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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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2
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Shoeman RL, Hartmann E, Schlichting I. Growing and making nano- and microcrystals. Nat Protoc 2023; 18:854-882. [PMID: 36451055 DOI: 10.1038/s41596-022-00777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 08/22/2022] [Indexed: 12/02/2022]
Abstract
Thanks to recent technological advances in X-ray and micro-electron diffraction and solid-state NMR, structural information can be obtained by using much smaller crystals. Thus, microcrystals have become a valuable commodity rather than a mere stepping stone toward obtaining macroscopic crystals. Microcrystals are particularly useful for structure determination using serial data collection approaches at synchrotrons and X-ray free-electron lasers. The latter's enormous peak brilliance and short X-ray pulse duration mean that structural information can be obtained before the effects of radiation damage are seen; these properties also facilitate time-resolved crystallography. To establish defined reaction initiation conditions, microcrystals with a desired and narrow size distribution are critical. Here, we describe milling and seeding techniques as well as filtration approaches for the reproducible and size-adjustable preparation of homogeneous nano- and microcrystals. Nanocrystals and crystal seeds can be obtained by milling using zirconium beads and the BeadBug homogenizer; fragmentation of large crystals yields micro- or nanocrystals by flowing crystals through stainless steel filters by using an HPLC pump. The approaches can be scaled to generate micro- to milliliter quantities of microcrystals, starting from macroscopic crystals. The procedure typically takes 3-5 d, including the time required to grow the microcrystals.
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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: 26] [Impact Index Per Article: 13.0] [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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4
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Nakatsu T. What Kind of Measurements Can Be Made with an X-ray Free Electron Laser at SACLA? YAKUGAKU ZASSHI 2022; 142:479-485. [DOI: 10.1248/yakushi.21-00203-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Toru Nakatsu
- Graduate School of Pharmaceutical Sciences, Kyoto University
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5
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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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Nam Y, Keefer D, Nenov A, Conti I, Aleotti F, Segatta F, Lee JY, Garavelli M, Mukamel S. Conical Intersection Passages of Molecules Probed by X-ray Diffraction and Stimulated Raman Spectroscopy. J Phys Chem Lett 2021; 12:12300-12309. [PMID: 34931839 DOI: 10.1021/acs.jpclett.1c03814] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Conical intersections (CoIns) play an important role in ultrafast relaxation channels. Their monitoring remains a formidable experimental challenge. We theoretically compare the probing of the S2 → S1 CoIn passage in 4-thiouracil by monitoring its vibronic coherences, using off-resonant X-ray-stimulated Raman spectroscopy (TRUECARS) and time-resolved X-ray diffraction (TRXD). The quantum nuclear wavepacket (WP) dynamics provides an accurate picture of the photoinduced dynamics. Upon photoexcitation, the WP oscillates among the Franck-Condon point, the S2 minimum, and the CoIn with a 70 fs period. A vibronic coherence first emerges at 20 fs and can be observed until the S2 state is fully depopulated. The distribution of the vibronic frequencies involved in the coherence is recorded by the TRUECARS spectrogram. The TRXD signal provides spatial images of electron densities associated with the CoIn. In combination, the two signals provide a complementary picture of the nonadiabatic passage, which helps in the study of the underlying photophysics in thiobases.
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Affiliation(s)
- Yeonsig Nam
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
- Convergence Research Center for Energy and Environmental Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Daniel Keefer
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Flavia Aleotti
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Jin Yong Lee
- Convergence Research Center for Energy and Environmental Sciences, Sungkyunkwan University, Suwon 16419, Korea
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Korea
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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7
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Imaging conical intersection dynamics during azobenzene photoisomerization by ultrafast X-ray diffraction. Proc Natl Acad Sci U S A 2021; 118:2022037118. [PMID: 33436412 DOI: 10.1073/pnas.2022037118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
X-ray diffraction is routinely used for structure determination of stationary molecular samples. Modern X-ray photon sources, e.g., from free-electron lasers, enable us to add temporal resolution to these scattering events, thereby providing a movie of atomic motions. We simulate and decipher the various contributions to the X-ray diffraction pattern for the femtosecond isomerization of azobenzene, a textbook photochemical process. A wealth of information is encoded besides real-time monitoring of the molecular charge density for the cis to trans isomerization. In particular, vibronic coherences emerge at the conical intersection, contributing to the total diffraction signal by mixed elastic and inelastic photon scattering. They cause distinct phase modulations in momentum space, which directly reflect the real-space phase modulation of the electronic transition density during the nonadiabatic passage. To overcome the masking by the intense elastic scattering contributions from the electronic populations in the total diffraction signal, we discuss how this information can be retrieved, e.g., by employing very hard X-rays to record large scattering momentum transfers.
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Nguyen C, Gonen T. Beyond protein structure determination with MicroED. Curr Opin Struct Biol 2020; 64:51-58. [PMID: 32610218 PMCID: PMC7321661 DOI: 10.1016/j.sbi.2020.05.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022]
Abstract
Microcrystal electron diffraction (MicroED) was first coined and developed in 2013 at the Janelia Research Campus as a new modality in electron cryomicroscopy (cryoEM). Since then, MicroED has not only made important contributions in pushing the resolution limits of cryoEM protein structure characterization but also of peptides, small-organic and inorganic molecules, and natural-products that have resisted structure determination by other methods. This review showcases important recent developments in MicroED, highlighting the importance of the technique in fields of studies beyond protein structure determination where MicroED is beginning to have paradigm shifting roles.
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Affiliation(s)
- Chi Nguyen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA90095, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA90095, United States; Department of Physiology, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA90095, United States; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA90095, United States.
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9
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Cheng R, Huang C, Hennig M, Nar H, Schnapp G. In situ
crystallography as an emerging method for structure solution of membrane proteins: the case of CCR2A. FEBS J 2019; 287:866-873. [DOI: 10.1111/febs.15098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/10/2019] [Accepted: 10/15/2019] [Indexed: 12/27/2022]
Affiliation(s)
| | - Chia‐Ying Huang
- Swiss Light Source Paul Scherrer Institute Villigen Switzerland
| | | | - Herbert Nar
- Boehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Gisela Schnapp
- Boehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
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10
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The cryo-EM method microcrystal electron diffraction (MicroED). Nat Methods 2019; 16:369-379. [PMID: 31040436 PMCID: PMC6568260 DOI: 10.1038/s41592-019-0395-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 03/25/2019] [Indexed: 01/07/2023]
Abstract
In 2013 we established a cryo-electron microscopy (cryo-EM) technique called microcrystal electron diffraction (MicroED). Since that time, data collection and analysis schemes have been fine-tuned, and structures for more than 40 different proteins, oligopeptides and organic molecules have been determined. Here we review the MicroED technique and place it in context with other structure-determination methods. We showcase example structures solved by MicroED and provide practical advice to prospective users.
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Abstract
A review that summarizes the most recent technological developments in the field of ultrafast structural dynamics with focus on the use of ultrashort X-ray and electron pulses follows. Atomistic views of chemical processes and phase transformations have long been the exclusive domain of computer simulators. The advent of femtosecond (fs) hard X-ray and fs-electron diffraction techniques made it possible to bring such a level of scrutiny to the experimental area. The following review article provides a summary of the main ultrafast techniques that enabled the generation of atomically resolved movies utilizing ultrashort X-ray and electron pulses. Recent advances are discussed with emphasis on synchrotron-based methods, tabletop fs-X-ray plasma sources, ultrabright fs-electron diffractometers, and timing techniques developed to further improve the temporal resolution and fully exploit the use of intense and ultrashort X-ray free electron laser (XFEL) pulses.
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12
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I Ciftci H, G Sierra R, Yoon CH, Su Z, Tateishi H, Koga R, Kotaro K, Yumoto F, Senda T, Liang M, Wakatsuki S, Otsuka M, Fujita M, DeMirci H. Serial Femtosecond X-Ray Diffraction of HIV-1 Gag MA-IP6 Microcrystals at Ambient Temperature. Int J Mol Sci 2019; 20:ijms20071675. [PMID: 30987231 PMCID: PMC6479536 DOI: 10.3390/ijms20071675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/22/2019] [Accepted: 04/01/2019] [Indexed: 01/24/2023] Open
Abstract
The Human immunodeficiency virus-1 (HIV-1) matrix (MA) domain is involved in the highly regulated assembly process of the virus particles that occur at the host cell’s plasma membrane. High-resolution structures of the MA domain determined using cryo X-ray crystallography have provided initial insights into the possible steps in the viral assembly process. However, these structural studies have relied on large and frozen crystals in order to reduce radiation damage caused by the intense X-rays. Here, we report the first X-ray free-electron laser (XFEL) study of the HIV-1 MA domain’s interaction with inositol hexaphosphate (IP6), a phospholipid headgroup mimic. We also describe the purification, characterization and microcrystallization of two MA crystal forms obtained in the presence of IP6. In addition, we describe the capabilities of serial femtosecond X-ray crystallography (SFX) using an XFEL to elucidate the diffraction data of MA-IP6 complex microcrystals in liquid suspension at ambient temperature. Two different microcrystal forms of the MA-IP6 complex both diffracted to beyond 3.5 Å resolution, demonstrating the feasibility of using SFX to study the complexes of MA domain of HIV-1 Gag polyprotein with IP6 at near-physiological temperatures. Further optimization of the experimental and data analysis procedures will lead to better understanding of the MA domain of HIV-1 Gag and IP6 interaction at high resolution and will provide basis for optimization of the lead compounds for efficient inhibition of the Gag protein recruitment to the plasma membrane prior to virion formation.
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Affiliation(s)
- Halil I Ciftci
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan.
- Department of Bioorganic Medicinal Chemistry, School of Pharmacy, Kumamoto University, Kumamoto 862-0973, Japan.
- Stanford PULSE Institute, 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.
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
| | - Hiroshi Tateishi
- Department of Bioorganic Medicinal Chemistry, School of Pharmacy, Kumamoto University, Kumamoto 862-0973, Japan.
| | - Ryoko Koga
- Department of Bioorganic Medicinal Chemistry, School of Pharmacy, Kumamoto University, Kumamoto 862-0973, Japan.
| | - Koiwai Kotaro
- Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0034, Japan.
| | - Fumiaki Yumoto
- Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0034, Japan.
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0034, Japan.
| | - Mengling Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Soichi Wakatsuki
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Masami Otsuka
- Department of Bioorganic Medicinal Chemistry, School of Pharmacy, Kumamoto University, Kumamoto 862-0973, Japan.
| | - Mikako Fujita
- Research Institute for Drug Discovery, School of Pharmacy, Kumamoto University, Kumamoto 862-0973, Japan.
| | - Hasan DeMirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
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13
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Mosslehy W, Voskoboynikova N, Colbasevici A, Ricke A, Klose D, Klare JP, Mulkidjanian AY, Steinhoff HJ. Conformational Dynamics of Sensory Rhodopsin II in Nanolipoprotein and Styrene-Maleic Acid Lipid Particles. Photochem Photobiol 2019; 95:1195-1204. [PMID: 30849183 DOI: 10.1111/php.13096] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/03/2019] [Indexed: 02/01/2023]
Abstract
Styrene-maleic acid lipid particles (SMALPs) provide stable water-soluble nanocontainers for lipid-encased membrane proteins. Possible effects of the SMA-stabilized lipid environment on the interaction dynamics between functionally coupled membrane proteins remain to be elucidated. The photoreceptor sensory rhodopsin II, NpSRII and its cognate transducer, NpHtrII, of Natronomonas pharaonis form a transmembrane complex, NpSRII2 /NpHtrII2 that plays a key role in negative phototaxis and provides a unique model system to study the light-induced transfer of a conformational signal between two integral membrane proteins. Photon absorption induces transient structural changes in NpSRII comprising an outward movement of helix F that cause further conformational alterations in NpHtrII. We applied site-directed spin labeling and time-resolved optical and EPR spectroscopy to compare the conformational dynamics of NpSRII2 /NpHtrII2 reconstituted in SMALPs with that of nanolipoprotein particle and liposome preparations. NpSRII and NpSRII2 /NpHtrII2 show similar photocycles in liposomes and nanolipoprotein particles. An accelerated decay of the M photointermediate found for SMALPs can be explained by a high local proton concentration provided by the carboxylic groups of the SMA polymer. Light-induced large-scale conformational changes of NpSRII2 /NpHtrII2 observed in liposomes and nanolipoprotein particles are affected in SMALPs, indicating restrictions of the protein's conformational freedom.
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Affiliation(s)
- Wageiha Mosslehy
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | | | | | - Adrian Ricke
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Daniel Klose
- Department of Physics, University of Osnabrück, Osnabrück, Germany.,Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Johann P Klare
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Armen Y Mulkidjanian
- Department of Physics, University of Osnabrück, Osnabrück, Germany.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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14
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Nastou KC, Batskinis MA, Litou ZI, Hamodrakas SJ, Iconomidou VA. Analysis of Single-Nucleotide Polymorphisms in Human Voltage-Gated Ion Channels. J Proteome Res 2019; 18:2310-2320. [DOI: 10.1021/acs.jproteome.9b00121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Katerina C. Nastou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| | - Michail A. Batskinis
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| | - Zoi I. Litou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| | - Stavros J. Hamodrakas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| | - Vassiliki A. Iconomidou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
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15
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Nam KH. Sample Delivery Media for Serial Crystallography. Int J Mol Sci 2019; 20:ijms20051094. [PMID: 30836596 PMCID: PMC6429298 DOI: 10.3390/ijms20051094] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 01/19/2023] Open
Abstract
X-ray crystallographic methods can be used to visualize macromolecules at high resolution. This provides an understanding of molecular mechanisms and an insight into drug development and rational engineering of enzymes used in the industry. Although conventional synchrotron-based X-ray crystallography remains a powerful tool for understanding molecular function, it has experimental limitations, including radiation damage, cryogenic temperature, and static structural information. Serial femtosecond crystallography (SFX) using X-ray free electron laser (XFEL) and serial millisecond crystallography (SMX) using synchrotron X-ray have recently gained attention as research methods for visualizing macromolecules at room temperature without causing or reducing radiation damage, respectively. These techniques provide more biologically relevant structures than traditional X-ray crystallography at cryogenic temperatures using a single crystal. Serial femtosecond crystallography techniques visualize the dynamics of macromolecules through time-resolved experiments. In serial crystallography (SX), one of the most important aspects is the delivery of crystal samples efficiently, reliably, and continuously to an X-ray interaction point. A viscous delivery medium, such as a carrier matrix, dramatically reduces sample consumption, contributing to the success of SX experiments. This review discusses the preparation and criteria for the selection and development of a sample delivery medium and its application for SX.
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Affiliation(s)
- Ki Hyun Nam
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea.
- Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Korea.
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16
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Shoji M, Isobe H, Yamanaka S, Umena Y, Kawakami K, Kamiya N, Yamaguchi K. Theoretical Elucidation of Geometrical Structures of the CaMn4O5 Cluster in Oxygen Evolving Complex of Photosystem II Scope and Applicability of Estimation Formulae of Structural Deformations via the Mixed-Valence and Jahn–Teller Effects. ADVANCES IN QUANTUM CHEMISTRY 2019. [DOI: 10.1016/bs.aiq.2018.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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17
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Dao EH, Poitevin F, Sierra RG, Gati C, Rao Y, Ciftci HI, Akşit F, McGurk A, Obrinski T, Mgbam P, Hayes B, De Lichtenberg C, Pardo-Avila F, Corsepius N, Zhang L, Seaberg MH, Hunter MS, Liang M, Koglin JE, Wakatsuki S, Demirci H. Structure of the 30S ribosomal decoding complex at ambient temperature. RNA (NEW YORK, N.Y.) 2018; 24:1667-1676. [PMID: 30139800 PMCID: PMC6239188 DOI: 10.1261/rna.067660.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/14/2018] [Indexed: 05/29/2023]
Abstract
The ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New light sources like the X-ray free electron laser (XFEL) have enabled data collection from macromolecular crystals at ambient temperature. Here, we report an X-ray crystal structure of the Thermus thermophilus 30S ribosomal subunit decoding complex to 3.45 Å resolution using data obtained at ambient temperature at the Linac Coherent Light Source (LCLS). We find that this ambient-temperature structure is largely consistent with existing cryogenic-temperature crystal structures, with key residues of the decoding complex exhibiting similar conformations, including adenosine residues 1492 and 1493. Minor variations were observed, namely an alternate conformation of cytosine 1397 near the mRNA channel and the A-site. Our serial crystallography experiment illustrates the amenability of ribosomal microcrystals to routine structural studies at ambient temperature, thus overcoming a long-standing experimental limitation to structural studies of RNA and RNA-protein complexes at near-physiological temperatures.
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Affiliation(s)
- E Han Dao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Frédéric Poitevin
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
| | - Raymond G Sierra
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Cornelius Gati
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
- Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Yashas Rao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Halil Ibrahim Ciftci
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Fulya Akşit
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Alex McGurk
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Trevor Obrinski
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Paul Mgbam
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Casper De Lichtenberg
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE-901 87 Umeå, Sweden
| | - Fatima Pardo-Avila
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
| | - Nicholas Corsepius
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
| | - Lindsey Zhang
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Matthew H Seaberg
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Mengling Liang
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
- Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Hasan Demirci
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
- Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA
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18
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Genoni A, Bučinský L, Claiser N, Contreras-García J, Dittrich B, Dominiak PM, Espinosa E, Gatti C, Giannozzi P, Gillet JM, Jayatilaka D, Macchi P, Madsen AØ, Massa L, Matta CF, Merz KM, Nakashima PNH, Ott H, Ryde U, Schwarz K, Sierka M, Grabowsky S. Quantum Crystallography: Current Developments and Future Perspectives. Chemistry 2018; 24:10881-10905. [PMID: 29488652 DOI: 10.1002/chem.201705952] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/27/2018] [Indexed: 11/09/2022]
Abstract
Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huang, direct extraction of wavefunctions or density matrices from measured intensities of reflections or, conversely, ad hoc quantum mechanical calculations to enhance the accuracy of the crystallographic refinement are implicated. Nevertheless, many other active and emerging research areas involving quantum mechanics and scattering experiments are not covered by the original definition although they enable to observe and explain quantum phenomena as accurately and successfully as the original strategies. Therefore, we give an overview over current research that is related to a broader notion of QCr, and discuss options how QCr can evolve to become a complete and independent domain of natural sciences. The goal of this paper is to initiate discussions around QCr, but not to find a final definition of the field.
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Affiliation(s)
- Alessandro Genoni
- Université de Lorraine, CNRS, Laboratoire LPCT, 1 Boulevard Arago, F-57078, Metz, France
| | - Lukas Bučinský
- Institute of Physical Chemistry and Chemical Physics, Slovak University of Technology, FCHPT SUT, Radlinského 9, SK-812 37, Bratislava, Slovakia
| | - Nicolas Claiser
- Université de Lorraine, CNRS, Laboratoire CRM2, Boulevard des Aiguillettes, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Julia Contreras-García
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire de Chimie Théorique (LCT), 4 Place Jussieu, F-75252, Paris Cedex 05, France
| | - Birger Dittrich
- Anorganische und Strukturchemie II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland
| | - Enrique Espinosa
- Université de Lorraine, CNRS, Laboratoire CRM2, Boulevard des Aiguillettes, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Carlo Gatti
- CNR-ISTM Istituto di Scienze e Tecnologie Molecolari, via Golgi 19, Milano, I-20133, Italy.,Istituto Lombardo Accademia di Scienze e Lettere, via Brera 28, 20121, Milano, Italy
| | - Paolo Giannozzi
- Department of Mathematics, Computer Science and Physics, University of Udine, Via delle Scienze 208, I-33100, Udine, Italy
| | - Jean-Michel Gillet
- Structure, Properties and Modeling of Solids Laboratory, CentraleSupelec, Paris-Saclay University, 3 rue Joliot-Curie, 91191, Gif-sur-Yvette, France
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Anders Ø Madsen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Lou Massa
- Hunter College & the Ph.D. Program of the Graduate Center, City University of New York, New York, USA
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, B3M 2J6, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4J3, Canada.,Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada.,Département de Chimie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan, 48824, USA.,Institute for Cyber Enabled Research, Michigan State University, 567 Wilson Road, Room 1440, East Lansing, Michigan, 48824, USA
| | - Philip N H Nakashima
- Department of Materials Science and Engineering, Monash University, Victoria, 3800, Australia
| | - Holger Ott
- Bruker AXS GmbH, Östliche Rheinbrückenstraße 49, 76187, Karlsruhe, Germany
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-22100, Lund, Sweden
| | - Karlheinz Schwarz
- Technische Universität Wien, Institut für Materialwissenschaften, Getreidemarkt 9, A-1060, Vienna, Austria
| | - Marek Sierka
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, Löbdergraben 32, 07743, Jena, Germany
| | - Simon Grabowsky
- Fachbereich 2-Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Str. 3, 28359, Bremen, Germany
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19
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von Ardenne B, Mechelke M, Grubmüller H. Structure determination from single molecule X-ray scattering with three photons per image. Nat Commun 2018; 9:2375. [PMID: 29915244 PMCID: PMC6006178 DOI: 10.1038/s41467-018-04830-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 05/01/2018] [Indexed: 01/30/2023] Open
Abstract
Scattering experiments with femtosecond high-intensity free-electron laser pulses provide a new route to macromolecular structure determination. While currently limited to nano-crystals or virus particles, the ultimate goal is scattering on single biomolecules. The main challenges in these experiments are the extremely low signal-to-noise ratio due to the very low expected photon count per scattering image, often well below 100, as well as the random orientation of the molecule in each shot. Here we present a de novo correlation-based approach and show that three coherently scattered photons per image suffice for structure determination. Using synthetic scattering data of a small protein, we demonstrate near-atomic resolution of 3.3 Å using 3.3 × 1010 coherently scattered photons from 3.3 × 109 images, which is within experimental reach. Further, our three-photon correlation approach is robust to additional noise from incoherent scattering; the number of disordered solvent molecules attached to the macromolecular surface should be kept small. Existing methods to extract structural information from single-molecule scattering measurements require large number of photons per image. Here the authors discuss a method to reconstruct the structure of a molecule from X-ray scattering data by using only three photons per image.
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Affiliation(s)
- Benjamin von Ardenne
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Martin Mechelke
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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20
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Monitoring molecular nonadiabatic dynamics with femtosecond X-ray diffraction. Proc Natl Acad Sci U S A 2018; 115:6538-6547. [PMID: 29891703 DOI: 10.1073/pnas.1805335115] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ultrafast time-resolved X-ray scattering, made possible by free-electron laser sources, provides a wealth of information about electronic and nuclear dynamical processes in molecules. The technique provides stroboscopic snapshots of the time-dependent electronic charge density traditionally used in structure determination and reflects the interplay of elastic and inelastic processes, nonadiabatic dynamics, and electronic populations and coherences. The various contributions to ultrafast off-resonant diffraction from populations and coherences of molecules in crystals, in the gas phase, or from single molecules are surveyed for core-resonant and off-resonant diffraction. Single-molecule [Formula: see text] scaling and two-molecule [Formula: see text] scaling contributions, where N is the number of active molecules, are compared. Simulations are presented for the excited-state nonadiabatic dynamics of the electron harpooning at the avoided crossing in NaF. We show how a class of multiple diffraction signals from a single molecule can reveal charge-density fluctuations through multidimensional correlation functions of the charge density.
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21
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Birch J, Axford D, Foadi J, Meyer A, Eckhardt A, Thielmann Y, Moraes I. The fine art of integral membrane protein crystallisation. Methods 2018; 147:150-162. [PMID: 29778646 DOI: 10.1016/j.ymeth.2018.05.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/13/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022] Open
Abstract
Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral membrane proteins has proven to be far from trivial, hence they are underrepresented in the protein data bank. Low expression levels, insolubility and instability are just a few of the many hurdles one faces when studying these proteins. X-ray crystallography has been the most used method to determine atomic structures of membrane proteins. However, the production of high quality membrane protein crystals is always very challenging, often seen more as art than a rational experiment. Here we review valuable approaches, methods and techniques to successful membrane protein crystallisation.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK
| | - James Foadi
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Arne Meyer
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Annette Eckhardt
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Yvonne Thielmann
- Max Planck Institute of Biophysics, Molecular Membrane Biology, Max-von-Laue-Strasse 3, 60438 Frankfurt, Germany
| | - Isabel Moraes
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK; Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK; National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
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22
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Seddon EA, Clarke JA, Dunning DJ, Masciovecchio C, Milne CJ, Parmigiani F, Rugg D, Spence JCH, Thompson NR, Ueda K, Vinko SM, Wark JS, Wurth W. Short-wavelength free-electron laser sources and science: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2017; 80:115901. [PMID: 29059048 DOI: 10.1088/1361-6633/aa7cca] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
This review is focused on free-electron lasers (FELs) in the hard to soft x-ray regime. The aim is to provide newcomers to the area with insights into: the basic physics of FELs, the qualities of the radiation they produce, the challenges of transmitting that radiation to end users and the diversity of current scientific applications. Initial consideration is given to FEL theory in order to provide the foundation for discussion of FEL output properties and the technical challenges of short-wavelength FELs. This is followed by an overview of existing x-ray FEL facilities, future facilities and FEL frontiers. To provide a context for information in the above sections, a detailed comparison of the photon pulse characteristics of FEL sources with those of other sources of high brightness x-rays is made. A brief summary of FEL beamline design and photon diagnostics then precedes an overview of FEL scientific applications. Recent highlights are covered in sections on structural biology, atomic and molecular physics, photochemistry, non-linear spectroscopy, shock physics, solid density plasmas. A short industrial perspective is also included to emphasise potential in this area.
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Affiliation(s)
- E A Seddon
- ASTeC, STFC Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Cheshire, WA4 4AD, United Kingdom. The School of Physics and Astronomy and Photon Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. The Cockcroft Institute, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Cheshire, WA4 4AD, United Kingdom
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23
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Mylona A, Carr S, Aller P, Moraes I, Treisman R, Evans G, Foadi J. A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software. CRYSTALS 2017; 7:242. [PMID: 29456874 PMCID: PMC5813789 DOI: 10.3390/cryst7080242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present article describes how to use the computer program BLEND to help assemble complete datasets for the solution of macromolecular structures, starting from partial or complete datasets, derived from data collection from multiple crystals. The program is demonstrated on more than two hundred X-ray diffraction datasets obtained from 50 crystals of a complex formed between the SRF transcription factor, its cognate DNA, and a peptide from the SRF cofactor MRTF-A. This structure is currently in the process of being fully solved. While full details of the structure are not yet available, the repeated application of BLEND on data from this structure, as they have become available, has made it possible to produce electron density maps clear enough to visualise the potential location of MRTF sequences.
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Affiliation(s)
- Anastasia Mylona
- Signalling and Transcription Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Pierre Aller
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Isabel Moraes
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Richard Treisman
- Signalling and Transcription Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - James Foadi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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24
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Adawy A, Amghouz Z, van Hest JCM, Wilson DA. Sub-Micron Polymeric Stomatocytes as Promising Templates for Confined Crystallization and Diffraction Experiments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1700642. [PMID: 28558135 DOI: 10.1002/smll.201700642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 04/06/2017] [Indexed: 06/07/2023]
Abstract
The possibility of using sub-micrometer polymeric stomatocytes is investigated to effectuate confined crystallization of inorganic compounds. These bowl-shaped polymeric compartments facilitate confined crystallization while their glassy surfaces provide their crystalline cargos with convenient shielding from the electron beam's harsh effects during transmission electron microscopy experiments. Stomatocytes host the growth of a single nanocrystal per nanocavity, and the electron diffraction experiments reveal that their glassy membranes do not interfere with the diffraction patterns obtained from their crystalline cargos. Therefore, it is expected that the encapsulation and crystallization within these compartments can be considered as a promising template (nanovials) that hold and protect nanocrystals and protein clusters from the direct radiation damage before data acquisition, while they are examined by modern crystallography methodologies such as serial femtosecond crystallography.
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Affiliation(s)
- Alaa Adawy
- Institute for Molecules and Materials, Radboud University, 6525, AJ, Nijmegen, The Netherlands
| | - Zakariae Amghouz
- HRTEM Laboratory, Scientific-Technical Services, University of Oviedo-CINN, Oviedo, 33006, Spain
| | - Jan C M van Hest
- Institute for Molecules and Materials, Radboud University, 6525, AJ, Nijmegen, The Netherlands
| | - Daniela A Wilson
- Institute for Molecules and Materials, Radboud University, 6525, AJ, Nijmegen, The Netherlands
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25
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Dörner K, Martin-Garcia JM, Kupitz C, Gong Z, Mallet TC, Chen L, Wachter RM, Fromme P. Characterization of Protein Nanocrystals Based on the Reversibility of Crystallization. CRYSTAL GROWTH & DESIGN 2016; 16:3838-3845. [PMID: 29056873 PMCID: PMC5649632 DOI: 10.1021/acs.cgd.6b00384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A new approach is described to screen for protein nanocrystals based on the reversibility of crystallization. Methods to characterize nanocrystals are in strong need to facilitate sample preparation for serial femtosecond X-ray nanocrystallography (SFX). SFX enables protein structure determination by collecting X-ray diffraction from nano- and microcrystals using a free electron laser. This technique is especially valuable for challenging proteins as for example membrane proteins and is in general a powerful method to overcome the radiation damage problem and to perform time-resolved structure analysis. Nanocrystal growth cannot be monitored with common methods used in protein crystallography, as the resolution of bright field microscopy is not sufficient. A high-performance method to screen for nanocrystals is second order nonlinear imaging of chiral crystals (SONICC). However, the high cost prevents its use in every laboratory, and some protein nanocrystals may be "invisible" to SONICC. In this work using a crystallization robot and a common imaging system precipitation comprised of nanocrystals and precipitation caused by aggregated protein can be distinguished.
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Affiliation(s)
- Katerina Dörner
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - Jose M. Martin-Garcia
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, United States
| | - Christopher Kupitz
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - Zhen Gong
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - T. Conn Mallet
- Life Science, Rigaku Americas Corporation, 9009 New Trails Drive, The Woodlands, Texas 77381, United States
| | - Liqing Chen
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - Rebekka M. Wachter
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, United States
- Corresponding Author: Address: School of Molecular Sciences, Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University P.O. Box 85287-1604 Tempe, AZ 85287-1604, USA. Phone +1 (480)-965-9028. Fax: +1 (480)-965-2747. . Web: http://www.public.asu.edu/∼pfromme/
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26
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Molnár J, Szakács G, Tusnády GE. Characterization of Disease-Associated Mutations in Human Transmembrane Proteins. PLoS One 2016; 11:e0151760. [PMID: 26986070 PMCID: PMC4795776 DOI: 10.1371/journal.pone.0151760] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 03/03/2016] [Indexed: 11/21/2022] Open
Abstract
Transmembrane protein coding genes are commonly associated with human diseases. We characterized disease causing mutations and natural polymorphisms in transmembrane proteins by mapping missense genetic variations from the UniProt database on the transmembrane protein topology listed in the Human Transmembrane Proteome database. We found characteristic differences in the spectrum of amino acid changes within transmembrane regions: in the case of disease associated mutations the non-polar to non-polar and non-polar to charged amino acid changes are equally frequent. In contrast, in the case of natural polymorphisms non-polar to charged amino acid changes are rare while non-polar to non-polar changes are common. The majority of disease associated mutations result in glycine to arginine and leucine to proline substitutions. Mutations to positively charged amino acids are more common in the center of the lipid bilayer, where they cause more severe structural and functional anomalies. Our analysis contributes to the better understanding of the effect of disease associated mutations in transmembrane proteins, which can help prioritize genetic variations in personal genomic investigations.
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Affiliation(s)
- János Molnár
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
| | - Gábor E. Tusnády
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
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27
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Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nat Commun 2015; 5:3309. [PMID: 24525480 DOI: 10.1038/ncomms4309] [Citation(s) in RCA: 442] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/24/2014] [Indexed: 01/23/2023] Open
Abstract
Lipidic cubic phase (LCP) crystallization has proven successful for high-resolution structure determination of challenging membrane proteins. Here we present a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providing a continuously renewed source of material for serial femtosecond crystallography. Data collected from sub-10-μm-sized crystals produced with less than 0.5 mg of purified protein yield structural insights regarding cyclopamine binding to the Smoothened receptor.
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28
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Liekhus-Schmaltz CE, Tenney I, Osipov T, Sanchez-Gonzalez A, Berrah N, Boll R, Bomme C, Bostedt C, Bozek JD, Carron S, Coffee R, Devin J, Erk B, Ferguson KR, Field RW, Foucar L, Frasinski LJ, Glownia JM, Gühr M, Kamalov A, Krzywinski J, Li H, Marangos JP, Martinez TJ, McFarland BK, Miyabe S, Murphy B, Natan A, Rolles D, Rudenko A, Siano M, Simpson ER, Spector L, Swiggers M, Walke D, Wang S, Weber T, Bucksbaum PH, Petrovic VS. Ultrafast isomerization initiated by X-ray core ionization. Nat Commun 2015; 6:8199. [DOI: 10.1038/ncomms9199] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 07/28/2015] [Indexed: 11/09/2022] Open
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29
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Abdallah BG, Zatsepin NA, Roy-Chowdhury S, Coe J, Conrad CE, Dörner K, Sierra RG, Stevenson HP, Camacho-Alanis F, Grant TD, Nelson G, James D, Calero G, Wachter RM, Spence JCH, Weierstall U, Fromme P, Ros A. Microfluidic sorting of protein nanocrystals by size for X-ray free-electron laser diffraction. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041719. [PMID: 26798818 PMCID: PMC4711642 DOI: 10.1063/1.4928688] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/05/2015] [Indexed: 05/23/2023]
Abstract
The advent and application of the X-ray free-electron laser (XFEL) has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity, where variations in crystal size (among other factors) lead to the requirement of large data sets (and thus 10-100 mg of protein) for determining accurate structure factors. To decrease sample dispersity, we developed a high-throughput microfluidic sorter operating on the principle of dielectrophoresis, whereby polydisperse particles can be transported into various fluid streams for size fractionation. Using this microsorter, we isolated several milliliters of photosystem I nanocrystal fractions ranging from 200 to 600 nm in size as characterized by dynamic light scattering, nanoparticle tracking, and electron microscopy. Sorted nanocrystals were delivered in a liquid jet via the gas dynamic virtual nozzle into the path of the XFEL at the Linac Coherent Light Source. We obtained diffraction to ∼4 Å resolution, indicating that the small crystals were not damaged by the sorting process. We also observed the shape transforms of photosystem I nanocrystals, demonstrating that our device can optimize data collection for the shape transform-based phasing method. Using simulations, we show that narrow crystal size distributions can significantly improve merged data quality in serial crystallography. From this proof-of-concept work, we expect that the automated size-sorting of protein crystals will become an important step for sample production by reducing the amount of protein needed for a high quality final structure and the development of novel phasing methods that exploit inter-Bragg reflection intensities or use variations in beam intensity for radiation damage-induced phasing. This method will also permit an analysis of the dependence of crystal quality on crystal size.
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Affiliation(s)
| | | | | | | | | | | | - Raymond G Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Hilary P Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, USA
| | - Fernanda Camacho-Alanis
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, USA
| | - Thomas D Grant
- Hauptman-Woodward Medical Research Institute, University at Buffalo , Buffalo, New York 14203, USA
| | | | | | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, USA
| | - Rebekka M Wachter
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, USA
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30
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Hao Y, Inhester L, Hanasaki K, Son SK, Santra R. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041707. [PMID: 26798806 PMCID: PMC4711638 DOI: 10.1063/1.4919794] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 04/24/2015] [Indexed: 05/16/2023]
Abstract
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.
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31
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Guo F, Zhou W, Li P, Mao Z, Yennawar N, French JB, Jun Huang T. Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:2733-7. [PMID: 25641793 PMCID: PMC4478196 DOI: 10.1002/smll.201403262] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/19/2014] [Indexed: 05/20/2023]
Abstract
Advances in modern X-ray sources and detector technology have made it possible for crystallographers to collect usable data on crystals of only a few micrometers or less in size. Despite these developments, sample handling techniques have significantly lagged behind and often prevent the full realization of current beamline capabilities. In order to address this shortcoming, a surface acoustic wave-based method for manipulating and patterning crystals is developed. This method, which does not damage the fragile protein crystals, can precisely manipulate and pattern micrometer and submicrometer-sized crystals for data collection and screening. The technique is robust, inexpensive, and easy to implement. This method not only promises to significantly increase efficiency and throughput of both conventional and serial crystallography experiments, but will also make it possible to collect data on samples that were previously intractable.
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Affiliation(s)
- Feng Guo
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Weijie Zhou
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Peng Li
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Zhangming Mao
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Neela Yennawar
- Huck Institutes for Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jarrod B. French
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Tony Jun Huang
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
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32
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Struts AV, Barmasov AV, Brown MF. SPECTRAL METHODS FOR STUDY OF THE G-PROTEIN-COUPLED RECEPTOR RHODOPSIN. I. VIBRATIONAL AND ELECTRONIC SPECTROSCOPY. OPTICS AND SPECTROSCOPY 2015; 118:711-717. [PMID: 28260815 PMCID: PMC5334778 DOI: 10.1134/s0030400x15050240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Here we review the application of modern spectral methods for the study of G-protein-coupled receptors (GPCRs) using rhodopsin as a prototype. Because X-ray analysis gives us immobile snapshots of protein conformations, it is imperative to apply spectroscopic methods for elucidating their function: vibrational (Raman, FTIR), electronic (UV-visible absorption, fluorescence) spectroscopies, and magnetic resonance (electron paramagnetic resonance, EPR), and nuclear magnetic resonance, NMR). In the first of the two companion articles, we discuss the application of optical spectroscopy for studying rhodopsin in a membrane environment. Information is obtained regarding the time-ordered sequence of events in rhodopsin activation. Isomerization of the chromophore and deprotonation of the retinal Schiff base leads to a structural change of the protein involving the motion of helices H5 and H6 in a pH-dependent process. Information is obtained that is unavailable from X-ray crystallography, which can be combined with spectroscopic studies to achieve a more complete understanding of GPCR function.
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Affiliation(s)
- A V Struts
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia; University of Arizona, Tucson, AZ 85721 USA
| | - A V Barmasov
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia
| | - M F Brown
- University of Arizona, Tucson, AZ 85721 USA
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33
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Bennett K, Biggs JD, Zhang Y, Dorfman KE, Mukamel S. Time-, frequency-, and wavevector-resolved x-ray diffraction from single molecules. J Chem Phys 2015; 140:204311. [PMID: 24880284 DOI: 10.1063/1.4878377] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Using a quantum electrodynamic framework, we calculate the off-resonant scattering of a broadband X-ray pulse from a sample initially prepared in an arbitrary superposition of electronic states. The signal consists of single-particle (incoherent) and two-particle (coherent) contributions that carry different particle form factors that involve different material transitions. Single-molecule experiments involving incoherent scattering are more influenced by inelastic processes compared to bulk measurements. The conditions under which the technique directly measures charge densities (and can be considered as diffraction) as opposed to correlation functions of the charge-density are specified. The results are illustrated with time- and wavevector-resolved signals from a single amino acid molecule (cysteine) following an impulsive excitation by a stimulated X-ray Raman process resonant with the sulfur K-edge. Our theory and simulations can guide future experimental studies on the structures of nano-particles and proteins.
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Affiliation(s)
- Kochise Bennett
- University of California, Irvine, California 92697-2025, USA
| | - Jason D Biggs
- University of California, Irvine, California 92697-2025, USA
| | - Yu Zhang
- University of California, Irvine, California 92697-2025, USA
| | | | - Shaul Mukamel
- University of California, Irvine, California 92697-2025, USA
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34
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Abdallah BG, Roy-Chowdhury S, Coe J, Fromme P, Ros A. High throughput protein nanocrystal fractionation in a microfluidic sorter. Anal Chem 2015; 87:4159-67. [PMID: 25794348 DOI: 10.1021/acs.analchem.5b00589] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein crystallography is transitioning into a new generation with the introduction of the X-ray free electron laser, which can be used to solve the structures of complex proteins via serial femtosecond crystallography. Sample characteristics play a critical role in successful implementation of this new technology, whereby a small, narrow protein crystal size distribution is desired to provide high quality diffraction data. To provide such a sample, we developed a microfluidic device that facilitates dielectrophoretic sorting of heterogeneous particle mixtures into various size fractions. The first generation device demonstrated great potential and success toward this endeavor; thus, in this work, we present a comprehensive optimization study to improve throughput and control over sorting outcomes. First, device geometry was designed considering a variety of criteria, and applied potentials were modeled to determine the scheme achieving the largest sorting efficiency for isolating nanoparticles from microparticles. Further, to investigate sorting efficiency within the nanoparticle regime, critical geometrical dimensions and input parameters were optimized to achieve high sorting efficiencies. Experiments revealed fractionation of nanobeads from microbeads in the optimized device with high sorting efficiencies, and protein crystals were sorted into submicrometer size fractions as desired for future serial femtosecond crystallography experiments.
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Affiliation(s)
- Bahige G Abdallah
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States.,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Shatabdi Roy-Chowdhury
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States.,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Jesse Coe
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States.,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States.,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Alexandra Ros
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States.,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
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35
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Nogly P, James D, Wang D, White TA, Zatsepin N, Shilova A, Nelson G, Liu H, Johansson L, Heymann M, Jaeger K, Metz M, Wickstrand C, Wu W, Båth P, Berntsen P, Oberthuer D, Panneels V, Cherezov V, Chapman H, Schertler G, Neutze R, Spence J, Moraes I, Burghammer M, Standfuss J, Weierstall U. Lipidic cubic phase serial millisecond crystallography using synchrotron radiation. IUCRJ 2015; 2:168-76. [PMID: 25866654 PMCID: PMC4392771 DOI: 10.1107/s2052252514026487] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/01/2014] [Indexed: 05/19/2023]
Abstract
Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway.
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Affiliation(s)
- Przemyslaw Nogly
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Daniel James
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Dingjie Wang
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Anastasya Shilova
- European Synchrotron Radiation Facility, Grenoble Cedex 9, F-38043, France
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Haiguang Liu
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Linda Johansson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California USA
| | - Michael Heymann
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
| | - Kathrin Jaeger
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Markus Metz
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
- Centre for Ultrafast Imaging, Hamburg 22607, Germany
| | - Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Wenting Wu
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
- Centre for Ultrafast Imaging, Hamburg 22607, Germany
| | - Valerie Panneels
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Vadim Cherezov
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California USA
| | - Henry Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
- Department of Physics, University of Hamburg, Hamburg 22607, Germany
| | - Gebhard Schertler
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
- Deparment of Biology, ETH Zurich, Zürich 8093, Switzerland
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - John Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Isabel Moraes
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Oxfordshire OX11 0DE, England
- Department of Life Sciences, Imperial College London, London, England
- Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Didcot, Oxfordshire OX11 0FA, England
| | - Manfred Burghammer
- European Synchrotron Radiation Facility, Grenoble Cedex 9, F-38043, France
- Department of Analytical Chemistry, Ghent University, Ghent B-9000, Belgium
| | - Joerg Standfuss
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
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Schlichting I. Serial femtosecond crystallography: the first five years. IUCRJ 2015; 2:246-55. [PMID: 25866661 PMCID: PMC4392417 DOI: 10.1107/s205225251402702x] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/09/2014] [Indexed: 05/18/2023]
Abstract
Protein crystallography using synchrotron radiation sources has had a tremendous impact on biology, having yielded the structures of thousands of proteins and given detailed insight into their mechanisms. However, the technique is limited by the requirement for macroscopic crystals, which can be difficult to obtain, as well as by the often severe radiation damage caused in diffraction experiments, in particular when using tiny crystals. To slow radiation damage, data collection is typically performed at cryogenic temperatures. With the advent of free-electron lasers (FELs) capable of delivering extremely intense femtosecond X-ray pulses, this situation appears to be remedied, allowing the structure determination of undamaged macromolecules using either macroscopic or microscopic crystals. The latter are exposed to the FEL beam in random orientations and their diffraction data are collected at cryogenic or room temperature in a serial fashion, since each crystal is destroyed upon a single exposure. The new approaches required for crystal growth and delivery, and for diffraction data analysis, including de novo phasing, are reviewed. The opportunities and challenges of SFX are described, including applications such as time-resolved measurements and the analysis of radiation damage-prone systems.
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Affiliation(s)
- Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
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37
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Jönsson HO, Tîmneanu N, Östlin C, Scott HA, Caleman C. Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:256-66. [PMID: 25723927 DOI: 10.1107/s1600577515002878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 02/10/2015] [Indexed: 05/07/2023]
Abstract
Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 10(4) to 10(7) J cm(-2) with photon energies from 2 to 12 keV, up to 100 fs long. Radiation damage in the form of sample heating that will lead to a loss of crystalline periodicity and changes in scattering factor due to electronic reconfigurations of ionized atoms are considered here. The simulations show differences in the dynamics of the radiation damage processes for different temporal pulse profiles and intensities, where ionization or atomic motion could be predominant. The different dynamics influence the recorded diffracted signal in any given resolution and will affect the subsequent structure determination.
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Affiliation(s)
- H Olof Jönsson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Nicuşor Tîmneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Christofer Östlin
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Howard A Scott
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
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38
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Kupitz C, Grotjohann I, Conrad CE, Roy-Chowdhury S, Fromme R, Fromme P. Microcrystallization techniques for serial femtosecond crystallography using photosystem II from Thermosynechococcus elongatus as a model system. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130316. [PMID: 24914149 DOI: 10.1098/rstb.2013.0316] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Serial femtosecond crystallography (SFX) is a new emerging method, where X-ray diffraction data are collected from a fully hydrated stream of nano- or microcrystals of biomolecules in their mother liquor using high-energy, X-ray free-electron lasers. The success of SFX experiments strongly depends on the ability to grow large amounts of well-ordered nano/microcrystals of homogeneous size distribution. While methods to grow large single crystals have been extensively explored in the past, method developments to grow nano/microcrystals in sufficient amounts for SFX experiments are still in their infancy. Here, we describe and compare three methods (batch, free interface diffusion (FID) and FID centrifugation) for growth of nano/microcrystals for time-resolved SFX experiments using the large membrane protein complex photosystem II as a model system.
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Affiliation(s)
- Christopher Kupitz
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85281, USA
| | - Ingo Grotjohann
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85281, USA
| | - Chelsie E Conrad
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85281, USA
| | - Shatabdi Roy-Chowdhury
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85281, USA
| | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85281, USA
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85281, USA
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39
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40
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A Study on the Energy Transition of All-α Proteins by Molecular Dynamics Simulation. ACTA POLYM SIN 2014. [DOI: 10.3724/sp.j.1105.2014.13169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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Nannenga BL, Gonen T. Protein structure determination by MicroED. Curr Opin Struct Biol 2014; 27:24-31. [PMID: 24709395 PMCID: PMC5656570 DOI: 10.1016/j.sbi.2014.03.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/21/2014] [Accepted: 03/07/2014] [Indexed: 11/17/2022]
Abstract
In this review we discuss the current advances relating to structure determination from protein microcrystals with special emphasis on the newly developed method called MicroED. This method uses a transmission electron cryo-microscope to collect electron diffraction data from extremely small 3-dimensional (3D) crystals. MicroED has been used to solve the 3D structure of the model protein lysozyme to 2.9Å resolution. As the method further matures, MicroED promises to offer a unique and widely applicable approach to protein crystallography using nanocrystals.
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Affiliation(s)
- Brent L Nannenga
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Tamir Gonen
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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42
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Howard JAK, Probert MR. Cutting-Edge Techniques Used for the Structural Investigation of Single Crystals. Science 2014; 343:1098-102. [DOI: 10.1126/science.1247252] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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43
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High-resolution NMR reveals secondary structure and folding of amino acid transporter from outer chloroplast membrane. PLoS One 2013; 8:e78116. [PMID: 24205117 PMCID: PMC3812221 DOI: 10.1371/journal.pone.0078116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 09/16/2013] [Indexed: 12/05/2022] Open
Abstract
Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein.
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44
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Abdallah BG, Chao TC, Kupitz C, Fromme P, Ros A. Dielectrophoretic sorting of membrane protein nanocrystals. ACS NANO 2013; 7:9129-37. [PMID: 24004002 PMCID: PMC3894612 DOI: 10.1021/nn403760q] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Structure elucidation of large membrane protein complexes is still a considerable challenge, yet is a key factor in drug development and disease combat. Femtosecond nanocrystallography is an emerging technique with which structural information of membrane proteins is obtained without the need to grow large crystals, thus overcoming the experimental riddle faced in traditional crystallography methods. Here, we demonstrate for the first time a microfluidic device capable of sorting membrane protein crystals based on size using dielectrophoresis. We demonstrate the excellent sorting power of this new approach with numerical simulations of selected submicrometer beads in excellent agreement with experimental observations. Crystals from batch crystallization broths of the huge membrane protein complex photosystem I were sorted without further treatment, resulting in a high degree of monodispersity and crystallinity in the ~100 nm size range. Microfluidic integration, continuous sorting, and nanometer-sized crystal fractions make this method ideal for direct coupling to femtosecond nanocrystallography.
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Affiliation(s)
| | - Tzu-Chiao Chao
- Department of Biology, University of Regina, Regina, SK, S4S0A2, Canada
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Dynamic structural science: recent developments in time-resolved spectroscopy and X-ray crystallography. Biochem Soc Trans 2013; 41:1260-4. [DOI: 10.1042/bst20130125] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To understand the mechanism of biological processes, time-resolved methodologies are required to investigate how functionality is linked to changes in molecular structure. A number of spectroscopic techniques are available that probe local structural rearrangements with high temporal resolution. However, for macromolecules, these techniques do not yield an overall high-resolution description of the structure. Time-resolved X-ray crystallographic methods exist, but, due to both instrument availability and stringent sample requirements, they have not been widely applied to macromolecular systems, especially for time resolutions below 1 s. Recently, there has been a resurgent interest in time-resolved structural science, fuelled by the recognition that both chemical and life scientists face many of the same challenges. In the present article, we review the current state-of-the-art in dynamic structural science, highlighting applications to enzymes. We also look to the future and discuss current method developments with the potential to widen access to time-resolved studies across discipline boundaries.
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Demirci H, Sierra RG, Laksmono H, Shoeman RL, Botha S, Barends TRM, Nass K, Schlichting I, Doak RB, Gati C, Williams GJ, Boutet S, Messerschmidt M, Jogl G, Dahlberg AE, Gregory ST, Bogan MJ. Serial femtosecond X-ray diffraction of 30S ribosomal subunit microcrystals in liquid suspension at ambient temperature using an X-ray free-electron laser. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1066-9. [PMID: 23989164 PMCID: PMC3758164 DOI: 10.1107/s174430911302099x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/27/2013] [Indexed: 12/03/2022]
Abstract
High-resolution ribosome structures determined by X-ray crystallography have provided important insights into the mechanism of translation. Such studies have thus far relied on large ribosome crystals kept at cryogenic temperatures to reduce radiation damage. Here, the application of serial femtosecond X-ray crystallography (SFX) using an X-ray free-electron laser (XFEL) to obtain diffraction data from ribosome microcrystals in liquid suspension at ambient temperature is described. 30S ribosomal subunit microcrystals diffracted to beyond 6 Å resolution, demonstrating the feasibility of using SFX for ribosome structural studies. The ability to collect diffraction data at near-physiological temperatures promises to provide fundamental insights into the structural dynamics of the ribosome and its functional complexes.
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Affiliation(s)
- Hasan Demirci
- Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA.
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Xia Y, Peng L. Photoactivatable Lipid Probes for Studying Biomembranes by Photoaffinity Labeling. Chem Rev 2013; 113:7880-929. [DOI: 10.1021/cr300419p] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi Xia
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
| | - Ling Peng
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
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Abstract
Secondary active transporters exploit the electrochemical potential of solutes to shuttle specific substrate molecules across biological membranes, usually against their concentration gradient. Transporters of different functional families with little sequence similarity have repeatedly been found to exhibit similar folds, exemplified by the MFS, LeuT, and NhaA folds. Observations of multiple conformational states of the same transporter, represented by the LeuT superfamily members Mhp1, AdiC, vSGLT, and LeuT, led to proposals that structural changes are associated with substrate binding and transport. Despite recent biochemical and structural advances, our understanding of substrate recognition and energy coupling is rather preliminary. This review focuses on the common folds and shared transport mechanisms of secondary active transporters. Available structural information generally supports the alternating access model for substrate transport, with variations and extensions made by emerging structural, biochemical, and computational evidence.
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Affiliation(s)
- Yigong Shi
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.
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Kissick DJ, Dettmar CM, Becker M, Mulichak AM, Cherezov V, Ginell SL, Battaile KP, Keefe LJ, Fischetti RF, Simpson GJ. Towards protein-crystal centering using second-harmonic generation (SHG) microscopy. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:843-51. [PMID: 23633594 PMCID: PMC3640472 DOI: 10.1107/s0907444913002746] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 01/28/2013] [Indexed: 11/10/2022]
Abstract
The potential of second-harmonic generation (SHG) microscopy for automated crystal centering to guide synchrotron X-ray diffraction of protein crystals was explored. These studies included (i) comparison of microcrystal positions in cryoloops as determined by SHG imaging and by X-ray diffraction rastering and (ii) X-ray structure determinations of selected proteins to investigate the potential for laser-induced damage from SHG imaging. In studies using β2 adrenergic receptor membrane-protein crystals prepared in lipidic mesophase, the crystal locations identified by SHG images obtained in transmission mode were found to correlate well with the crystal locations identified by raster scanning using an X-ray minibeam. SHG imaging was found to provide about 2 µm spatial resolution and shorter image-acquisition times. The general insensitivity of SHG images to optical scatter enabled the reliable identification of microcrystals within opaque cryocooled lipidic mesophases that were not identified by conventional bright-field imaging. The potential impact of extended exposure of protein crystals to five times a typical imaging dose from an ultrafast laser source was also assessed. Measurements of myoglobin and thaumatin crystals resulted in no statistically significant differences between structures obtained from diffraction data acquired from exposed and unexposed regions of single crystals. Practical constraints for integrating SHG imaging into an active beamline for routine automated crystal centering are discussed.
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Affiliation(s)
- David J. Kissick
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Michael Becker
- GM/CA-CAT at the APS, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Anne M. Mulichak
- IMCA-CAT, Hauptman–Woodward Medical Research Institute, Argonne, IL 60439, USA
| | | | - Stephan L. Ginell
- SBC-CAT at the APS, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Kevin P. Battaile
- IMCA-CAT, Hauptman–Woodward Medical Research Institute, Argonne, IL 60439, USA
| | - Lisa J. Keefe
- IMCA-CAT, Hauptman–Woodward Medical Research Institute, Argonne, IL 60439, USA
| | - Robert F. Fischetti
- GM/CA-CAT at the APS, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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Sigfridsson KGV, Chernev P, Leidel N, Popović-Bijelić A, Gräslund A, Haumann M. Rapid X-ray photoreduction of dimetal-oxygen cofactors in ribonucleotide reductase. J Biol Chem 2013; 288:9648-9661. [PMID: 23400774 DOI: 10.1074/jbc.m112.438796] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prototypic dinuclear metal cofactors with varying metallation constitute a class of O2-activating catalysts in numerous enzymes such as ribonucleotide reductase. Reliable structures are required to unravel the reaction mechanisms. However, protein crystallography data may be compromised by x-ray photoreduction (XRP). We studied XPR of Fe(III)Fe(III) and Mn(III)Fe(III) sites in the R2 subunit of Chlamydia trachomatis ribonucleotide reductase using x-ray absorption spectroscopy. Rapid and biphasic x-ray photoreduction kinetics at 20 and 80 K for both cofactor types suggested sequential formation of (III,II) and (II,II) species and similar redox potentials of iron and manganese sites. Comparing with typical x-ray doses in crystallography implies that (II,II) states are reached in <1 s in such studies. First-sphere metal coordination and metal-metal distances differed after chemical reduction at room temperature and after XPR at cryogenic temperatures, as corroborated by model structures from density functional theory calculations. The inter-metal distances in the XPR-induced (II,II) states, however, are similar to R2 crystal structures. Therefore, crystal data of initially oxidized R2-type proteins mostly contain photoreduced (II,II) cofactors, which deviate from the native structures functional in O2 activation, explaining observed variable metal ligation motifs. This situation may be remedied by novel femtosecond free electron-laser protein crystallography techniques.
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Affiliation(s)
| | - Petko Chernev
- Free University Berlin, Institute of Experimental Physics, 14195 Berlin, Germany
| | - Nils Leidel
- Free University Berlin, Institute of Experimental Physics, 14195 Berlin, Germany
| | - Ana Popović-Bijelić
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Michael Haumann
- Free University Berlin, Institute of Experimental Physics, 14195 Berlin, Germany.
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