1
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Yoniles J, Summers JA, Zielinski KA, Antolini C, Panjalingam M, Lisova S, Moss FR, Di Perna MA, Kupitz C, Hunter MS, Pollack L, Wakatsuki S, Dahlberg PD. Time-resolved cryogenic electron tomography for the study of transient cellular processes. Mol Biol Cell 2024; 35:mr4. [PMID: 38717434 PMCID: PMC11244162 DOI: 10.1091/mbc.e24-01-0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/15/2024] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
Cryogenic electron tomography (cryo-ET) is the highest resolution imaging technique applicable to the life sciences, enabling subnanometer visualization of specimens preserved in their near native states. The rapid plunge freezing process used to prepare samples lends itself to time-resolved studies, which researchers have pursued for in vitro samples for decades. Here, we focus on developing a freezing apparatus for time-resolved studies in situ. The device mixes cellular samples with solution-phase stimulants before spraying them directly onto an electron microscopy grid that is transiting into cryogenic liquid ethane. By varying the flow rates of cell and stimulant solutions within the device, we can control the reaction time from tens of milliseconds to over a second before freezing. In a proof-of-principle demonstration, the freezing method is applied to a model bacterium, Caulobacter crescentus, mixed with an acidic buffer. Through cryo-ET we resolved structural changes throughout the cell, including surface-layer protein dissolution, outer membrane deformation, and cytosolic rearrangement, all within 1.5 s of reaction time. This new approach, Time-Resolved cryo-ET (TR-cryo-ET), enhances the capabilities of cryo-ET by incorporating a subsecond temporal axis and enables the visualization of induced structural changes at the molecular, organelle, or cellular level.
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Affiliation(s)
- Joseph Yoniles
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305
| | - Jacob A. Summers
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Kara A. Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Cali Antolini
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | | | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Frank R. Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | | | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Peter D. Dahlberg
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
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2
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Mous S, Poitevin F, Hunter MS, Asthagiri DN, Beck TL. Structural biology in the age of X-ray free-electron lasers and exascale computing. Curr Opin Struct Biol 2024; 86:102808. [PMID: 38547555 DOI: 10.1016/j.sbi.2024.102808] [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: 11/09/2023] [Revised: 02/07/2024] [Accepted: 03/07/2024] [Indexed: 05/19/2024]
Abstract
Serial femtosecond X-ray crystallography has emerged as a powerful method for investigating biomolecular structure and dynamics. With the new generation of X-ray free-electron lasers, which generate ultrabright X-ray pulses at megahertz repetition rates, we can now rapidly probe ultrafast conformational changes and charge movement in biomolecules. Over the last year, another innovation has been the deployment of Frontier, the world's first exascale supercomputer. Synergizing extremely high repetition rate X-ray light sources and exascale computing has the potential to accelerate discovery in biomolecular sciences. Here we outline our perspective on each of these remarkable innovations individually, and the opportunities and challenges in yoking them within an integrated research infrastructure.
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Affiliation(s)
- Sandra Mous
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA
| | - Frédéric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA.
| | - Dilipkumar N Asthagiri
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, 37830-6012, TN, USA
| | - Thomas L Beck
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, 37830-6012, TN, USA.
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3
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Lee Y, Oang KY, Kim D, Ihee H. A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:031301. [PMID: 38706888 PMCID: PMC11065455 DOI: 10.1063/4.0000249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
The structure of molecules, particularly the dynamic changes in structure, plays an essential role in understanding physical and chemical phenomena. Time-resolved (TR) scattering techniques serve as crucial experimental tools for studying structural dynamics, offering direct sensitivity to molecular structures through scattering signals. Over the past decade, the advent of x-ray free-electron lasers (XFELs) and mega-electron-volt ultrafast electron diffraction (MeV-UED) facilities has ushered TR scattering experiments into a new era, garnering significant attention. In this review, we delve into the basic principles of TR scattering experiments, especially focusing on those that employ x-rays and electrons. We highlight the variations in experimental conditions when employing x-rays vs electrons and discuss their complementarity. Additionally, cutting-edge XFELs and MeV-UED facilities for TR x-ray and electron scattering experiments and the experiments performed at those facilities are reviewed. As new facilities are constructed and existing ones undergo upgrades, the landscape for TR x-ray and electron scattering experiments is poised for further expansion. Through this review, we aim to facilitate the effective utilization of these emerging opportunities, assisting researchers in delving deeper into the intricate dynamics of molecular structures.
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Affiliation(s)
| | - Key Young Oang
- Radiation Center for Ultrafast Science, Korea Atomic Energy Research Institute (KAERI), Daejeon 34057, South Korea
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4
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Biener G, Malla TN, Schwander P, Schmidt M. KINNTREX: a neural network to unveil protein mechanisms from time-resolved X-ray crystallography. IUCRJ 2024; 11:405-422. [PMID: 38662478 PMCID: PMC11067743 DOI: 10.1107/s2052252524002392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/12/2024] [Indexed: 05/04/2024]
Abstract
Here, a machine-learning method based on a kinetically informed neural network (NN) is introduced. The proposed method is designed to analyze a time series of difference electron-density maps from a time-resolved X-ray crystallographic experiment. The method is named KINNTREX (kinetics-informed NN for time-resolved X-ray crystallography). To validate KINNTREX, multiple realistic scenarios were simulated with increasing levels of complexity. For the simulations, time-resolved X-ray data were generated that mimic data collected from the photocycle of the photoactive yellow protein. KINNTREX only requires the number of intermediates and approximate relaxation times (both obtained from a singular valued decomposition) and does not require an assumption of a candidate mechanism. It successfully predicts a consistent chemical kinetic mechanism, together with difference electron-density maps of the intermediates that appear during the reaction. These features make KINNTREX attractive for tackling a wide range of biomolecular questions. In addition, the versatility of KINNTREX can inspire more NN-based applications to time-resolved data from biological macromolecules obtained by other methods.
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Affiliation(s)
- Gabriel Biener
- Physics Department, University of Wisconsin–Milwaukee, Milwaukee, WI 53211, USA
| | - Tek Narsingh Malla
- Physics Department, University of Wisconsin–Milwaukee, Milwaukee, WI 53211, USA
| | - Peter Schwander
- Physics Department, University of Wisconsin–Milwaukee, Milwaukee, WI 53211, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin–Milwaukee, Milwaukee, WI 53211, USA
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5
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Stubbs J, Hornsey T, Hanrahan N, Esteban LB, Bolton R, Malý M, Basu S, Orlans J, de Sanctis D, Shim JU, Shaw Stewart PD, Orville AM, Tews I, West J. Droplet microfluidics for time-resolved serial crystallography. IUCRJ 2024; 11:237-248. [PMID: 38446456 PMCID: PMC10916287 DOI: 10.1107/s2052252524001799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
Serial crystallography requires large numbers of microcrystals and robust strategies to rapidly apply substrates to initiate reactions in time-resolved studies. Here, we report the use of droplet miniaturization for the controlled production of uniform crystals, providing an avenue for controlled substrate addition and synchronous reaction initiation. The approach was evaluated using two enzymatic systems, yielding 3 µm crystals of lysozyme and 2 µm crystals of Pdx1, an Arabidopsis enzyme involved in vitamin B6 biosynthesis. A seeding strategy was used to overcome the improbability of Pdx1 nucleation occurring with diminishing droplet volumes. Convection within droplets was exploited for rapid crystal mixing with ligands. Mixing times of <2 ms were achieved. Droplet microfluidics for crystal size engineering and rapid micromixing can be utilized to advance time-resolved serial crystallography.
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Affiliation(s)
- Jack Stubbs
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Theo Hornsey
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Niall Hanrahan
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Luis Blay Esteban
- Universitat Carlemany, Avenida Verge de Canolich, 47, Sant Julia de Loria, Principat d’Andorra AD600, Spain
| | - Rachel Bolton
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Martin Malý
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Shibom Basu
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble 38042, Cedex 9, France
| | - Julien Orlans
- European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, Grenoble 38042, Cedex 9, France
| | - Daniele de Sanctis
- European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, Grenoble 38042, Cedex 9, France
| | - Jung-uk Shim
- Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | | | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Ivo Tews
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Jonathan West
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, United Kingdom
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6
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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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7
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Caramello N, Royant A. From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons. Acta Crystallogr D Struct Biol 2024; 80:60-79. [PMID: 38265875 PMCID: PMC10836399 DOI: 10.1107/s2059798323011002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024] Open
Abstract
Over the last decade, the development of time-resolved serial crystallography (TR-SX) at X-ray free-electron lasers (XFELs) and synchrotrons has allowed researchers to study phenomena occurring in proteins on the femtosecond-to-minute timescale, taking advantage of many technical and methodological breakthroughs. Protein crystals of various sizes are presented to the X-ray beam in either a static or a moving medium. Photoactive proteins were naturally the initial systems to be studied in TR-SX experiments using pump-probe schemes, where the pump is a pulse of visible light. Other reaction initiations through small-molecule diffusion are gaining momentum. Here, selected examples of XFEL and synchrotron time-resolved crystallography studies will be used to highlight the specificities of the various instruments and methods with respect to time resolution, and are compared with cryo-trapping studies.
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Affiliation(s)
- Nicolas Caramello
- Structural Biology Group, European Synchrotron Radiation Facility, 1 Avenue des Martyrs, CS 40220, 38043 Grenoble CEDEX 9, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 1 Avenue des Martyrs, CS 40220, 38043 Grenoble CEDEX 9, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
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8
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Henning RW, Kosheleva I, Šrajer V, Kim IS, Zoellner E, Ranganathan R. BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:014301. [PMID: 38304444 PMCID: PMC10834067 DOI: 10.1063/4.0000238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024]
Abstract
A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods-UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.
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Affiliation(s)
- Robert W. Henning
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Irina Kosheleva
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Vukica Šrajer
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - In-Sik Kim
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Eric Zoellner
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rama Ranganathan
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
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9
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Botha S, Fromme P. Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook. Structure 2023; 31:1306-1319. [PMID: 37898125 PMCID: PMC10842180 DOI: 10.1016/j.str.2023.10.005] [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: 07/18/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/30/2023]
Abstract
Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions.
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Affiliation(s)
- Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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10
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Malla TN, Zielinski K, Aldama L, Bajt S, Feliz D, Hayes B, Hunter M, Kupitz C, Lisova S, Knoska J, Martin-Garcia JM, Mariani V, Pandey S, Poudyal I, Sierra RG, Tolstikova A, Yefanov O, Yoon CH, Ourmazd A, Fromme P, Schwander P, Barty A, Chapman HN, Stojkovic EA, Batyuk A, Boutet S, Phillips GN, Pollack L, Schmidt M. Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam. Nat Commun 2023; 14:5507. [PMID: 37679343 PMCID: PMC10485065 DOI: 10.1038/s41467-023-41246-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/27/2023] [Indexed: 09/09/2023] Open
Abstract
For decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals. Here, we report in atomic detail (between 2.2 and 2.7 Å resolution) by room-temperature, time-resolved crystallography with millisecond time-resolution (with timepoints between 3 ms and 700 ms) how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating, cooperativity, induced fit, and conformational selection all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme noncovalently before reacting to a trans-enamine. This was made possible in part by the application of singular value decomposition to the MISC data using a program that remains functional even if unit cell parameters change up to 3 Å during the reaction.
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Affiliation(s)
- Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Kara Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Luis Aldama
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Sasa Bajt
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Denisse Feliz
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Brendon Hayes
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark Hunter
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christopher Kupitz
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Stella Lisova
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Jose Manuel Martin-Garcia
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
| | - Valerio Mariani
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ishwor Poudyal
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Raymond G Sierra
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Chung Hong Yoon
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Abbas Ourmazd
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, 20 Arizona State University, Tempe, AZ, USA
| | - Peter Schwander
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Anton Barty
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Emina A Stojkovic
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Alexander Batyuk
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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11
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Vakili M, Han H, Schmidt C, Wrona A, Kloos M, de Diego I, Dörner K, Geng T, Kim C, Koua FHM, Melo DVM, Rappas M, Round A, Round E, Sikorski M, Valerio J, Zhou T, Lorenzen K, Schulz J. Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography. J Appl Crystallogr 2023; 56:1038-1045. [PMID: 37555221 PMCID: PMC10405586 DOI: 10.1107/s1600576723004405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/21/2023] [Indexed: 08/10/2023] Open
Abstract
Time-resolved crystallography enables the visualization of protein molecular motion during a reaction. Although light is often used to initiate reactions in time-resolved crystallography, only a small number of proteins can be activated by light. However, many biological reactions can be triggered by the interaction between proteins and ligands. The sample delivery method presented here uses a mix-and-extrude approach based on 3D-printed microchannels in conjunction with a micronozzle. The diffusive mixing enables the study of the dynamics of samples in viscous media. The device design allows mixing of the ligands and protein crystals in 2 to 20 s. The device characterization using a model system (fluorescence quenching of iq-mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within lipidic cubic phase, can be mixed efficiently. The potential of this approach for time-resolved membrane protein crystallography to support the development of new drugs is discussed.
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Affiliation(s)
| | - Huijong Han
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | | | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | - Iñaki de Diego
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | - Tian Geng
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Chan Kim
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | | | - Mathieu Rappas
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | | | - Joana Valerio
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | - Tiankun Zhou
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | | | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
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12
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Kalkan Ö, Kantamneni S, Brings L, Han H, Bean R, Mancuso AP, Koua FHM. Heterologous expression, purification and structural features of native Dictyostelium discoideum dye-decolorizing peroxidase bound to a natively incorporated heme. Front Chem 2023; 11:1220543. [PMID: 37593106 PMCID: PMC10427876 DOI: 10.3389/fchem.2023.1220543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
The Dictyostelium discoideum dye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily. DdDyP catalyzes the H2O2-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism of DdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a heme in vitro reconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing the DdDyP peroxidase in ×2 YT enriched medium at low temperature (20°C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure of DdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of native DdDyP active site and its implication on DyP catalysis.
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Affiliation(s)
- Özlem Kalkan
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Türkiye
| | | | - Lea Brings
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
| | - Huijong Han
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
| | - Richard Bean
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
| | - Adrian P. Mancuso
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, United Kingdom
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13
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Doppler D, Sonker M, Egatz-Gomez A, Grieco A, Zaare S, Jernigan R, Meza-Aguilar JD, Rabbani MT, Manna A, Alvarez RC, Karpos K, Cruz Villarreal J, Nelson G, Yang JH, Carrion J, Morin K, Ketawala GK, Pey AL, Ruiz-Fresneda MA, Pacheco-Garcia JL, Hermoso JA, Nazari R, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Lisova S, Mariani V, Boutet S, Fromme R, Grant TD, Botha S, Fromme P, Kirian RA, Martin-Garcia JM, Ros A. Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme. LAB ON A CHIP 2023; 23:3016-3033. [PMID: 37294576 PMCID: PMC10503405 DOI: 10.1039/d3lc00176h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.
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Affiliation(s)
- Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Alice Grieco
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Sahba Zaare
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Rebecca Jernigan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Jose Domingo Meza-Aguilar
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Mohammad T Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Abhik Manna
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Roberto C Alvarez
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Garrett Nelson
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Jay-How Yang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Jackson Carrion
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Katherine Morin
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Gihan K Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - Miguel Angel Ruiz-Fresneda
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Juan Luis Pacheco-Garcia
- Departamento de Química Física, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Reza Nazari
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Raymond Sierra
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Mark S Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Alexander Batyuk
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Christopher J Kupitz
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Robert E Sublett
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Stella Lisova
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Valerio Mariani
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, 955 Main St, Buffalo, NY, 14203, USA
| | - Sabine Botha
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Richard A Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Jose Manuel Martin-Garcia
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
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14
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Abstract
Proteins guide the flows of information, energy, and matter that make life possible by accelerating transport and chemical reactions, by allosterically modulating these reactions, and by forming dynamic supramolecular assemblies. In these roles, conformational change underlies functional transitions. Time-resolved X-ray diffraction methods characterize these transitions either by directly triggering sequences of functionally important motions or, more broadly, by capturing the motions of which proteins are capable. To date, most successful have been experiments in which conformational change is triggered in light-dependent proteins. In this review, I emphasize emerging techniques that probe the dynamic basis of function in proteins lacking natively light-dependent transitions and speculate about extensions and further possibilities. In addition, I review how the weaker and more distributed signals in these data push the limits of the capabilities of analytical methods. Taken together, these new methods are beginning to establish a powerful paradigm for the study of the physics of protein function.
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Affiliation(s)
- Doeke R Hekstra
- Department of Molecular and Cellular Biology and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA;
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15
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Zielinski KA, Katz AM, Calvey GD, Pabit SA, Milano SK, Aplin C, San Emeterio J, Cerione RA, Pollack L. Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering. IUCRJ 2023; 10:363-375. [PMID: 37144817 PMCID: PMC10161774 DOI: 10.1107/s2052252523003482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/17/2023] [Indexed: 05/06/2023]
Abstract
Advances in time-resolved structural techniques, mainly in macromolecular crystallography and small-angle X-ray scattering (SAXS), allow for a detailed view of the dynamics of biological macromolecules and reactions between binding partners. Of particular promise, are mix-and-inject techniques, which offer a wide range of experimental possibility as microfluidic mixers are used to rapidly combine two species just prior to data collection. Most mix-and-inject approaches rely on diffusive mixers, which have been effectively used within crystallography and SAXS for a variety of systems, but their success is dependent on a specific set of conditions to facilitate fast diffusion for mixing. The use of a new chaotic advection mixer designed for microfluidic applications helps to further broaden the types of systems compatible with time-resolved mixing experiments. The chaotic advection mixer can create ultra-thin, alternating layers of liquid, enabling faster diffusion so that even more slowly diffusing molecules, like proteins or nucleic acids, can achieve fast mixing on timescales relevant to biological reactions. This mixer was first used in UV-vis absorbance and SAXS experiments with systems of a variety of molecular weights, and thus diffusion speeds. Careful effort was also dedicated to making a loop-loading sample-delivery system that consumes as little sample as possible, enabling the study of precious, laboratory-purified samples. The combination of the versatile mixer with low sample consumption opens the door to many new applications for mix-and-inject studies.
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Affiliation(s)
- Kara A. Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York USA
| | - Andrea M. Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York USA
| | - George D. Calvey
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York USA
| | - Suzette A. Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York USA
| | - Shawn K. Milano
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York USA
| | - Cody Aplin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York USA
| | - Josue San Emeterio
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York USA
| | - Richard A. Cerione
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York USA
- Department of Molecular Medicine, Cornell University, Ithaca, New York USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York USA
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16
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Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography. Nat Commun 2023; 14:903. [PMID: 36807348 PMCID: PMC9936131 DOI: 10.1038/s41467-023-36481-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
The binding and release of ligands from their protein targets is central to fundamental biological processes as well as to drug discovery. Photopharmacology introduces chemical triggers that allow the changing of ligand affinities and thus biological activity by light. Insight into the molecular mechanisms of photopharmacology is largely missing because the relevant transitions during the light-triggered reaction cannot be resolved by conventional structural biology. Using time-resolved serial crystallography at a synchrotron and X-ray free-electron laser, we capture the release of the anti-cancer compound azo-combretastatin A4 and the resulting conformational changes in tubulin. Nine structural snapshots from 1 ns to 100 ms complemented by simulations show how cis-to-trans isomerization of the azobenzene bond leads to a switch in ligand affinity, opening of an exit channel, and collapse of the binding pocket upon ligand release. The resulting global backbone rearrangements are related to the action mechanism of microtubule-destabilizing drugs.
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17
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Jernigan RJ, Logeswaran D, Doppler D, Nagaratnam N, Sonker M, Yang JH, Ketawala G, Martin-Garcia JM, Shelby ML, Grant TD, Mariani V, Tolstikova A, Sheikh MZ, Yung MC, Coleman MA, Zaare S, Kaschner EK, Rabbani MT, Nazari R, Zacks MA, Hayes B, Sierra RG, Hunter MS, Lisova S, Batyuk A, Kupitz C, Boutet S, Hansen DT, Kirian RA, Schmidt M, Fromme R, Frank M, Ros A, Chen JJL, Botha S, Fromme P. Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser. Structure 2023; 31:138-151.e5. [PMID: 36630960 PMCID: PMC9830665 DOI: 10.1016/j.str.2022.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/08/2022] [Accepted: 12/14/2022] [Indexed: 01/11/2023]
Abstract
NendoU from SARS-CoV-2 is responsible for the virus's ability to evade the innate immune system by cleaving the polyuridine leader sequence of antisense viral RNA. Here we report the room-temperature structure of NendoU, solved by serial femtosecond crystallography at an X-ray free-electron laser to 2.6 Å resolution. The room-temperature structure provides insight into the flexibility, dynamics, and other intrinsic properties of NendoU, with indications that the enzyme functions as an allosteric switch. Functional studies examining cleavage specificity in solution and in crystals support the uridine-purine cleavage preference, and we demonstrate that enzyme activity is fully maintained in crystal form. Optimizing the purification of NendoU and identifying suitable crystallization conditions set the benchmark for future time-resolved serial femtosecond crystallography studies. This could advance the design of antivirals with higher efficacy in treating coronaviral infections, since drugs that block allosteric conformational changes are less prone to drug resistance.
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Affiliation(s)
- Rebecca J Jernigan
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Dhenugen Logeswaran
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Diandra Doppler
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Nirupa Nagaratnam
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Mukul Sonker
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Jay-How Yang
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Gihan Ketawala
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Jose M Martin-Garcia
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Megan L Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, 955 Main Street, Buffalo, NY 14203, USA
| | - Valerio Mariani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Michelle Z Sheikh
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Mimi Cho Yung
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Sahba Zaare
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Fulton School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Emily K Kaschner
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Mohammad Towshif Rabbani
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Reza Nazari
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Michele A Zacks
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sebastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Debra T Hansen
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Richard A Kirian
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Avenue, Milwaukee, WI 53211, USA
| | - Raimund Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Alexandra Ros
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Julian J-L Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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18
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Hough MA, Prischi F, Worrall JAR. Perspective: Structure determination of protein-ligand complexes at room temperature using X-ray diffraction approaches. Front Mol Biosci 2023; 10:1113762. [PMID: 36756363 PMCID: PMC9899996 DOI: 10.3389/fmolb.2023.1113762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/12/2023] [Indexed: 01/24/2023] Open
Abstract
The interaction between macromolecular proteins and small molecule ligands is an essential component of cellular function. Such ligands may include enzyme substrates, molecules involved in cellular signalling or pharmaceutical drugs. Together with biophysical techniques used to assess the thermodynamic and kinetic properties of ligand binding to proteins, methodology to determine high-resolution structures that enable atomic level interactions between protein and ligand(s) to be directly visualised is required. Whilst such structural approaches are well established with high throughput X-ray crystallography routinely used in the pharmaceutical sector, they provide only a static view of the complex. Recent advances in X-ray structural biology methods offer several new possibilities that can examine protein-ligand complexes at ambient temperature rather than under cryogenic conditions, enable transient binding sites and interactions to be characterised using time-resolved approaches and combine spectroscopic measurements from the same crystal that the structures themselves are determined. This Perspective reviews several recent developments in these areas and discusses new possibilities for applications of these advanced methodologies to transform our understanding of protein-ligand interactions.
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Affiliation(s)
- Michael A. Hough
- School of Life Sciences, University of Essex, Colchester, United Kingdom,Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, United Kingdom,*Correspondence: Michael A. Hough, ; Jonathan A. R. Worrall,
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Jonathan A. R. Worrall
- School of Life Sciences, University of Essex, Colchester, United Kingdom,*Correspondence: Michael A. Hough, ; Jonathan A. R. Worrall,
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19
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Schmidt M, Malla TN, Zielinski K, Aldama L, Bajt S, Feliz D, Hayes B, Hunter M, Kupitz C, Lisova S, Knoska J, Martin-Garcia J, Mariani V, Pandey S, Poudyal I, Sierra R, Tolstikova A, Yefanov O, Yoon CH, Ourmazd A, Fromme P, Schwander P, Barty A, Chapman H, Stojković E, Batyuk A, Boutet S, Phillips G, Pollack L. Heterogeneity in the M. tuberculosis β-Lactamase Inhibition by Sulbactam. RESEARCH SQUARE 2023:rs.3.rs-2334665. [PMID: 36712138 PMCID: PMC9882615 DOI: 10.21203/rs.3.rs-2334665/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
For decades, researchers have been determined to elucidate essential enzymatic functions on the atomic lengths scale by tracing atomic positions in real time. Our work builds on new possibilities unleashed by mix-and-inject serial crystallography (MISC) 1-5 at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals 6 . Here, we report in atomic detail and with millisecond time-resolution how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating 7-9 , cooperativity, induced fit 10,11 and conformational selection 11-13 all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme non-covalently before reacting to a trans- enamine. This was made possible in part by the application of the singular value decomposition 14 to the MISC data using a newly developed program that remains functional even if unit cell parameters change during the reaction.
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20
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Thorne RE. Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization. Acta Crystallogr D Struct Biol 2023; 79:78-94. [PMID: 36601809 PMCID: PMC9815097 DOI: 10.1107/s2059798322011652] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/04/2022] [Indexed: 01/05/2023] Open
Abstract
For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein-solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54, e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.
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Affiliation(s)
- Robert E. Thorne
- Physics Department, Cornell University, Ithaca, NY 14853, USA
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
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21
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Schmidt M. Biological function investigated by time-resolved structure determination. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:010901. [PMID: 36846099 PMCID: PMC9946696 DOI: 10.1063/4.0000177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Inspired by recent progress in time-resolved x-ray crystallography and the adoption of time-resolution by cryo-electronmicroscopy, this article enumerates several approaches developed to become bigger/smaller, faster, and better to gain new insight into the molecular mechanisms of life. This is illustrated by examples where chemical and physical stimuli spawn biological responses on various length and time-scales, from fractions of Ångströms to micro-meters and from femtoseconds to hours.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, USA
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22
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Sonker M, Doppler D, Egatz-Gomez A, Zaare S, Rabbani MT, Manna A, Cruz Villarreal J, Nelson G, Ketawala GK, Karpos K, Alvarez RC, Nazari R, Thifault D, Jernigan R, Oberthür D, Han H, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Poitevin F, Lisova S, Mariani V, Tolstikova A, Boutet S, Messerschmidt M, Meza-Aguilar JD, Fromme R, Martin-Garcia JM, Botha S, Fromme P, Grant TD, Kirian RA, Ros A. Electrically stimulated droplet injector for reduced sample consumption in serial crystallography. BIOPHYSICAL REPORTS 2022; 2:100081. [PMID: 36425668 PMCID: PMC9680787 DOI: 10.1016/j.bpr.2022.100081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
With advances in X-ray free-electron lasers (XFELs), serial femtosecond crystallography (SFX) has enabled the static and dynamic structure determination for challenging proteins such as membrane protein complexes. In SFX with XFELs, the crystals are typically destroyed after interacting with a single XFEL pulse. Therefore, thousands of new crystals must be sequentially introduced into the X-ray beam to collect full data sets. Because of the serial nature of any SFX experiment, up to 99% of the sample delivered to the X-ray beam during its "off-time" between X-ray pulses is wasted due to the intrinsic pulsed nature of all current XFELs. To solve this major problem of large and often limiting sample consumption, we report on improvements of a revolutionary sample-saving method that is compatible with all current XFELs. We previously reported 3D-printed injection devices coupled with gas dynamic virtual nozzles (GDVNs) capable of generating samples containing droplets segmented by an immiscible oil phase for jetting crystal-laden droplets into the path of an XFEL. Here, we have further improved the device design by including metal electrodes inducing electrowetting effects for improved control over droplet generation frequency to stimulate the droplet release to matching the XFEL repetition rate by employing an electrical feedback mechanism. We report the improvements in this electrically triggered segmented flow approach for sample conservation in comparison with a continuous GDVN injection using the microcrystals of lysozyme and 3-deoxy-D-manno-octulosonate 8-phosphate synthase and report the segmented flow approach for sample injection applied at the Macromolecular Femtosecond Crystallography instrument at the Linear Coherent Light Source for the first time.
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Affiliation(s)
- Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Sahba Zaare
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Mohammad T. Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Abhik Manna
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Gihan K. Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Roberto C. Alvarez
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Reza Nazari
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Darren Thifault
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Rebecca Jernigan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | | | - Raymond Sierra
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Mark S. Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Alexander Batyuk
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Christopher J. Kupitz
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Robert E. Sublett
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Frederic Poitevin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Stella Lisova
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Valerio Mariani
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Sebastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - J. Domingo Meza-Aguilar
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Jose M. Martin-Garcia
- Institute Physical-Chemistry Rocasolano, Spanish National Research Council, Madrid, Spain
| | - Sabine Botha
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Thomas D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York
| | - Richard A. Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
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23
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Worrall JAR, Hough MA. Serial femtosecond crystallography approaches to understanding catalysis in iron enzymes. Curr Opin Struct Biol 2022; 77:102486. [PMID: 36274419 DOI: 10.1016/j.sbi.2022.102486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/11/2022] [Accepted: 09/16/2022] [Indexed: 12/14/2022]
Abstract
Enzymes with iron-containing active sites play crucial roles in catalysing a myriad of oxidative reactions essential to aerobic life. Defining the three-dimensional structures of iron enzymes in resting, oxy-bound intermediate and substrate-bound states is particularly challenging, not least because of the extreme susceptibility of the Fe(III) and Fe(IV) redox states to radiation-induced chemistry caused by intense X-ray or electron beams. The availability of novel sources such as X-ray free electron lasers has enabled structures that are effectively free of the effects of radiation-induced chemistry and allows time-resolved structures to be determined. Important to both applications is the ability to obtain in crystallo spectroscopic data to identify the redox state of the iron in any particular structure or timepoint.
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Affiliation(s)
- Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK; Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK.
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24
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Wilamowski M, Sherrell DA, Kim Y, Lavens A, Henning RW, Lazarski K, Shigemoto A, Endres M, Maltseva N, Babnigg G, Burdette SC, Srajer V, Joachimiak A. Time-resolved β-lactam cleavage by L1 metallo-β-lactamase. Nat Commun 2022; 13:7379. [PMID: 36450742 PMCID: PMC9712583 DOI: 10.1038/s41467-022-35029-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
Serial x-ray crystallography can uncover binding events, and subsequent chemical conversions occurring during enzymatic reaction. Here, we reveal the structure, binding and cleavage of moxalactam antibiotic bound to L1 metallo-β-lactamase (MBL) from Stenotrophomonas maltophilia. Using time-resolved serial synchrotron crystallography, we show the time course of β-lactam hydrolysis and determine ten snapshots (20, 40, 60, 80, 100, 150, 300, 500, 2000 and 4000 ms) at 2.20 Å resolution. The reaction is initiated by laser pulse releasing Zn2+ ions from a UV-labile photocage. Two metal ions bind to the active site, followed by binding of moxalactam and the intact β-lactam ring is observed for 100 ms after photolysis. Cleavage of β-lactam is detected at 150 ms and the ligand is significantly displaced. The reaction product adjusts its conformation reaching steady state at 2000 ms corresponding to the relaxed state of the enzyme. Only small changes are observed in the positions of Zn2+ ions and the active site residues. Mechanistic details captured here can be generalized to other MBLs.
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Affiliation(s)
- M Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology of Jagiellonian University, 30387, Krakow, Poland
| | - D A Sherrell
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Y Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - A Lavens
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - R W Henning
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL, 60637, USA
| | - K Lazarski
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - A Shigemoto
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - M Endres
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - N Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - G Babnigg
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - S C Burdette
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - V Srajer
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL, 60637, USA
| | - A Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
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25
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Aplin C, Milano SK, Zielinski KA, Pollack L, Cerione RA. Evolving Experimental Techniques for Structure-Based Drug Design. J Phys Chem B 2022; 126:6599-6607. [PMID: 36029222 PMCID: PMC10161966 DOI: 10.1021/acs.jpcb.2c04344] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-based drug design (SBDD) is a prominent method in rational drug development and has traditionally benefitted from the atomic models of protein targets obtained using X-ray crystallography at cryogenic temperatures. In this perspective, we highlight recent advances in the development of structural techniques that are capable of probing dynamic information about protein targets. First, we discuss advances in the field of X-ray crystallography including serial room-temperature crystallography as a method for obtaining high-resolution conformational dynamics of protein-inhibitor complexes. Next, we look at cryogenic electron microscopy (cryoEM), another high-resolution technique that has recently been used to study proteins and protein complexes that are too difficult to crystallize. Finally, we present small-angle X-ray scattering (SAXS) as a potential high-throughput screening tool to identify inhibitors that target protein complexes and protein oligomerization.
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Affiliation(s)
- Cody Aplin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Shawn K Milano
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kara A Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Richard A Cerione
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Department of Molecular Medicine, Cornell University, Ithaca, New York 14853, United States
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26
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Hammarström B, Lane TJ, Batili H, Sierra R, Wiklund M, Sellberg JA. Acoustic Focusing of Protein Crystals for In-Line Monitoring and Up-Concentration during Serial Crystallography. Anal Chem 2022; 94:12645-12656. [PMID: 36054318 PMCID: PMC9494305 DOI: 10.1021/acs.analchem.2c01701] [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] [Indexed: 11/30/2022]
Abstract
Serial femtosecond crystallography (SFX) has become one of the standard techniques at X-ray free-electron lasers (XFELs) to obtain high-resolution structural information from microcrystals of proteins. Nevertheless, reliable sample delivery is still often limiting data collection, as microcrystals can clog both field- and flow-focusing nozzles despite in-line filters. In this study, we developed acoustic 2D focusing of protein microcrystals in capillaries that enables real-time online characterization of crystal size and shape in the sample delivery line after the in-line filter. We used a piezoelectric actuator to create a standing wave perpendicular to the crystal flow, which focused lysozyme microcrystals into a single line inside a silica capillary so that they can be imaged using a high-speed camera. We characterized the acoustic contrast factor, focus size, and the coaxial flow lines and developed a splitting union that enables up-concentration to at least a factor of five. The focus size, flow rates, and geometry may enable an upper limit of up-concentration as high as 200 fold. The novel feedback and concentration control could be implemented for serial crystallography at synchrotrons with minor modifications. It will also aid the development of improved sample delivery systems that will increase SFX data collection rates at XFELs, with potential applications to many proteins that can only be purified and crystallized in small amounts.
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Affiliation(s)
- Björn Hammarström
- Department of Applied Physics, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Thomas J Lane
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Hazal Batili
- Department of Applied Physics, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Raymond Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Martin Wiklund
- Department of Applied Physics, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Jonas A Sellberg
- Department of Applied Physics, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
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27
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Barends TR, Stauch B, Cherezov V, Schlichting I. Serial femtosecond crystallography. NATURE REVIEWS. METHODS PRIMERS 2022; 2:59. [PMID: 36643971 PMCID: PMC9833121 DOI: 10.1038/s43586-022-00141-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
With the advent of X-ray Free Electron Lasers (XFELs), new, high-throughput serial crystallography techniques for macromolecular structure determination have emerged. Serial femtosecond crystallography (SFX) and related methods provide possibilities beyond canonical, single-crystal rotation crystallography by mitigating radiation damage and allowing time-resolved studies with unprecedented temporal resolution. This primer aims to assist structural biology groups with little or no experience in serial crystallography planning and carrying out a successful SFX experiment. It discusses the background of serial crystallography and its possibilities. Microcrystal growth and characterization methods are discussed, alongside techniques for sample delivery and data processing. Moreover, it gives practical tips for preparing an experiment, what to consider and do during a beamtime and how to conduct the final data analysis. Finally, the Primer looks at various applications of SFX, including structure determination of membrane proteins, investigation of radiation damage-prone systems and time-resolved studies.
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Affiliation(s)
- Thomas R.M. Barends
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Benjamin Stauch
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Vadim Cherezov
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Ilme Schlichting
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany,
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28
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Malla TN, Schmidt M. Transient state measurements on proteins by time-resolved crystallography. Curr Opin Struct Biol 2022; 74:102376. [DOI: 10.1016/j.sbi.2022.102376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022]
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29
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Foos N, Rizk M, Nanao MH. Single-support serial isomorphous replacement phasing. Acta Crystallogr D Struct Biol 2022; 78:716-724. [PMID: 35647919 PMCID: PMC9159287 DOI: 10.1107/s2059798322003977] [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: 08/24/2021] [Accepted: 04/11/2022] [Indexed: 11/11/2022] Open
Abstract
A simple method for serial single isomorphous replacement, which exploits natural differences in heavy-atom occupancy, is presented. The use of single isomorphous replacement (SIR) has become less widespread due to difficulties in sample preparation and the identification of isomorphous native and derivative data sets. Non-isomorphism becomes even more problematic in serial experiments, because it adds natural inter-crystal non-isomorphism to heavy-atom-soaking-induced non-isomorphism. Here, a method that can successfully address these issues (and indeed can benefit from differences in heavy-atom occupancy) and additionally significantly simplifies the SIR experiment is presented. A single heavy-atom soak into a microcrystalline slurry is performed, followed by automated serial data collection of partial data sets. This produces a set of data collections with a gradient of heavy-atom occupancies, which are reflected in differential merging statistics. These differences can be exploited by an optimized genetic algorithm to segregate the pool of data sets into ‘native’ and ‘derivative’ groups, which can then be used to successfully determine phases experimentally by SIR.
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30
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Vakili M, Bielecki J, Knoška J, Otte F, Han H, Kloos M, Schubert R, Delmas E, Mills G, de Wijn R, Letrun R, Dold S, Bean R, Round A, Kim Y, Lima FA, Dörner K, Valerio J, Heymann M, Mancuso AP, Schulz J. 3D printed devices and infrastructure for liquid sample delivery at the European XFEL. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:331-346. [PMID: 35254295 PMCID: PMC8900844 DOI: 10.1107/s1600577521013370] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
The Sample Environment and Characterization (SEC) group of the European X-ray Free-Electron Laser (EuXFEL) develops sample delivery systems for the various scientific instruments, including systems for the injection of liquid samples that enable serial femtosecond X-ray crystallography (SFX) and single-particle imaging (SPI) experiments, among others. For rapid prototyping of various device types and materials, sub-micrometre precision 3D printers are used to address the specific experimental conditions of SFX and SPI by providing a large number of devices with reliable performance. This work presents the current pool of 3D printed liquid sample delivery devices, based on the two-photon polymerization (2PP) technique. These devices encompass gas dynamic virtual nozzles (GDVNs), mixing-GDVNs, high-viscosity extruders (HVEs) and electrospray conical capillary tips (CCTs) with highly reproducible geometric features that are suitable for time-resolved SFX and SPI experiments at XFEL facilities. Liquid sample injection setups and infrastructure on the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument are described, this being the instrument which is designated for biological structure determination at the EuXFEL.
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Affiliation(s)
| | | | - Juraj Knoška
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Florian Otte
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Physics, TU Dortmund, Otto-Hahn-Straße 4, 44221 Dortmund, Germany
| | - Huijong Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Elisa Delmas
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Grant Mills
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Simon Dold
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- School of Chemical and Physical Sciences, Keele University, Staffordshire ST5 5AZ, United Kingdom
| | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Michael Heymann
- Institute for Biomaterials and Biomolecular Systems (IBBS), University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Adrian P. Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne 3086, Australia
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31
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Potential of Time-Resolved Serial Femtosecond Crystallography Using High Repetition Rate XFEL Sources. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052551] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This perspective review describes emerging techniques and future opportunities for time-resolved serial femtosecond crystallography (TR-SFX) experiments using high repetition rate XFEL sources. High repetition rate sources are becoming more available with the European XFEL in operation and the recently upgraded LCLS-II will be available in the near future. One efficient use of these facilities for TR-SFX relies on pump–probe experiments using a laser to trigger a reaction of light-responsive proteins or mix-and-inject experiments for light-unresponsive proteins. With the view to widen the application of TR-SFX, the promising field of photocaged compounds is under development, which allows the very fast laser triggering of reactions that is no longer limited to naturally light-responsive samples. In addition to reaction triggering, a key concern when performing an SFX experiment is efficient sample usage, which is a main focus of new high repetition rate-compatible sample delivery methods.
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32
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Doppler D, Rabbani MT, Letrun R, Cruz Villarreal J, Kim DH, Gandhi S, Egatz-Gomez A, Sonker M, Chen J, Koua FHM, Yang J, Youssef M, Mazalova V, Bajt S, Shelby ML, Coleman MA, Wiedorn MO, Knoska J, Schön S, Sato T, Hunter MS, Hosseinizadeh A, Kuptiz C, Nazari R, Alvarez RC, Karpos K, Zaare S, Dobson Z, Discianno E, Zhang S, Zook JD, Bielecki J, de Wijn R, Round AR, Vagovic P, Kloos M, Vakili M, Ketawala GK, Stander NE, Olson TL, Morin K, Mondal J, Nguyen J, Meza-Aguilar JD, Kodis G, Vaiana S, Martin-Garcia JM, Mariani V, Schwander P, Schmidt M, Messerschmidt M, Ourmazd A, Zatsepin N, Weierstall U, Bruce BD, Mancuso AP, Grant T, Barty A, Chapman HN, Frank M, Fromme R, Spence JCH, Botha S, Fromme P, Kirian RA, Ros A. Co-flow injection for serial crystallography at X-ray free-electron lasers. J Appl Crystallogr 2022; 55:1-13. [PMID: 35153640 PMCID: PMC8805165 DOI: 10.1107/s1600576721011079] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/22/2021] [Indexed: 02/03/2023] Open
Abstract
Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macro-molecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.
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Affiliation(s)
- Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mohammad T. Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | | | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Dai Hyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Sahir Gandhi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Joe Chen
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Faisal H. M. Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Jayhow Yang
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mohamed Youssef
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Victoria Mazalova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Saša Bajt
- Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Megan L. Shelby
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Matt A. Coleman
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Silvan Schön
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Christopher Kuptiz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Reza Nazari
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Roberto C. Alvarez
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sahba Zaare
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Zachary Dobson
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Erin Discianno
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Shangji Zhang
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - James D. Zook
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | | | | | - Adam R. Round
- European XFEL, Schenefeld, Germany,School of Chemical and Physical Sciences, Keele University, Staffordshire, UK
| | - Patrik Vagovic
- European XFEL, Schenefeld, Germany,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | | | - Gihan K. Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Natasha E. Stander
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Tien L. Olson
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Katherine Morin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jyotirmory Mondal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jonathan Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - José Domingo Meza-Aguilar
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,European XFEL, Schenefeld, Germany
| | - Gerdenis Kodis
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sara Vaiana
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Jose M. Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Crystallography and Structural Biology, Institute of Physical Chemistry ‘Rocasolano’, CSIC, Madrid, Spain
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Uwe Weierstall
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Barry D. Bruce
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Adrian P. Mancuso
- European XFEL, Schenefeld, Germany,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Thomas Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - John C. H. Spence
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sabine Botha
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Richard A. Kirian
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Correspondence e-mail:
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33
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Abstract
Serial crystallography (SX) is an emerging technique to determine macromolecules at room temperature. SX with a pump–probe experiment provides the time-resolved dynamics of target molecules. SX has developed rapidly over the past decade as a technique that not only provides room-temperature structures with biomolecules, but also has the ability to time-resolve their molecular dynamics. The serial femtosecond crystallography (SFX) technique using an X-ray free electron laser (XFEL) has now been extended to serial synchrotron crystallography (SSX) using synchrotron X-rays. The development of a variety of sample delivery techniques and data processing programs is currently accelerating SX research, thereby increasing the research scope. In this editorial, I briefly review some of the experimental techniques that have contributed to advances in the field of SX research and recent major research achievements. This Special Issue will contribute to the field of SX research.
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34
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Garratt RC. Protein structure, dynamics, and function-a 20th IUPAB Congress symposium. Biophys Rev 2021; 13:867-869. [PMID: 35059010 PMCID: PMC8724499 DOI: 10.1007/s12551-021-00889-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 10/19/2022] Open
Abstract
A wide range of topics was raised by the four invited speakers who took part in the session on protein structure, dynamics, and function during the 20th IUPAB Congress. Most of the emphasis was placed on understanding the underlying biological phenomena of interest although applications in drug development were also mentioned. For both these purposes, it was clear that a complete description of the dynamics of the system was as important as the structures themselves. The subjects covered included antibiotic peptides, sodium channels, the synthesis of the bacterial cell wall, and protein dynamics using X-FELs.
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Affiliation(s)
- Richard C. Garratt
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
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