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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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2
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Chretien A, Nagel MF, Botha S, de Wijn R, Brings L, Dörner K, Han H, Koliyadu JCP, Letrun R, Round A, Sato T, Schmidt C, Secareanu RC, von Stetten D, Vakili M, Wrona A, Bean R, Mancuso A, Schulz J, Pearson AR, Kottke T, Lorenzen K, Schubert R. Light-induced Trp in/Met out Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC. J Mol Biol 2024; 436:168439. [PMID: 38185322 DOI: 10.1016/j.jmb.2024.168439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/28/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
The understanding of signal transduction mechanisms in photoreceptor proteins is essential for elucidating how living organisms respond to light as environmental stimuli. In this study, we investigated the ATP binding, photoactivation and signal transduction process in the photoactivatable adenylate cyclase from Oscillatoria acuminata (OaPAC) upon blue light excitation. Structural models with ATP bound in the active site of native OaPAC at cryogenic as well as room temperature are presented. ATP is found in one conformation at cryogenic- and in two conformations at ambient-temperature, and is bound in an energetically unfavorable conformation for the conversion to cAMP. However, FTIR spectroscopic experiments confirm that this conformation is the native binding mode in dark state OaPAC and that transition to a productive conformation for ATP turnover only occurs after light activation. A combination of time-resolved crystallography experiments at synchrotron and X-ray Free Electron Lasers sheds light on the early events around the Flavin Adenine Dinucleotide (FAD) chromophore in the light-sensitive BLUF domain of OaPAC. Early changes involve the highly conserved amino acids Tyr6, Gln48 and Met92. Crucially, the Gln48 side chain performs a 180° rotation during activation, leading to the stabilization of the FAD chromophore. Cryo-trapping experiments allowed us to investigate a late light-activated state of the reaction and revealed significant conformational changes in the BLUF domain around the FAD chromophore. In particular, a Trpin/Metout transition upon illumination is observed for the first time in the BLUF domain and its role in signal transmission via α-helix 3 and 4 in the linker region between sensor and effector domain is discussed.
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Affiliation(s)
- Anaïs Chretien
- European XFEL GmbH, Schenefeld, Germany; Department of Chemistry, Universität Hamburg, Hamburg, Germany
| | - Marius F Nagel
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | | | | | | | | | | | | | | | | | | | | | - David von Stetten
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | | | | | | | | | | | - Arwen R Pearson
- Institute for Nanostructure and Solid-State Physics, Universität Hamburg, Hamburg, Germany
| | - Tilman Kottke
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
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3
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Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers. CRYSTALS 2020. [DOI: 10.3390/cryst10070628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate. X-ray free electron lasers (XFELs) have enabled TRX experiments on previously uncharted femtosecond timescales. Here, we review the recent developments, opportunities, and challenges of pump-probe TRX at XFELs.
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4
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Srivastava A, Tiwari SP, Miyashita O, Tama F. Integrative/Hybrid Modeling Approaches for Studying Biomolecules. J Mol Biol 2020; 432:2846-2860. [DOI: 10.1016/j.jmb.2020.01.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/20/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
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Mehrabi P, Schulz EC, Dsouza R, Müller-Werkmeister HM, Tellkamp F, Miller RJD, Pai EF. Time-resolved crystallography reveals allosteric communication aligned with molecular breathing. Science 2019; 365:1167-1170. [DOI: 10.1126/science.aaw9904] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022]
Abstract
A comprehensive understanding of protein function demands correlating structure and dynamic changes. Using time-resolved serial synchrotron crystallography, we visualized half-of-the-sites reactivity and correlated molecular-breathing motions in the enzyme fluoroacetate dehalogenase. Eighteen time points from 30 milliseconds to 30 seconds cover four turnover cycles of the irreversible reaction. They reveal sequential substrate binding, covalent-intermediate formation, setup of a hydrolytic water molecule, and product release. Small structural changes of the protein mold and variations in the number and placement of water molecules accompany the various chemical steps of catalysis. Triggered by enzyme-ligand interactions, these repetitive changes in the protein framework’s dynamics and entropy constitute crucial components of the catalytic machinery.
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Zatsepin NA, Li C, Colasurd P, Nannenga BL. The complementarity of serial femtosecond crystallography and MicroED for structure determination from microcrystals. Curr Opin Struct Biol 2019; 58:286-293. [PMID: 31345629 DOI: 10.1016/j.sbi.2019.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 11/19/2022]
Abstract
In recent years, nano and microcrystals have emerged as a valuable source of high-resolution structural information owing to the invention of serial femtosecond crystallography (SFX) with X-ray free electron lasers and microcrystal electron diffraction (MicroED) using electron cryomicroscopes. Once considered useless for structure determination, nano/microcrystals now confer significant advantages for static and time-resolved structure determination from a wide variety of difficult-to-study targets. MicroED has been used to obtain sub-Ångstrom resolution maps in which hydrogen atoms can be clearly resolved from only a few nano/microcrystals, while SFX has been used to probe protein dynamics following reaction initiation on time scales from femtoseconds to minutes. We review these two complementary techniques and their abilities for high-resolution structure determination.
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Affiliation(s)
- Nadia A Zatsepin
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287, USA
| | - Paige Colasurd
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA.
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7
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Witkowska D, Rowińska-Żyrek M. Biophysical approaches for the study of metal-protein interactions. J Inorg Biochem 2019; 199:110783. [PMID: 31349072 DOI: 10.1016/j.jinorgbio.2019.110783] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions play important roles for a variety of cell functions, often involving metal ions; in fact, metal-ion binding mediates and regulates the activity of a wide range of biomolecules. Enlightening all of the specific features of metal-protein and metal-mediated protein-protein interactions can be a very challenging task; a detailed knowledge of the thermodynamic and spectroscopic parameters and the structural changes of the protein is normally required. For this purpose, many experimental techniques are employed, embracing all fields of Analytical and Bioinorganic Chemistry. In addition, the use of peptide models, reproducing the primary sequence of the metal-binding sites, is also proved to be useful. In this paper, a review of the most useful techniques for studying ligand-protein interactions with a special emphasis on metal-protein interactions is provided, with a critical summary of their strengths and limitations.
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Affiliation(s)
- Danuta Witkowska
- Public Higher Medical Professional School in Opole, Katowicka 68, 45060 Opole, Poland.
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Abstract
Classically, phenotype is what is observed, and genotype is the genetic makeup. Statistical studies aim to project phenotypic likelihoods of genotypic patterns. The traditional genotype-to-phenotype theory embraces the view that the encoded protein shape together with gene expression level largely determines the resulting phenotypic trait. Here, we point out that the molecular biology revolution at the turn of the century explained that the gene encodes not one but ensembles of conformations, which in turn spell all possible gene-associated phenotypes. The significance of a dynamic ensemble view is in understanding the linkage between genetic change and the gained observable physical or biochemical characteristics. Thus, despite the transformative shift in our understanding of the basis of protein structure and function, the literature still commonly relates to the classical genotype-phenotype paradigm. This is important because an ensemble view clarifies how even seemingly small genetic alterations can lead to pleiotropic traits in adaptive evolution and in disease, why cellular pathways can be modified in monogenic and polygenic traits, and how the environment may tweak protein function.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
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Schmidt M. Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources. Int J Mol Sci 2019; 20:ijms20061401. [PMID: 30897736 PMCID: PMC6470897 DOI: 10.3390/ijms20061401] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 11/30/2022] Open
Abstract
The focus of structural biology is shifting from the determination of static structures to the investigation of dynamical aspects of macromolecular function. With time-resolved macromolecular crystallography (TRX), intermediates that form and decay during the macromolecular reaction can be investigated, as well as their reaction dynamics. Time-resolved crystallographic methods were initially developed at synchrotrons. However, about a decade ago, extremely brilliant, femtosecond-pulsed X-ray sources, the free electron lasers for hard X-rays, became available to a wider community. TRX is now possible with femtosecond temporal resolution. This review provides an overview of methodological aspects of TRX, and at the same time, aims to outline the frontiers of this method at modern pulsed X-ray sources.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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Cerutti DS, Case DA. Molecular Dynamics Simulations of Macromolecular Crystals. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018; 9. [PMID: 31662799 DOI: 10.1002/wcms.1402] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The structures of biological macromolecules would not be known to their present extent without X-ray crystallography. Most simulations of globular proteins in solution begin by surrounding the crystal structure of the monomer in a bath of water molecules, but the standard simulation employing periodic boundary conditions is already close to a crystal lattice environment. With simple protocols, the same software and molecular models can perform simulations of the crystal lattice, including all asymmetric units and solvent to fill the box. Throughout the history of molecular dynamics, studies of crystal lattices have served to investigate the quality of the underlying force fields, correlate the simulated ensembles to experimental structure factors, and extrapolate the behavior in lattices to behavior in solution. Powerful new computers are enabling molecular simulations with greater realism and statistical convergence. Meanwhile, the advent of exciting new methods in crystallography, including femtosecond free-electron lasers and image reconstruction for time-resolved crystallography on slurries of small crystals, is expanding the range of structures accessible to X-ray diffraction. We review past fusions of simulations and crystallography, then look ahead to the ways that simulations of crystal structures will enhance structural biology in the future.
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Affiliation(s)
- David S Cerutti
- Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8066
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8066
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11
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A modeling and simulation perspective on the mechanism and function of respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:510-523. [DOI: 10.1016/j.bbabio.2018.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022]
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12
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Seddon EA, Clarke JA, Dunning DJ, Masciovecchio C, Milne CJ, Parmigiani F, Rugg D, Spence JCH, Thompson NR, Ueda K, Vinko SM, Wark JS, Wurth W. Short-wavelength free-electron laser sources and science: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2017; 80:115901. [PMID: 29059048 DOI: 10.1088/1361-6633/aa7cca] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
This review is focused on free-electron lasers (FELs) in the hard to soft x-ray regime. The aim is to provide newcomers to the area with insights into: the basic physics of FELs, the qualities of the radiation they produce, the challenges of transmitting that radiation to end users and the diversity of current scientific applications. Initial consideration is given to FEL theory in order to provide the foundation for discussion of FEL output properties and the technical challenges of short-wavelength FELs. This is followed by an overview of existing x-ray FEL facilities, future facilities and FEL frontiers. To provide a context for information in the above sections, a detailed comparison of the photon pulse characteristics of FEL sources with those of other sources of high brightness x-rays is made. A brief summary of FEL beamline design and photon diagnostics then precedes an overview of FEL scientific applications. Recent highlights are covered in sections on structural biology, atomic and molecular physics, photochemistry, non-linear spectroscopy, shock physics, solid density plasmas. A short industrial perspective is also included to emphasise potential in this area.
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Affiliation(s)
- E A Seddon
- ASTeC, STFC Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Cheshire, WA4 4AD, United Kingdom. The School of Physics and Astronomy and Photon Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. The Cockcroft Institute, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Cheshire, WA4 4AD, United Kingdom
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13
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Beyerlein KR, Dierksmeyer D, Mariani V, Kuhn M, Sarrou I, Ottaviano A, Awel S, Knoska J, Fuglerud S, Jönsson O, Stern S, Wiedorn MO, Yefanov O, Adriano L, Bean R, Burkhardt A, Fischer P, Heymann M, Horke DA, Jungnickel KEJ, Kovaleva E, Lorbeer O, Metz M, Meyer J, Morgan A, Pande K, Panneerselvam S, Seuring C, Tolstikova A, Lieske J, Aplin S, Roessle M, White TA, Chapman HN, Meents A, Oberthuer D. Mix-and-diffuse serial synchrotron crystallography. IUCRJ 2017; 4:769-777. [PMID: 29123679 PMCID: PMC5668862 DOI: 10.1107/s2052252517013124] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/13/2017] [Indexed: 05/21/2023]
Abstract
Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzyme at a high level of detail. The success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.
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Affiliation(s)
- Kenneth R. Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Manuela Kuhn
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Angelica Ottaviano
- Department of Physics, California State University, Northridge, California, USA
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Silje Fuglerud
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Olof Jönsson
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Stephan Stern
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- European X-ray Free-Electron Laser Facility GmbH (XFEL), Schenefeld, Germany
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Luigi Adriano
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Richard Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anja Burkhardt
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Pontus Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Michael Heymann
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel A. Horke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | | | - Elena Kovaleva
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Olga Lorbeer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Markus Metz
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan Meyer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Andrew Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kanupriya Pande
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Julia Lieske
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Steve Aplin
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
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Kuramochi H, Fujisawa T, Takeuchi S, Tahara T. Broadband stimulated Raman spectroscopy in the deep ultraviolet region. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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Stepanenko OV, Stepanenko OV, Bublikov G, Kuznetsova I, Verkhusha V, Turoverov K. Stabilization of structure in near-infrared fluorescent proteins by binding of biliverdin chromophore. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Spence JCH. XFELs for structure and dynamics in biology. IUCRJ 2017; 4:322-339. [PMID: 28875020 PMCID: PMC5571796 DOI: 10.1107/s2052252517005760] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/17/2017] [Indexed: 05/20/2023]
Abstract
The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are outlined, and some grand challenges are suggested. By avoiding the need to cool samples to minimize damage, the XFEL has permitted atomic resolution imaging of molecular processes on the 100 fs timescale under near-physiological conditions and in the correct thermal bath in which molecular machines operate. Radiation damage, comparisons of XFEL and synchrotron work, single-particle diffraction, fast solution scattering, pump-probe studies on photosensitive proteins, mix-and-inject experiments, caged molecules, pH jump and other reaction-initiation methods, and the study of molecular machines are all discussed. Sample-delivery methods and data-analysis algorithms for the various modes, from serial femtosecond crystallo-graphy to fast solution scattering, fluctuation X-ray scattering, mixing jet experiments and single-particle diffraction, are also reviewed.
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Affiliation(s)
- J. C. H. Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
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17
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Abstract
Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers.
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Affiliation(s)
- Hosung Ki
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea; , , .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea
| | - Key Young Oang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea; , , .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, Incheon 402-751, South Korea;
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea; , , .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea
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18
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Abstract
Time-resolved macromolecular crystallography unifies protein structure determination with chemical kinetics. With the advent of fourth generation X-ray sources the time-resolution can be on the order of 10-40 fs, which opens the ultrafast time scale to structure determination. Fundamental motions and transitions associated with chemical reactions in proteins can now be observed. Moreover, new experimental approaches at synchrotrons allow for the straightforward investigation of all kind of reactions in biological macromolecules. Here, recent developments in the field are reviewed.
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Affiliation(s)
- Marius Schmidt
- Kenwood Interdisciplinary Research Complex, Physics Department, University of Wisconsin-Milwaukee, Room 3087, 3135 North Maryland Avenue, Milwaukee, WI, 53211, USA.
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19
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20
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Abstract
The walleye (Sander vitreus) is a golden yellow fish that inhabits the Northern American lakes. The recent sightings of the blue walleye and the correlation of its sighting to possible increased UV radiation have been proposed earlier. The underlying molecular basis of its adaptation to increased UV radiation is the presence of a protein (Sandercyanin)-ligand complex in the mucus of walleyes. Degradation of heme by UV radiation results in the formation of Biliverdin IXα (BLA), the chromophore bound to Sandercyanin. We show that Sandercyanin is a monomeric protein that forms stable homotetramers on addition of BLA to the protein. A structure of the Sandercyanin-BLA complex, purified from the fish mucus, reveals a glycosylated protein with a lipocalin fold. This protein-ligand complex absorbs light in the UV region (λmax of 375 nm) and upon excitation at this wavelength emits in the red region (λmax of 675 nm). Unlike all other known biliverdin-bound fluorescent proteins, the chromophore is noncovalently bound to the protein. We provide here a molecular rationale for the observed spectral properties of Sandercyanin.
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21
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Abstract
Serial crystallography at a synchrotron has been used to obtain time-resolved atomic resolution density maps of enzyme catalysis in copper nitrite reductase. Similar XFEL studies, intended to out-run radiation damage, will also soon appear.
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Affiliation(s)
- John Spence
- Physics, Arizona State University, Rural Rd, Tempe, 85287-1504, USA
| | - Eaton Lattman
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203-1101, USA
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22
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Abstract
A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last twenty years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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23
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Stepanenko OV, Baloban M, Bublikov GS, Shcherbakova DM, Stepanenko OV, Turoverov KK, Kuznetsova IM, Verkhusha VV. Allosteric effects of chromophore interaction with dimeric near-infrared fluorescent proteins engineered from bacterial phytochromes. Sci Rep 2016; 6:18750. [PMID: 26725513 PMCID: PMC4698714 DOI: 10.1038/srep18750] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/25/2015] [Indexed: 01/02/2023] Open
Abstract
Fluorescent proteins (FPs) engineered from bacterial phytochromes attract attention as probes for in vivo imaging due to their near-infrared (NIR) spectra and use of available in mammalian cells biliverdin (BV) as chromophore. We studied spectral properties of the iRFP670, iRFP682 and iRFP713 proteins and their mutants having Cys residues able to bind BV either in both PAS (Cys15) and GAF (Cys256) domains, in one of these domains, or without these Cys residues. We show that the absorption and fluorescence spectra and the chromophore binding depend on the location of the Cys residues. Compared with NIR FPs in which BV covalently binds to Cys15 or those that incorporate BV noncovalently, the proteins with BV covalently bound to Cys256 have blue-shifted spectra and higher quantum yield. In dimeric NIR FPs without Cys15, the covalent binding of BV to Сys256 in one monomer allosterically inhibits the covalent binding of BV to the other monomer, whereas the presence of Cys15 allosterically promotes BV binding to Cys256 in both monomers. The NIR FPs with both Cys residues have the narrowest blue-shifted spectra and the highest quantum yield. Our analysis resulted in the iRFP713/Val256Cys protein with the highest brightness in mammalian cells among available NIR FPs.
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Affiliation(s)
- Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russian Federation
| | - Mikhail Baloban
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Grigory S Bublikov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russian Federation
| | - Daria M Shcherbakova
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russian Federation
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russian Federation.,Department of Biophysics, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 194064, Russian Federation
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russian Federation
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
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24
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Gupta PK, Meuwly M. Ligand and interfacial dynamics in a homodimeric hemoglobin. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:012003. [PMID: 26958581 PMCID: PMC4760971 DOI: 10.1063/1.4940228] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/08/2016] [Indexed: 05/18/2023]
Abstract
The structural dynamics of dimeric hemoglobin (HbI) from Scapharca inaequivalvis in different ligand-binding states is studied from atomistic simulations on the μs time scale. The intermediates are between the fully ligand-bound (R) and ligand-free (T) states. Tertiary structural changes, such as rotation of the side chain of Phe97, breaking of the Lys96-heme salt bridge, and the Fe-Fe separation, are characterized and the water dynamics along the R-T transition is analyzed. All these properties for the intermediates are bracketed by those determined experimentally for the fully ligand-bound and ligand-free proteins, respectively. The dynamics of the two monomers is asymmetric on the 100 ns timescale. Several spontaneous rotations of the Phe97 side chain are observed which suggest a typical time scale of 50-100 ns for this process. Ligand migration pathways include regions between the B/G and C/G helices and, if observed, take place in the 100 ns time scale.
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Affiliation(s)
- Prashant Kumar Gupta
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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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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Moffat K. 66 Design of light-sensitive molecules for time-resolved crystallography and optogenetics. J Biomol Struct Dyn 2015. [DOI: 10.1080/07391102.2015.1032683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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27
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Affiliation(s)
- John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85282, USA
| | - Henry N Chapman
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg 22607, Germany
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28
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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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29
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Wang D, Weierstall U, Pollack L, Spence J. Double-focusing mixing jet for XFEL study of chemical kinetics. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:1364-6. [PMID: 25343806 PMCID: PMC4211133 DOI: 10.1107/s160057751401858x] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 08/14/2014] [Indexed: 05/19/2023]
Abstract
Several liquid sample injection methods have been developed to satisfy the requirements for serial femtosecond X-ray nanocrystallography, which enables radiation-damage-free determination of molecular structure at room temperature. Time-resolved nanocrystallography would combine structure analysis with chemical kinetics by determining the structures of the transient states and chemical kinetic mechanisms simultaneously. A windowless liquid mixing jet device has been designed for this purpose. It achieves fast uniform mixing of substrates and enzymes in the jet within 250 µs, with an adjustable delay between mixing and probing by the X-ray free-electron laser beam of up to 1 s for each frame of a `movie'. The principle of the liquid mixing jet device is illustrated using numerical simulation, and experimental results are presented using a fluorescent dye.
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Affiliation(s)
- Dingjie Wang
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, 254 Clark Hall, Ithaca, NY 14853, USA
| | - John Spence
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
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30
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