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Gul M, Ayan E, Destan E, Johnson JA, Shafiei A, Kepceoğlu A, Yilmaz M, Ertem FB, Yapici İ, Tosun B, Baldir N, Tokay N, Nergiz Z, Karakadioğlu G, Paydos SS, Kulakman C, Ferah CK, Güven Ö, Atalay N, Akcan EK, Cetinok H, Arslan NE, Şabanoğlu K, Aşci B, Tavli S, Gümüsboğa H, Altuntaş S, Otsuka M, Fujita M, Teki N Ş, Çi Ftçi H, Durdaği S, Karaca E, Kaplan Türköz B, Kabasakal BV, Kati A, DeMi Rci H. Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source. Sci Rep 2023; 13:8123. [PMID: 37208392 DOI: 10.1038/s41598-023-33989-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/21/2023] [Indexed: 05/21/2023] Open
Abstract
High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.
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Affiliation(s)
- Mehmet Gul
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Esra Ayan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Ebru Destan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - J Austin Johnson
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Alaleh Shafiei
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Abdullah Kepceoğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Koç University Surface Science and Technology Center (KUYTAM), Koç University, Istanbul, Türkiye
| | - Merve Yilmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Fatma Betül Ertem
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - İlkin Yapici
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Bilge Tosun
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Nilüfer Baldir
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Nurettin Tokay
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Zeliş Nergiz
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Koç University Isbank Center for Infectious Diseases (KUISCID), Koç University, Istanbul, Türkiye
| | - Gözde Karakadioğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Seyide Seda Paydos
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Cahine Kulakman
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Cengiz Kaan Ferah
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Ömür Güven
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Necati Atalay
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Science, Gebze Technical University, Kocaeli, Türkiye
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Enver Kamil Akcan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Türkiye
| | - Haluk Cetinok
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Nazlı Eylül Arslan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Arel University, Istanbul, Türkiye
| | - Kardelen Şabanoğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yıldız Technical University, Istanbul, Türkiye
| | - Bengisu Aşci
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Serra Tavli
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Helin Gümüsboğa
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Sevde Altuntaş
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
- Department of Tissue Engineering, Hamidiye Institute of Health Sciences, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
- Department of Drug Discovery, Science Farm Ltd., Kumamoto, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Şaban Teki N
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
- The Scientific and Technological Research Council of Türkiye (TÜBİTAK) Marmara Research Center (MAM), Life Sciences, Kocaeli, Türkiye
- Department of Basic Medical Sciences, Division of Medical Biology, Faculty of Medicine, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Halilibrahim Çi Ftçi
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
- Department of Drug Discovery, Science Farm Ltd., Kumamoto, Japan
| | - Serdar Durdaği
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Türkiye
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye
| | - Burcu Kaplan Türköz
- Department of Food Engineering, Faculty of Engineering, Ege University, Izmir, Türkiye
| | - Burak Veli Kabasakal
- Turkish Accelerator and Radiation Laboratory (TARLA), Ankara University, Ankara, Türkiye
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Ahmet Kati
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
- Department of Biotechnology, Hamidiye Institute of Health Sciences, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Hasan DeMi Rci
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye.
- Koç University Isbank Center for Infectious Diseases (KUISCID), Koç University, Istanbul, Türkiye.
- SLAC National Laboratory, Stanford PULSE Institute, Menlo Park, CA, USA.
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Abstract
The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction.
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3
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Khakurel KP, Angelov B, Andreasson J. Macromolecular Nanocrystal Structural Analysis with Electron and X-Rays: A Comparative Review. Molecules 2019; 24:E3490. [PMID: 31561479 PMCID: PMC6804143 DOI: 10.3390/molecules24193490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 01/10/2023] Open
Abstract
Crystallography has long been the unrivaled method that can provide the atomistic structural models of macromolecules, using either X-rays or electrons as probes. The methodology has gone through several revolutionary periods, driven by the development of new sources, detectors, and other instrumentation. Novel sources of both X-ray and electrons are constantly emerging. The increase in brightness of these sources, complemented by the advanced detection techniques, has relaxed the traditionally strict need for large, high quality, crystals. Recent reports suggest high-quality diffraction datasets from crystals as small as a few hundreds of nanometers can be routinely obtained. This has resulted in the genesis of a new field of macromolecular nanocrystal crystallography. Here we will make a brief comparative review of this growing field focusing on the use of X-rays and electrons sources.
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Affiliation(s)
- Krishna P Khakurel
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
| | - Borislav Angelov
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
| | - Jakob Andreasson
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
- Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
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4
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O'Sullivan ME, Poitevin F, Sierra RG, Gati C, Dao EH, Rao Y, Aksit F, Ciftci H, Corsepius N, Greenhouse R, Hayes B, Hunter MS, Liang M, McGurk A, Mbgam P, Obrinsky T, Pardo-Avila F, Seaberg MH, Cheng AG, Ricci AJ, DeMirci H. Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature. Nucleic Acids Res 2019; 46:9793-9804. [PMID: 30113694 PMCID: PMC6182148 DOI: 10.1093/nar/gky693] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/19/2018] [Indexed: 11/21/2022] Open
Abstract
The bacterial 30S ribosomal subunit is a primary antibiotic target. Despite decades of discovery, the mechanisms by which antibiotic binding induces ribosomal dysfunction are not fully understood. Ambient temperature crystallographic techniques allow more biologically relevant investigation of how local antibiotic binding site interactions trigger global subunit rearrangements that perturb protein synthesis. Here, the structural effects of 2-deoxystreptamine (paromomycin and sisomicin), a novel sisomicin derivative, N1-methyl sulfonyl sisomicin (N1MS) and the non-deoxystreptamine (streptomycin) aminoglycosides on the ribosome at ambient and cryogenic temperatures were examined. Comparative studies led to three main observations. First, individual aminoglycoside–ribosome interactions in the decoding center were similar for cryogenic versus ambient temperature structures. Second, analysis of a highly conserved GGAA tetraloop of h45 revealed aminoglycoside-specific conformational changes, which are affected by temperature only for N1MS. We report the h44–h45 interface in varying states, i.e. engaged, disengaged and in equilibrium. Third, we observe aminoglycoside-induced effects on 30S domain closure, including a novel intermediary closure state, which is also sensitive to temperature. Analysis of three ambient and five cryogenic crystallography datasets reveal a correlation between h44–h45 engagement and domain closure. These observations illustrate the role of ambient temperature crystallography in identifying dynamic mechanisms of ribosomal dysfunction induced by local drug-binding site interactions. Together, these data identify tertiary ribosomal structural changes induced by aminoglycoside binding that provides functional insight and targets for drug design.
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Affiliation(s)
- Mary E O'Sullivan
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA, 94305
| | - Frédéric Poitevin
- Department of Structural Biology, Stanford University, Palo Alto, CA, USA, 94305.,Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Cornelius Gati
- Department of Structural Biology, Stanford University, Palo Alto, CA, USA, 94305.,Biosciences Division, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - E Han Dao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Yashas Rao
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Fulya Aksit
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Halilibrahim Ciftci
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Nicholas Corsepius
- Department of Structural Biology, Stanford University, Palo Alto, CA, USA, 94305
| | - Robert Greenhouse
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA, 94305
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Mengling Liang
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Alex McGurk
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Paul Mbgam
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Trevor Obrinsky
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Fátima Pardo-Avila
- Department of Structural Biology, Stanford University, Palo Alto, CA, USA, 94305
| | - Matthew H Seaberg
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Alan G Cheng
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA, 94305
| | - Anthony J Ricci
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA, 94305
| | - Hasan DeMirci
- Department of Structural Biology, Stanford University, Palo Alto, CA, USA, 94305.,Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, USA, 94025.,Biosciences Division, SLAC National Laboratory, Menlo Park, CA, USA, 94025
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5
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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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6
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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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7
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X-ray free electron laser: opportunities for drug discovery. Essays Biochem 2017; 61:529-542. [PMID: 29118098 DOI: 10.1042/ebc20170031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 01/16/2023]
Abstract
Past decades have shown the impact of structural information derived from complexes of drug candidates with their protein targets to facilitate the discovery of safe and effective medicines. Despite recent developments in single particle cryo-electron microscopy, X-ray crystallography has been the main method to derive structural information. The unique properties of X-ray free electron laser (XFEL) with unmet peak brilliance and beam focus allow X-ray diffraction data recording and successful structure determination from smaller and weaker diffracting crystals shortening timelines in crystal optimization. To further capitalize on the XFEL advantage, innovations in crystal sample delivery for the X-ray experiment, data collection and processing methods are required. This development was a key contributor to serial crystallography allowing structure determination at room temperature yielding physiologically more relevant structures. Adding the time resolution provided by the femtosecond X-ray pulse will enable monitoring and capturing of dynamic processes of ligand binding and associated conformational changes with great impact to the design of candidate drug compounds.
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8
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Sui S, Wang Y, Kolewe KW, Srajer V, Henning R, Schiffman JD, Dimitrakopoulos C, Perry SL. Graphene-based microfluidics for serial crystallography. LAB ON A CHIP 2016; 16:3082-96. [PMID: 27241728 PMCID: PMC4970872 DOI: 10.1039/c6lc00451b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Microfluidic strategies to enable the growth and subsequent serial crystallographic analysis of micro-crystals have the potential to facilitate both structural characterization and dynamic structural studies of protein targets that have been resistant to single-crystal strategies. However, adapting microfluidic crystallization platforms for micro-crystallography requires a dramatic decrease in the overall device thickness. We report a robust strategy for the straightforward incorporation of single-layer graphene into ultra-thin microfluidic devices. This architecture allows for a total material thickness of only ∼1 μm, facilitating on-chip X-ray diffraction analysis while creating a sample environment that is stable against significant water loss over several weeks. We demonstrate excellent signal-to-noise in our X-ray diffraction measurements using a 1.5 μs polychromatic X-ray exposure, and validate our approach via on-chip structure determination using hen egg white lysozyme (HEWL) as a model system. Although this work is focused on the use of graphene for protein crystallography, we anticipate that this technology should find utility in a wide range of both X-ray and other lab on a chip applications.
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Affiliation(s)
- Shuo Sui
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Yuxi Wang
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Kristopher W Kolewe
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Vukica Srajer
- BioCARS Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL 60439, USA
| | - Robert Henning
- BioCARS Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL 60439, USA
| | - Jessica D Schiffman
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Christos Dimitrakopoulos
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Sarah L Perry
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
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9
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Martin-Garcia JM, Conrad CE, Coe J, Roy-Chowdhury S, Fromme P. Serial femtosecond crystallography: A revolution in structural biology. Arch Biochem Biophys 2016; 602:32-47. [PMID: 27143509 DOI: 10.1016/j.abb.2016.03.036] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 10/21/2022]
Abstract
Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein.
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Affiliation(s)
- Jose M Martin-Garcia
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Chelsie E Conrad
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Jesse Coe
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA.
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10
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Roessler CG, Agarwal R, Allaire M, Alonso-Mori R, Andi B, Bachega JFR, Bommer M, Brewster AS, Browne MC, Chatterjee R, Cho E, Cohen AE, Cowan M, Datwani S, Davidson VL, Defever J, Eaton B, Ellson R, Feng Y, Ghislain LP, Glownia JM, Han G, Hattne J, Hellmich J, Héroux A, Ibrahim M, Kern J, Kuczewski A, Lemke HT, Liu P, Majlof L, McClintock WM, Myers S, Nelsen S, Olechno J, Orville AM, Sauter NK, Soares AS, Soltis SM, Song H, Stearns RG, Tran R, Tsai Y, Uervirojnangkoorn M, Wilmot CM, Yachandra V, Yano J, Yukl ET, Zhu D, Zouni A. Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography. Structure 2016; 24:631-640. [PMID: 26996959 DOI: 10.1016/j.str.2016.02.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/25/2015] [Accepted: 02/17/2016] [Indexed: 02/01/2023]
Abstract
X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallization conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. We report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). Additional samples were screened to demonstrate that these methods can be applied to rare samples.
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Affiliation(s)
- Christian G Roessler
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Rakhi Agarwal
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Marc Allaire
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Babak Andi
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - José F R Bachega
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos, CEP: 13560-970, Brazil
| | - Martin Bommer
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Michael C Browne
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ruchira Chatterjee
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Eunsun Cho
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Matthew Cowan
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | | | - Victor L Davidson
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816-2364, USA
| | - Jim Defever
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | | | - Yiping Feng
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - James M Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Guangye Han
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Julia Hellmich
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Annie Héroux
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Anthony Kuczewski
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Henrik T Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
| | | | | | - Stuart Myers
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Silke Nelsen
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Allen M Orville
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Alexei S Soares
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Heng Song
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
| | | | - Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Yingssu Tsai
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Department of Chemistry, Stanford University, Stanford, CA 94305-4401, USA
| | | | - Carrie M Wilmot
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vittal Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Erik T Yukl
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
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11
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Dilanian RA, Williams SR, Martin AV, Streltsov VA, Quiney HM. Whole-pattern fitting technique in serial femtosecond nanocrystallography. IUCRJ 2016; 3:127-38. [PMID: 27006776 PMCID: PMC4775161 DOI: 10.1107/s2052252516001238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 01/19/2016] [Indexed: 05/31/2023]
Abstract
Serial femtosecond X-ray crystallography (SFX) has created new opportunities in the field of structural analysis of protein nanocrystals. The intensity and timescale characteristics of the X-ray free-electron laser sources used in SFX experiments necessitate the analysis of a large collection of individual crystals of variable shape and quality to ultimately solve a single, average crystal structure. Ensembles of crystals are commonly encountered in powder diffraction, but serial crystallography is different because each crystal is measured individually and can be oriented via indexing and merged into a three-dimensional data set, as is done for conventional crystallography data. In this way, serial femtosecond crystallography data lie in between conventional crystallography data and powder diffraction data, sharing features of both. The extremely small sizes of nanocrystals, as well as the possible imperfections of their crystallite structure, significantly affect the diffraction pattern and raise the question of how best to extract accurate structure-factor moduli from serial crystallography data. Here it is demonstrated that whole-pattern fitting techniques established for one-dimensional powder diffraction analysis can be feasibly extended to higher dimensions for the analysis of merged SFX diffraction data. It is shown that for very small crystals, whole-pattern fitting methods are more accurate than Monte Carlo integration methods that are currently used.
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Affiliation(s)
- Ruben A. Dilanian
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sophie R. Williams
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrew V. Martin
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Harry M. Quiney
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
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12
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Jaeger K, Dworkowski F, Nogly P, Milne C, Wang M, Standfuss J. Serial Millisecond Crystallography of Membrane Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:137-149. [DOI: 10.1007/978-3-319-35072-1_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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13
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Sierra RG, Gati C, Laksmono H, Dao EH, Gul S, Fuller F, Kern J, Chatterjee R, Ibrahim M, Brewster AS, Young ID, Michels-Clark T, Aquila A, Liang M, Hunter MS, Koglin JE, Boutet S, Junco EA, Hayes B, Bogan MJ, Hampton CY, Puglisi EV, Sauter NK, Stan CA, Zouni A, Yano J, Yachandra VK, Soltis SM, Puglisi JD, DeMirci H. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nat Methods 2016; 13:59-62. [PMID: 26619013 PMCID: PMC4890631 DOI: 10.1038/nmeth.3667] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/14/2015] [Indexed: 01/30/2023]
Abstract
We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).
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Affiliation(s)
- Raymond G. Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - E. Han Dao
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sheraz Gul
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Jan Kern
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Mohamed Ibrahim
- Institute für Biologie, Humboldt University of Berlin, Berlin, Germany
| | | | - Iris D. Young
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Jason E. Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Elia A. Junco
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Michael J. Bogan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christina Y. Hampton
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Elisabetta V. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Claudiu A. Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Athina Zouni
- Institute für Biologie, Humboldt University of Berlin, Berlin, Germany
| | - Junko Yano
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - S. Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Joseph D. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hasan DeMirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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14
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Kroon-Batenburg LMJ, Schreurs AMM, Ravelli RBG, Gros P. Accounting for partiality in serial crystallography using ray-tracing principles. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1799-811. [PMID: 26327370 PMCID: PMC4556312 DOI: 10.1107/s1399004715011803] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/19/2015] [Indexed: 02/04/2023]
Abstract
Serial crystallography generates `still' diffraction data sets that are composed of single diffraction images obtained from a large number of crystals arbitrarily oriented in the X-ray beam. Estimation of the reflection partialities, which accounts for the expected observed fractions of diffraction intensities, has so far been problematic. In this paper, a method is derived for modelling the partialities by making use of the ray-tracing diffraction-integration method EVAL. The method estimates partialities based on crystal mosaicity, beam divergence, wavelength dispersion, crystal size and the interference function, accounting for crystallite size. It is shown that modelling of each reflection by a distribution of interference-function weighted rays yields a `still' Lorentz factor. Still data are compared with a conventional rotation data set collected from a single lysozyme crystal. Overall, the presented still integration method improves the data quality markedly. The R factor of the still data compared with the rotation data decreases from 26% using a Monte Carlo approach to 12% after applying the Lorentz correction, to 5.3% when estimating partialities by EVAL and finally to 4.7% after post-refinement. The merging R(int) factor of the still data improves from 105 to 56% but remains high. This suggests that the accuracy of the model parameters could be further improved. However, with a multiplicity of around 40 and an R(int) of ∼50% the merged still data approximate the quality of the rotation data. The presented integration method suitably accounts for the partiality of the observed intensities in still diffraction data, which is a critical step to improve data quality in serial crystallography.
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Affiliation(s)
- Loes M. J. Kroon-Batenburg
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Antoine M. M. Schreurs
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Raimond B. G. Ravelli
- M4I Division of Nanoscopy, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Piet Gros
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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15
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Pawate AS, Šrajer V, Schieferstein J, Guha S, Henning R, Kosheleva I, Schmidt M, Ren Z, Kenis PJA, Perry SL. Towards time-resolved serial crystallography in a microfluidic device. Acta Crystallogr F Struct Biol Commun 2015; 71:823-30. [PMID: 26144226 PMCID: PMC4498702 DOI: 10.1107/s2053230x15009061] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/11/2015] [Indexed: 11/10/2022] Open
Abstract
Serial methods for crystallography have the potential to enable dynamic structural studies of protein targets that have been resistant to single-crystal strategies. The use of serial data-collection strategies can circumvent challenges associated with radiation damage and repeated reaction initiation. This work utilizes a microfluidic crystallization platform for the serial time-resolved Laue diffraction analysis of macroscopic crystals of photoactive yellow protein (PYP). Reaction initiation was achieved via pulsed laser illumination, and the resultant electron-density difference maps clearly depict the expected pR(1)/pR(E46Q) and pR(2)/pR(CW) states at 10 µs and the pB1 intermediate at 1 ms. The strategies presented here have tremendous potential for extension to chemical triggering methods for reaction initiation and for extension to dynamic, multivariable analyses.
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Affiliation(s)
- Ashtamurthy S. Pawate
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Vukica Šrajer
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
| | - Jeremy Schieferstein
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sudipto Guha
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
| | - Marius Schmidt
- Department of Physics, The University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA
| | - Zhong Ren
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
- Renz Research Inc., Westmont, Illinois, USA
| | - Paul J. A. Kenis
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sarah L. Perry
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, Massachusetts, USA
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16
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Dao EH, Sierra RG, Laksmono H, Lemke HT, Alonso-Mori R, Coey A, Larsen K, Baxter EL, Cohen AE, Soltis SM, DeMirci H. Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041706. [PMID: 26798805 PMCID: PMC4711619 DOI: 10.1063/1.4919407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/20/2015] [Indexed: 06/05/2023]
Abstract
In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS) using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecond X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.
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Affiliation(s)
- E Han Dao
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Raymond G Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Henrik T Lemke
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Aaron Coey
- Biophysics Program, Stanford University School of Medicine , Stanford, California 94305, USA
| | - Kevin Larsen
- Biophysics Program, Stanford University School of Medicine , Stanford, California 94305, USA
| | - Elizabeth L Baxter
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
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17
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Tono K, Nango E, Sugahara M, Song C, Park J, Tanaka T, Tanaka R, Joti Y, Kameshima T, Ono S, Hatsui T, Mizohata E, Suzuki M, Shimamura T, Tanaka Y, Iwata S, Yabashi M. Diverse application platform for hard X-ray diffraction in SACLA (DAPHNIS): application to serial protein crystallography using an X-ray free-electron laser. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:532-7. [PMID: 25931065 PMCID: PMC4817517 DOI: 10.1107/s1600577515004464] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/03/2015] [Indexed: 05/06/2023]
Abstract
An experimental system for serial femtosecond crystallography using an X-ray free-electron laser (XFEL) has been developed. It basically consists of a sample chamber, fluid injectors and a two-dimensional detector. The chamber and the injectors are operated under helium atmosphere at 1 atm. The ambient pressure operation facilitates applications to fluid samples. Three kinds of injectors are employed to feed randomly oriented crystals in aqueous solution or highly viscous fluid. Experiments on lysozyme crystals were performed by using the 10 keV XFEL of the SPring-8 Angstrom Compact free-electron LAser (SACLA). The structure of model protein lysozyme from 1 µm crystals at a resolution of 2.4 Å was obtained.
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Affiliation(s)
- Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5198, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | | | - Changyong Song
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | - Jaehyun Park
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5198, Japan
| | - Takashi Kameshima
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5198, Japan
| | - Shun Ono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | - Takaki Hatsui
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mamoru Suzuki
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tatsuro Shimamura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshiki Tanaka
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
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18
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Liang M, Williams GJ, Messerschmidt M, Seibert MM, Montanez PA, Hayes M, Milathianaki D, Aquila A, Hunter MS, Koglin JE, Schafer DW, Guillet S, Busse A, Bergan R, Olson W, Fox K, Stewart N, Curtis R, Miahnahri AA, Boutet S. The Coherent X-ray Imaging instrument at the Linac Coherent Light Source. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:514-9. [PMID: 25931062 PMCID: PMC4416669 DOI: 10.1107/s160057751500449x] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/04/2015] [Indexed: 05/19/2023]
Abstract
The Coherent X-ray Imaging (CXI) instrument specializes in hard X-ray, in-vacuum, high power density experiments in all areas of science. Two main sample chambers, one containing a 100 nm focus and one a 1 µm focus, are available, each with multiple diagnostics, sample injection, pump-probe and detector capabilities. The flexibility of CXI has enabled it to host a diverse range of experiments, from biological to extreme matter.
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Affiliation(s)
- Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth J. Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - M. Marvin Seibert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Paul A. Montanez
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matt Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Despina Milathianaki
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason E. Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Donald W. Schafer
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Serge Guillet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Armin Busse
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Robert Bergan
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - William Olson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Kay Fox
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Nathaniel Stewart
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Robin Curtis
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Alireza Alan Miahnahri
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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19
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Abstract
Next-generation synchrotron radiation sources, such as X-ray free-electron lasers, energy recovery linacs, and ultra-low-emittance storage rings, are catalyzing novel methods of biomolecular microcrystallography and solution scattering. These methods are described and future trends are predicted. Importantly, there is a growing realization that serial microcrystallography and certain cutting-edge solution scattering experiments can be performed at existing storage ring sources by utilizing new technology. In this sense, next-generation sources are serving two distinct functions, namely, provision of new capabilities that require the newer sources and inspiration of new methods that can be performed at existing sources.
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20
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Perry SL, Guha S, Pawate AS, Henning R, Kosheleva I, Srajer V, Kenis PJA, Ren Z. In situ serial Laue diffraction on a microfluidic crystallization device. J Appl Crystallogr 2014; 47:1975-1982. [PMID: 25484843 PMCID: PMC4248567 DOI: 10.1107/s1600576714023322] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/22/2014] [Indexed: 11/10/2022] Open
Abstract
Renewed interest in room-temperature diffraction has been prompted by the desire to observe structural dynamics of proteins as they function. Serial crystallography, an experimental strategy that aggregates small pieces of data from a large uniform pool of crystals, has been demonstrated at synchrotrons and X-ray free-electron lasers. This work utilizes a microfluidic crystallization platform for serial Laue diffraction from macroscopic crystals and proposes that a collection of small slices of Laue data from many individual crystals is a realistic solution to the difficulties in dynamic studies of irreversible biochemical reactions.
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Affiliation(s)
- Sarah L. Perry
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA, USA
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Sudipto Guha
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Ashtamurthy S. Pawate
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
| | - Vukica Srajer
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
| | - Paul J. A. Kenis
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Zhong Ren
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
- Renz Research Inc., Westmont, IL, USA
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21
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Cantara WA, Olson ED, Musier-Forsyth K. Progress and outlook in structural biology of large viral RNAs. Virus Res 2014; 193:24-38. [PMID: 24956407 PMCID: PMC4252365 DOI: 10.1016/j.virusres.2014.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/11/2014] [Accepted: 06/12/2014] [Indexed: 02/05/2023]
Abstract
The field of viral molecular biology has reached a precipice for which pioneering studies on the structure of viral RNAs are beginning to bridge the gap. It has become clear that viral genomic RNAs are not simply carriers of hereditary information, but rather are active players in many critical stages during replication. Indeed, functions such as cap-independent translation initiation mechanisms are, in some cases, primarily driven by RNA structural determinants. Other stages including reverse transcription initiation in retroviruses, nuclear export and viral packaging are specifically dependent on the proper 3-dimensional folding of multiple RNA domains to recruit necessary viral and host factors required for activity. Furthermore, a large-scale conformational change within the 5'-untranslated region of HIV-1 has been proposed to regulate the temporal switch between viral protein synthesis and packaging. These RNA-dependent functions are necessary for replication of many human disease-causing viruses such as severe acute respiratory syndrome (SARS)-associated coronavirus, West Nile virus, and HIV-1. The potential for antiviral development is currently hindered by a poor understanding of RNA-driven molecular mechanisms, resulting from a lack of structural information on large RNAs and ribonucleoprotein complexes. Herein, we describe the recent progress that has been made on characterizing these large RNAs and provide brief descriptions of the techniques that will be at the forefront of future advances. Ongoing and future work will contribute to a more complete understanding of the lifecycles of retroviruses and RNA viruses and potentially lead to novel antiviral strategies.
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Affiliation(s)
| | | | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
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22
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Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam. Proc Natl Acad Sci U S A 2014; 111:12769-74. [PMID: 25136092 DOI: 10.1073/pnas.1413456111] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has long been known that toxins produced by Bacillus thuringiensis (Bt) are stored in the bacterial cells in crystalline form. Here we describe the structure determination of the Cry3A toxin found naturally crystallized within Bt cells. When whole Bt cells were streamed into an X-ray free-electron laser beam we found that scattering from other cell components did not obscure diffraction from the crystals. The resolution limits of the best diffraction images collected from cells were the same as from isolated crystals. The integrity of the cells at the moment of diffraction is unclear; however, given the short time (∼ 5 µs) between exiting the injector to intersecting with the X-ray beam, our result is a 2.9-Å-resolution structure of a crystalline protein as it exists in a living cell. The study suggests that authentic in vivo diffraction studies can produce atomic-level structural information.
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23
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Feld GK, Frank M. Enabling membrane protein structure and dynamics with X-ray free electron lasers. Curr Opin Struct Biol 2014; 27:69-78. [PMID: 24930119 DOI: 10.1016/j.sbi.2014.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Determining the three-dimensional structures and dynamics of membrane proteins remains one of the great challenges of modern biology. The recent availability of X-ray free electron laser (XFEL) light sources has opened the door to a new and revolutionary approach to performing X-ray analysis of these important biomolecules. Recent advances in sample delivery, data reduction, and phasing have enabled the high-resolution structural probing of membrane proteins at room temperature. While considerable challenges remain, the recent developments described in this review may ultimately provide structural biologists with powerful tools for obtaining unprecedented atomic-scale and dynamic visualization of membrane proteins at near-physiological conditions.
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Affiliation(s)
- Geoffrey K Feld
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Matthias Frank
- Physics Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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24
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Structural analysis of base substitutions in Thermus thermophilus 16S rRNA conferring streptomycin resistance. Antimicrob Agents Chemother 2014; 58:4308-17. [PMID: 24820088 DOI: 10.1128/aac.02857-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Streptomycin is a bactericidal antibiotic that induces translational errors. It binds to the 30S ribosomal subunit, interacting with ribosomal protein S12 and with 16S rRNA through contacts with the phosphodiester backbone. To explore the structural basis for streptomycin resistance, we determined the X-ray crystal structures of 30S ribosomal subunits from six streptomycin-resistant mutants of Thermus thermophilus both in the apo form and in complex with streptomycin. Base substitutions at highly conserved residues in the central pseudoknot of 16S rRNA produce novel hydrogen-bonding and base-stacking interactions. These rearrangements in secondary structure produce only minor adjustments in the three-dimensional fold of the pseudoknot. These results illustrate how antibiotic resistance can occur as a result of small changes in binding site conformation.
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