HbII requires quaternary transitions hampered by crystal lattice and gel encapsulation, revealing greater complexity in cooperative function than the direct communication across a dimeric interface observed in HbI.
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Affiliation(s)
- Luca Ronda
- Department of Pharmacy, University of Parma , Parco Area delle Scienze, 23/A, 43124 Parma, Italy
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36
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Neutze R, Moffat K. Time-resolved structural studies at synchrotrons and X-ray free electron lasers: opportunities and challenges. Curr Opin Struct Biol 2012; 22:651-9. [PMID: 23021004 PMCID: PMC3520507 DOI: 10.1016/j.sbi.2012.08.006] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 08/27/2012] [Accepted: 08/31/2012] [Indexed: 11/19/2022]
Abstract
X-ray free electron lasers (XFELs) are potentially revolutionary X-ray sources because of their very short pulse duration, extreme peak brilliance and high spatial coherence, features that distinguish them from today's synchrotron sources. We review recent time-resolved Laue diffraction and time-resolved wide angle X-ray scattering (WAXS) studies at synchrotron sources, and initial static studies at XFELs. XFELs have the potential to transform the field of time-resolved structural biology, yet many challenges arise in devising and adapting hardware, experimental design and data analysis strategies to exploit their unusual properties. Despite these challenges, we are confident that XFEL sources are poised to shed new light on ultrafast protein reaction dynamics.
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Affiliation(s)
- Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden.
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37
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Kim K, Muniyappan S, Oang KY, Kim JG, Nozawa S, Sato T, Koshihara SY, Henning R, Kosheleva I, Ki H, Kim Y, Kim TW, Kim J, Adachi SI, Ihee H. Direct observation of cooperative protein structural dynamics of homodimeric hemoglobin from 100 ps to 10 ms with pump-probe X-ray solution scattering. J Am Chem Soc 2012; 134:7001-8. [PMID: 22494177 PMCID: PMC3337689 DOI: 10.1021/ja210856v] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Indexed: 01/11/2023]
Abstract
Proteins serve as molecular machines in performing their biological functions, but the detailed structural transitions are difficult to observe in their native aqueous environments in real time. For example, despite extensive studies, the solution-phase structures of the intermediates along the allosteric pathways for the transitions between the relaxed (R) and tense (T) forms have been elusive. In this work, we employed picosecond X-ray solution scattering and novel structural analysis to track the details of the structural dynamics of wild-type homodimeric hemoglobin (HbI) from the clam Scapharca inaequivalvis and its F97Y mutant over a wide time range from 100 ps to 56.2 ms. From kinetic analysis of the measured time-resolved X-ray solution scattering data, we identified three structurally distinct intermediates (I(1), I(2), and I(3)) and their kinetic pathways common for both the wild type and the mutant. The data revealed that the singly liganded and unliganded forms of each intermediate share the same structure, providing direct evidence that the ligand photolysis of only a single subunit induces the same structural change as the complete photolysis of both subunits does. In addition, by applying novel structural analysis to the scattering data, we elucidated the detailed structural changes in the protein, including changes in the heme-heme distance, the quaternary rotation angle of subunits, and interfacial water gain/loss. The earliest, R-like I(1) intermediate is generated within 100 ps and transforms to the R-like I(2) intermediate with a time constant of 3.2 ± 0.2 ns. Subsequently, the late, T-like I(3) intermediate is formed via subunit rotation, a decrease in the heme-heme distance, and substantial gain of interfacial water and exhibits ligation-dependent formation kinetics with time constants of 730 ± 120 ns for the fully photolyzed form and 5.6 ± 0.8 μs for the partially photolyzed form. For the mutant, the overall kinetics are accelerated, and the formation of the T-like I(3) intermediate involves interfacial water loss (instead of water entry) and lacks the contraction of the heme-heme distance, thus underscoring the dramatic effect of the F97Y mutation. The ability to keep track of the detailed movements of the protein in aqueous solution in real time provides new insights into the protein structural dynamics.
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Affiliation(s)
- Kyung
Hwan Kim
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Srinivasan Muniyappan
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Key Young Oang
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Jong Goo Kim
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Shunsuke Nozawa
- Photon Factory,
Institute of
Materials Structure Science, High Energy Accelerator
Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki
305-0801, Japan
| | - Tokushi Sato
- Photon Factory,
Institute of
Materials Structure Science, High Energy Accelerator
Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki
305-0801, Japan
| | - Shin-ya Koshihara
- Department
of Chemistry and Materials
Science, Tokyo Institute of Technology and
CREST, Japan Science and Technology Agency (JST), Meguro-ku, Tokyo 152-8551, Japan
| | - Robert Henning
- Center for Advanced Radiation
Sources, The University of Chicago, Chicago,
Illinois 60637, United States
| | - Irina Kosheleva
- Center for Advanced Radiation
Sources, The University of Chicago, Chicago,
Illinois 60637, United States
| | - Hosung Ki
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Youngmin Kim
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Tae Wu Kim
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Jeongho Kim
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Shin-ichi Adachi
- Photon Factory,
Institute of
Materials Structure Science, High Energy Accelerator
Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki
305-0801, Japan
- PRESTO, Japan Science
and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi,
Saitama 332-0012, Japan
| | - Hyotcherl Ihee
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
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