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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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Birch J, Kwan TOC, Judge PJ, Axford D, Aller P, Butryn A, Reis RI, Bada Juarez JF, Vinals J, Owen RL, Nango E, Tanaka R, Tono K, Joti Y, Tanaka T, Owada S, Sugahara M, Iwata S, Orville AM, Watts A, Moraes I. A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography. J Appl Crystallogr 2023; 56:1361-1370. [PMID: 37791355 PMCID: PMC10543674 DOI: 10.1107/s1600576723006428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/24/2023] [Indexed: 10/05/2023] Open
Abstract
Serial crystallography has emerged as an important tool for structural studies of integral membrane proteins. The ability to collect data from micrometre-sized weakly diffracting crystals at room temperature with minimal radiation damage has opened many new opportunities in time-resolved studies and drug discovery. However, the production of integral membrane protein microcrystals in lipidic cubic phase at the desired crystal density and quantity is challenging. This paper introduces VIALS (versatile approach to high-density microcrystals in lipidic cubic phase for serial crystallography), a simple, fast and efficient method for preparing hundreds of microlitres of high-density microcrystals suitable for serial X-ray diffraction experiments at both synchrotron and free-electron laser sources. The method is also of great benefit for rational structure-based drug design as it facilitates in situ crystal soaking and rapid determination of many co-crystal structures. Using the VIALS approach, room-temperature structures are reported of (i) the archaerhodopsin-3 protein in its dark-adapted state and 110 ns photocycle intermediate, determined to 2.2 and 1.7 Å, respectively, and (ii) the human A2A adenosine receptor in complex with two different ligands determined to a resolution of 3.5 Å.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Tristan O. C. Kwan
- ChemBio, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Peter J. Judge
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Pierre Aller
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Agata Butryn
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Rosana I. Reis
- ChemBio, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Juan F. Bada Juarez
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, Lausanne, CH-1015, Switzerland
| | - Javier Vinals
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Allen M. Orville
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Isabel Moraes
- ChemBio, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
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Kim H, Lim T, Ha GE, Lee JY, Kim JW, Chang N, Kim SH, Kim KH, Lee J, Cho Y, Kim BW, Abrahamsson A, Kim SH, Kim HJ, Park S, Lee SJ, Park J, Cheong E, Kim BM, Cho HS. Structure-based drug discovery of a corticotropin-releasing hormone receptor 1 antagonist using an X-ray free-electron laser. Exp Mol Med 2023; 55:2039-2050. [PMID: 37653040 PMCID: PMC10545732 DOI: 10.1038/s12276-023-01082-1] [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: 01/17/2023] [Revised: 05/24/2023] [Accepted: 06/27/2023] [Indexed: 09/02/2023] Open
Abstract
Thus far, attempts to develop drugs that target corticotropin-releasing hormone receptor 1 (CRF1R), a drug target in stress-related therapy, have been unsuccessful. Studies have focused on using high-resolution G protein-coupled receptor (GPCR) structures to develop drugs. X-ray free-electron lasers (XFELs), which prevent radiation damage and provide access to high-resolution compositions, have helped accelerate GPCR structural studies. We elucidated the crystal structure of CRF1R complexed with a BMK-I-152 antagonist at 2.75 Å using fixed-target serial femtosecond crystallography. The results revealed that two unique hydrogen bonds are present in the hydrogen bond network, the stalk region forms an alpha helix and the hydrophobic network contains an antagonist binding site. We then developed two antagonists-BMK-C203 and BMK-C205-and determined the CRF1R/BMK-C203 and CRF1R/BMK-C205 complex structures at 2.6 and 2.2 Å, respectively. BMK-C205 exerted significant antidepressant effects in mice and, thus, may be utilized to effectively identify structure-based drugs against CRF1R.
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Affiliation(s)
- Hoyoung Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea
| | - Taehyun Lim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Go Eun Ha
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jee-Young Lee
- New Drug Development Center (NDDC), Daegu Gyeongbuk Medical Innovation Foundation (K-Medi hub), 80 Chumbok-ro, Dong-gu, Daegu, 41061, Korea
| | - Jun-Woo Kim
- New Drug Development Center (NDDC), Daegu Gyeongbuk Medical Innovation Foundation (K-Medi hub), 80 Chumbok-ro, Dong-gu, Daegu, 41061, Korea
| | - Nienping Chang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea
| | - Si Hyun Kim
- Doping Control Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Ki Hun Kim
- Doping Control Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Jaeick Lee
- Doping Control Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Yongju Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea
| | - Byeong Wook Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Alva Abrahamsson
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung Hwan Kim
- New Drug Development Center (NDDC), Daegu Gyeongbuk Medical Innovation Foundation (K-Medi hub), 80 Chumbok-ro, Dong-gu, Daegu, 41061, Korea
| | - Hyo-Ji Kim
- New Drug Development Center (NDDC), Daegu Gyeongbuk Medical Innovation Foundation (K-Medi hub), 80 Chumbok-ro, Dong-gu, Daegu, 41061, Korea
| | - Sehan Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Republic of Korea
| | - Sang Jae Lee
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Republic of Korea
| | - Jaehyun Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Republic of Korea
| | - Eunji Cheong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
| | - B Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea.
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Shiriaeva A, Martynowycz MW, Nicolas WJ, Cherezov V, Gonen T. MicroED structure of the human vasopressin 1B receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547888. [PMID: 37461729 PMCID: PMC10350018 DOI: 10.1101/2023.07.05.547888] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
The small size and flexibility of G protein-coupled receptors (GPCRs) have long posed a significant challenge to determining their structures for research and therapeutic applications. Single particle cryogenic electron microscopy (cryoEM) is often out of reach due to the small size of the receptor without a signaling partner. Crystallization of GPCRs in lipidic cubic phase (LCP) often results in crystals that may be too small and difficult to analyze using X-ray microcrystallography at synchrotron sources or even serial femtosecond crystallography at X-ray free electron lasers. Here, we determine the previously unknown structure of the human vasopressin 1B receptor (V1BR) using microcrystal electron diffraction (MicroED). To achieve this, we grew V1BR microcrystals in LCP and transferred the material directly onto electron microscopy grids. The protein was labeled with a fluorescent dye prior to crystallization to locate the microcrystals using cryogenic fluorescence microscopy, and then the surrounding material was removed using a plasma-focused ion beam to thin the sample to a thickness amenable to MicroED. MicroED data from 14 crystalline lamellae were used to determine the 3.2 Å structure of the receptor in the crystallographic space group P 1. These results demonstrate the use of MicroED to determine previously unknown GPCR structures that, despite significant effort, were not tractable by other methods.
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Affiliation(s)
- Anna Shiriaeva
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Michael W. Martynowycz
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
| | - William J. Nicolas
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
| | - Vadim Cherezov
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Tamir Gonen
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
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5
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Doak RB, Shoeman RL, Gorel A, Barends TRM, Marekha B, Haacke S, Nizinski S, Schlichting I. Dynamic catcher for stabilization of high-viscosity extrusion jets. J Appl Crystallogr 2023; 56:903-907. [PMID: 37284264 PMCID: PMC10241051 DOI: 10.1107/s1600576723003795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/26/2023] [Indexed: 06/08/2023] Open
Abstract
A 'catcher' based on a revolving cylindrical collector is described. The simple and inexpensive device reduces free-jet instabilities inherent to high-viscosity extrusion injection, facilitating delivery of microcrystals for serial diffraction X-ray crystallography.
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Affiliation(s)
- R. Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Robert L. Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Alexander Gorel
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Bogdan Marekha
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institut de Physique et Chimie des Matériaux de Strasbourg, University of Strasbourg – CNRS, Strasbourg, France
| | - Stefan Haacke
- Institut de Physique et Chimie des Matériaux de Strasbourg, University of Strasbourg – CNRS, Strasbourg, France
| | - Stanislaw Nizinski
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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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: 5] [Impact Index Per Article: 5.0] [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: 43] [Impact Index Per Article: 21.5] [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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8
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Nam KH. Beef tallow injection matrix for serial crystallography. Sci Rep 2022; 12:694. [PMID: 35027663 PMCID: PMC8758675 DOI: 10.1038/s41598-021-04714-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 12/29/2021] [Indexed: 12/22/2022] Open
Abstract
Serial crystallography (SX) enables the visualization of the time-resolved molecular dynamics of macromolecular structures at room temperature while minimizing radiation damage. In SX experiments, the delivery of a large number of crystals into an X-ray interaction point in a serial and stable manner is key. Sample delivery using viscous medium maintains the stable injection stream at low flow rates, markedly reducing sample consumption compared with that of a liquid jet injector and is widely applied in SX experiments with low repetition rates. As the sample properties and experimental environment can affect the stability of the injection stream of a viscous medium, it is important to develop sample delivery media with various characteristics to optimize the experimental environment. In this study, a beef tallow injection matrix possessing a higher melting temperature than previously reported fat-based shortening and lard media was introduced as a sample delivery medium and applied to SX. Beef tallow was prepared by heat treating fats from cattle, followed by the removal of soluble impurities from the extract by phase separation. Beef tallow exhibited a very stable injection stream at room temperature and a flow rate of < 10 nL/min. The room-temperature structures of lysozyme and glucose isomerase embedded in beef tallow were successfully determined at 1.55 and 1.60 Å, respectively. The background scattering of beef tallow was higher than that of previously reported fat-based shortening and lard media but negligible for data processing. In conclusion, the beef tallow matrix can be employed for sample delivery in SX experiments conducted at temperatures exceeding room temperature.
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Affiliation(s)
- Ki Hyun Nam
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Korea. .,POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Korea.
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9
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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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Abstract
Microbial rhodopsins are light-sensitive transmembrane proteins, evolutionary adapted by various organisms like archaea, bacteria, simple eukaryote, and viruses to utilize solar energy for their survival. A complete understanding of functional mechanisms of these proteins is not possible without the knowledge of their high-resolution structures, which can be primarily obtained by X-ray crystallography. This technique, however, requires high-quality crystals, growing of which is a great challenge especially in case of membrane proteins. In this chapter, we summarize methods applied for crystallization of microbial rhodopsins with the emphasis on crystallization in lipidic mesophases, also known as in meso approach. In particular, we describe in detail the methods of crystallization using lipidic cubic phase to grow both large crystals optimized for traditional crystallographic data collection and microcrystals for serial crystallography.
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Affiliation(s)
- Kirill Kovalev
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Roman Astashkin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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11
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Gilbile D, Shelby ML, Lyubimov AY, Wierman JL, Monteiro DCF, Cohen AE, Russi S, Coleman MA, Frank M, Kuhl TL. Plug-and-play polymer microfluidic chips for hydrated, room temperature, fixed-target serial crystallography. LAB ON A CHIP 2021; 21:4831-4845. [PMID: 34821226 PMCID: PMC8915944 DOI: 10.1039/d1lc00810b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The practice of serial X-ray crystallography (SX) depends on efficient, continuous delivery of hydrated protein crystals while minimizing background scattering. Of the two major types of sample delivery devices, fixed-target devices offer several advantages over widely adopted jet injectors, including: lower sample consumption, clog-free delivery, and the ability to control on-chip crystal density to improve hit rates. Here we present our development of versatile, inexpensive, and robust polymer microfluidic chips for routine and reliable room temperature serial measurements at both synchrotrons and X-ray free electron lasers (XFELs). Our design includes highly X-ray-transparent enclosing thin film layers tuned to minimize scatter background, adaptable sample flow layers tuned to match crystal size, and a large sample area compatible with both raster scanning and rotation based serial data collection. The optically transparent chips can be used both for in situ protein crystallization (to eliminate crystal handling) or crystal slurry loading, with prepared samples stable for weeks in a humidified environment and for several hours in ambient conditions. Serial oscillation crystallography, using a multi-crystal rotational data collection approach, at a microfocus synchrotron beamline (SSRL, beamline 12-1) was used to benchmark the performance of the chips. High-resolution structures (1.3-2.7 Å) were collected from five different proteins - hen egg white lysozyme, thaumatin, bovine liver catalase, concanavalin-A (type VI), and SARS-CoV-2 nonstructural protein NSP5. Overall, our modular fabrication approach enables precise control over the cross-section of materials in the X-ray beam path and facilitates chip adaption to different sample and beamline requirements for user-friendly, straightforward diffraction measurements at room temperature.
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Affiliation(s)
- Deepshika Gilbile
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA.
| | - Megan L Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Artem Y Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Diana C F Monteiro
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Matthew A Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Radiation Oncology, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Matthias Frank
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Tonya L Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA.
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12
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Martynowycz MW, Shiriaeva A, Ge X, Hattne J, Nannenga BL, Cherezov V, Gonen T. MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP. Proc Natl Acad Sci U S A 2021; 118:e2106041118. [PMID: 34462357 PMCID: PMC8433539 DOI: 10.1073/pnas.2106041118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs), or seven-transmembrane receptors, are a superfamily of membrane proteins that are critically important to physiological processes in the human body. Determining high-resolution structures of GPCRs without bound cognate signaling partners, such as a G protein, requires crystallization in lipidic cubic phase (LCP). GPCR crystals grown in LCP are often too small for traditional X-ray crystallography. These microcrystals are ideal for investigation by microcrystal electron diffraction (MicroED), but the gel-like nature of LCP makes traditional approaches to MicroED sample preparation insurmountable. Here, we show that the structure of a human A2A adenosine receptor can be determined by MicroED after converting the LCP into the sponge phase followed by focused ion-beam milling. We determined the structure of the A2A adenosine receptor to 2.8-Å resolution and resolved an antagonist in its orthosteric ligand-binding site, as well as four cholesterol molecules bound around the receptor. This study lays the groundwork for future structural studies of lipid-embedded membrane proteins by MicroED using single microcrystals that would be impossible with other crystallographic methods.
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Affiliation(s)
- Michael W Martynowycz
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Anna Shiriaeva
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Xuanrui Ge
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90007
| | - Johan Hattne
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Vadim Cherezov
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007;
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Tamir Gonen
- HHMI, University of California, Los Angeles, CA 90095;
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Physiology, University of California, Los Angeles, CA 90095
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13
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Molecular basis for lipid recognition by the prostaglandin D 2 receptor CRTH2. Proc Natl Acad Sci U S A 2021; 118:2102813118. [PMID: 34341104 DOI: 10.1073/pnas.2102813118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Prostaglandin D2 (PGD2) signals through the G protein-coupled receptor (GPCR) CRTH2 to mediate various inflammatory responses. CRTH2 is the only member of the prostanoid receptor family that is phylogenetically distant from others, implying a nonconserved mechanism of lipid action on CRTH2. Here, we report a crystal structure of human CRTH2 bound to a PGD2 derivative, 15R-methyl-PGD2 (15mPGD2), by serial femtosecond crystallography. The structure revealed a "polar group in"-binding mode of 15mPGD2 contrasting the "polar group out"-binding mode of PGE2 in its receptor EP3. Structural comparison analysis suggested that these two lipid-binding modes, associated with distinct charge distributions of ligand-binding pockets, may apply to other lipid GPCRs. Molecular dynamics simulations together with mutagenesis studies also identified charged residues at the ligand entry port that function to capture lipid ligands of CRTH2 from the lipid bilayer. Together, our studies suggest critical roles of charge environment in lipid recognition by GPCRs.
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14
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Clabbers MTB, Holmes S, Muusse TW, Vajjhala PR, Thygesen SJ, Malde AK, Hunter DJB, Croll TI, Flueckiger L, Nanson JD, Rahaman MH, Aquila A, Hunter MS, Liang M, Yoon CH, Zhao J, Zatsepin NA, Abbey B, Sierecki E, Gambin Y, Stacey KJ, Darmanin C, Kobe B, Xu H, Ve T. MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography. Nat Commun 2021; 12:2578. [PMID: 33972532 PMCID: PMC8110528 DOI: 10.1038/s41467-021-22590-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/18/2021] [Indexed: 02/03/2023] Open
Abstract
MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.
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Affiliation(s)
- Max T B Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, USA
| | - Susannah Holmes
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Timothy W Muusse
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Parimala R Vajjhala
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sara J Thygesen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Alpeshkumar K Malde
- Institute for Glycomics, Griffith University, Southport, Queensland, Australia
| | - Dominic J B Hunter
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Tristan I Croll
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Leonie Flueckiger
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Md Habibur Rahaman
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jingjing Zhao
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Nadia A Zatsepin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Brian Abbey
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Yann Gambin
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Katryn J Stacey
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Connie Darmanin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, Queensland, Australia.
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15
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Polovinkin V, Khakurel K, Babiak M, Angelov B, Schneider B, Dohnalek J, Andreasson J, Hajdu J. Demonstration of electron diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures. J Appl Crystallogr 2020; 53:1416-1424. [PMID: 33304220 PMCID: PMC7710488 DOI: 10.1107/s1600576720013096] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/27/2020] [Indexed: 12/26/2022] Open
Abstract
Electron crystallography of sub-micrometre-sized 3D protein crystals has emerged recently as a valuable field of structural biology. In meso crystallization methods, utilizing lipidic mesophases, particularly lipidic cubic phases (LCPs), can produce high-quality 3D crystals of membrane proteins (MPs). A major step towards realizing 3D electron crystallography of MP crystals, grown in meso, is to demonstrate electron diffraction from such crystals. The first task is to remove the viscous and sticky lipidic matrix that surrounds the crystals without damaging the crystals. Additionally, the crystals have to be thin enough to let electrons traverse them without significant multiple scattering. In the present work, the concept that focused ion beam milling at cryogenic temperatures (cryo-FIB milling) can be used to remove excess host lipidic mesophase matrix is experimentally verified, and then the crystals are thinned to a thickness suitable for electron diffraction. In this study, bacteriorhodopsin (BR) crystals grown in a lipidic cubic mesophase of monoolein were used as a model system. LCP from a part of a hexagon-shaped plate-like BR crystal (∼10 µm in thickness and ∼70 µm in the longest dimension), which was flash-frozen in liquid nitro-gen, was milled away with a gallium FIB under cryogenic conditions, and a part of the crystal itself was thinned into a ∼210 nm-thick lamella with the ion beam. The frozen sample was then transferred into an electron cryo-microscope, and a nanovolume of ∼1400 × 1400 × 210 nm of the BR lamella was exposed to 200 kV electrons at a fluence of ∼0.06 e Å-2. The resulting electron diffraction peaks were detected beyond 2.7 Å resolution (with an average peak height to background ratio of >2) by a CMOS-based Ceta 16M camera. The results demonstrate that cryo-FIB milling produces high-quality lamellae from crystals grown in lipidic mesophases and pave the way for 3D electron crystallography on crystals grown or embedded in highly viscous media.
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Affiliation(s)
- Vitaly Polovinkin
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
| | - Krishna Khakurel
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
| | - Michal Babiak
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5/4, 62500 Brno, Czech Republic
| | - Borislav Angelov
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
| | - Jan Dohnalek
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
| | - Jakob Andreasson
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
| | - Janos Hajdu
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
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16
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Small-wedge synchrotron and serial XFEL datasets for Cysteinyl leukotriene GPCRs. Sci Data 2020; 7:388. [PMID: 33184270 PMCID: PMC7661540 DOI: 10.1038/s41597-020-00729-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/07/2020] [Indexed: 11/10/2022] Open
Abstract
Structural studies of challenging targets such as G protein-coupled receptors (GPCRs) have accelerated during the last several years due to the development of new approaches, including small-wedge and serial crystallography. Here, we describe the deposition of seven datasets consisting of X-ray diffraction images acquired from lipidic cubic phase (LCP) grown microcrystals of two human GPCRs, Cysteinyl leukotriene receptors 1 and 2 (CysLT1R and CysLT2R), in complex with various antagonists. Five datasets were collected using small-wedge synchrotron crystallography (SWSX) at the European Synchrotron Radiation Facility with multiple crystals under cryo-conditions. Two datasets were collected using X-ray free electron laser (XFEL) serial femtosecond crystallography (SFX) at the Linac Coherent Light Source, with microcrystals delivered at room temperature into the beam within LCP matrix by a viscous media microextrusion injector. All seven datasets have been deposited in the open-access databases Zenodo and CXIDB. Here, we describe sample preparation and annotate crystallization conditions for each partial and full datasets. We also document full processing pipelines and provide wrapper scripts for SWSX and SFX data processing. Measurement(s) | X-ray diffraction data • protein complex • protein structure data • protein crystallization | Technology Type(s) | small-wedge synchrotron crystallography • x-ray crystallography assay • X-ray free electron laser serial femtosecond crystallography | Factor Type(s) | type of G-protein-coupled receptor • type of antagonist |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13128758
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17
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Isoprenoid-chained lipid EROCOC 17+4: a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography. Sci Rep 2020; 10:19305. [PMID: 33168855 PMCID: PMC7652841 DOI: 10.1038/s41598-020-76277-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/26/2020] [Indexed: 11/08/2022] Open
Abstract
In meso crystallization of membrane proteins relies on the use of lipids capable of forming a lipidic cubic phase (LCP). However, almost all previous crystallization trials have used monoacylglycerols, with 1-(cis-9-octadecanoyl)-rac-glycerol (MO) being the most widely used lipid. We now report that EROCOC17+4 mixed with 10% (w/w) cholesterol (Fig. 1) serves as a new matrix for crystallization and a crystal delivery medium in the serial femtosecond crystallography of Adenosine A2A receptor (A2AR). The structures of EROCOC17+4-matrix grown A2AR crystals were determined at 2.0 Å resolution by serial synchrotron rotation crystallography at a cryogenic temperature, and at 1.8 Å by LCP-serial femtosecond crystallography, using an X-ray free-electron laser at 4 and 20 °C sample temperatures, and are comparable to the structure of the MO-matrix grown A2AR crystal (PDB ID: 4EIY). Moreover, X-ray scattering measurements indicated that the EROCOC17+4/water system did not form the crystalline LC phase at least down to - 20 °C, in marked contrast to the equilibrium MO/water system, which transforms into the crystalline LC phase below about 17 °C. As the LC phase formation within the LCP-matrix causes difficulties in protein crystallography experiments in meso, this feature of EROCOC17+4 will expand the utility of the in meso method.
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18
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Lee MY, Geiger J, Ishchenko A, Han GW, Barty A, White TA, Gati C, Batyuk A, Hunter MS, Aquila A, Boutet S, Weierstall U, Cherezov V, Liu W. Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase. IUCRJ 2020; 7:976-984. [PMID: 33209312 PMCID: PMC7642783 DOI: 10.1107/s2052252520012701] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/17/2020] [Indexed: 05/31/2023]
Abstract
Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A2A receptor (A2AAR) at 2.0 Å resolution is determined and compared with previous A2AAR structures determined in vacuum and/or at cryogenic temperatures. Specifically, the capability of utilizing high XFEL beam transmissions is demonstrated, in conjunction with a high dynamic range detector, to collect high-resolution SFX data while reducing crystalline material consumption and shortening the collection time required for a complete dataset. The experimental setup presented herein can be applied to future SFX applications for protein nanocrystal samples to aid in structure-based discovery efforts of therapeutic targets that are difficult to crystallize.
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Affiliation(s)
- Ming-Yue Lee
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James Geiger
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Andrii Ishchenko
- Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, 1002 W. Childs Way, Los Angeles, CA 90089, USA
| | - Gye Won Han
- Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, 1002 W. Childs Way, Los Angeles, CA 90089, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Cornelius Gati
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew Aquila
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Vadim Cherezov
- Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, 1002 W. Childs Way, Los Angeles, CA 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Wei Liu
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
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19
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Zhu L, Bu G, Jing L, Shi D, Lee MY, Gonen T, Liu W, Nannenga BL. Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED. Structure 2020; 28:1149-1159.e4. [PMID: 32735770 PMCID: PMC7544639 DOI: 10.1016/j.str.2020.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/02/2020] [Accepted: 07/13/2020] [Indexed: 01/22/2023]
Abstract
The lipidic cubic phase (LCP) technique has proved to facilitate the growth of high-quality crystals that are otherwise difficult to grow by other methods. However, the crystal size optimization process could be time and resource consuming, if it ever happens. Therefore, improved techniques for structure determination using these small crystals is an important strategy in diffraction technology development. Microcrystal electron diffraction (MicroED) is a technique that uses a cryo-transmission electron microscopy to collect electron diffraction data and determine high-resolution structures from very thin micro- and nanocrystals. In this work, we have used modified LCP and MicroED protocols to analyze crystals embedded in LCP converted by 2-methyl-2,4-pentanediol or lipase, including Proteinase K crystals grown in solution, cholesterol crystals, and human adenosine A2A receptor crystals grown in LCP. These results set the stage for the use of MicroED to analyze microcrystalline samples grown in LCP, especially for those highly challenging membrane protein targets.
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Affiliation(s)
- Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Guanhong Bu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Liang Jing
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Dan Shi
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Ming-Yue Lee
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA.
| | - Brent L Nannenga
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
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20
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Nam KH. Lard Injection Matrix for Serial Crystallography. Int J Mol Sci 2020; 21:ijms21175977. [PMID: 32825186 PMCID: PMC7504126 DOI: 10.3390/ijms21175977] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 02/08/2023] Open
Abstract
Serial crystallography (SX) using X-ray free electron laser or synchrotron X-ray allows for the determination of structures, at room temperature, with reduced radiation damage. Moreover, it allows for the study of structural dynamics of macromolecules using a time-resolved pump-probe, as well as mix-and-inject experiments. Delivering a crystal sample using a viscous medium decreases sample consumption by lowering the flow rate while being extruded from the injector or syringe as compared to a liquid jet injector. Since the environment of crystal samples varies, continuous development of the delivery medium is important for extended SX applications. Herein, I report the preparation and characterization of a lard-based sample delivery medium for SX. This material was obtained using heat treatment, and then the soluble impurities were removed through phase separation. The lard injection medium was highly stable and could be injected via a syringe needle extruded at room temperature with a flow rate < 200 nL/min. Serial millisecond crystallography experiments were performed using lard, and the room temperature structures of lysozyme and glucose isomerase embedded in lard at 1.75 and 1.80 Å, respectively, were determined. The lard medium showed X-ray background scattering similar or relatively lower than shortenings and lipidic cubic phase; therefore, it can be used as sample delivery medium in SX experiments.
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Affiliation(s)
- Ki Hyun Nam
- Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Korea
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21
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Clairfeuille T, Buchholz KR, Li Q, Verschueren E, Liu P, Sangaraju D, Park S, Noland CL, Storek KM, Nickerson NN, Martin L, Dela Vega T, Miu A, Reeder J, Ruiz-Gonzalez M, Swem D, Han G, DePonte DP, Hunter MS, Gati C, Shahidi-Latham S, Xu M, Skelton N, Sellers BD, Skippington E, Sandoval W, Hanan EJ, Payandeh J, Rutherford ST. Structure of the essential inner membrane lipopolysaccharide-PbgA complex. Nature 2020; 584:479-483. [PMID: 32788728 DOI: 10.1038/s41586-020-2597-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/10/2020] [Indexed: 12/21/2022]
Abstract
Lipopolysaccharide (LPS) resides in the outer membrane of Gram-negative bacteria where it is responsible for barrier function1,2. LPS can cause death as a result of septic shock, and its lipid A core is the target of polymyxin antibiotics3,4. Despite the clinical importance of polymyxins and the emergence of multidrug resistant strains5, our understanding of the bacterial factors that regulate LPS biogenesis is incomplete. Here we characterize the inner membrane protein PbgA and report that its depletion attenuates the virulence of Escherichia coli by reducing levels of LPS and outer membrane integrity. In contrast to previous claims that PbgA functions as a cardiolipin transporter6-9, our structural analyses and physiological studies identify a lipid A-binding motif along the periplasmic leaflet of the inner membrane. Synthetic PbgA-derived peptides selectively bind to LPS in vitro and inhibit the growth of diverse Gram-negative bacteria, including polymyxin-resistant strains. Proteomic, genetic and pharmacological experiments uncover a model in which direct periplasmic sensing of LPS by PbgA coordinates the biosynthesis of lipid A by regulating the stability of LpxC, a key cytoplasmic biosynthetic enzyme10-12. In summary, we find that PbgA has an unexpected but essential role in the regulation of LPS biogenesis, presents a new structural basis for the selective recognition of lipids, and provides opportunities for future antibiotic discovery.
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Affiliation(s)
| | - Kerry R Buchholz
- Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Qingling Li
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Erik Verschueren
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Peter Liu
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Dewakar Sangaraju
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA, USA
| | - Summer Park
- Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Cameron L Noland
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Kelly M Storek
- Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | | | - Lynn Martin
- BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | - Trisha Dela Vega
- BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | - Anh Miu
- Biochemical & Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
| | - Janina Reeder
- Bioinformatics & Computational Biology, Genentech Inc., South San Francisco, CA, USA
| | - Maria Ruiz-Gonzalez
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA
| | - Danielle Swem
- Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Guanghui Han
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Daniel P DePonte
- 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
| | - Cornelius Gati
- Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Stanford University, Department of Structural Biology, Stanford, CA, USA
| | | | - Min Xu
- Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Nicholas Skelton
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin D Sellers
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA
| | - Elizabeth Skippington
- Bioinformatics & Computational Biology, Genentech Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Emily J Hanan
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA.
| | - Jian Payandeh
- Structural Biology, Genentech Inc., South San Francisco, CA, USA. .,Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
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22
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Illumination guidelines for ultrafast pump-probe experiments by serial femtosecond crystallography. Nat Methods 2020; 17:681-684. [PMID: 32451477 DOI: 10.1038/s41592-020-0847-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 04/17/2020] [Indexed: 12/20/2022]
Abstract
Time-resolved crystallography with X-ray free-electron lasers enables structural characterization of light-induced reactions on ultrafast timescales. To be biologically and chemically relevant, such studies must be carried out in an appropriate photoexcitation regime to avoid multiphoton artifacts, a common issue in recent studies. We describe numerical and experimental approaches to determine how many photons are needed for single-photon excitation in microcrystals, taking into account losses by scattering.
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23
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Beyond structure: emerging approaches to study GPCR dynamics. Curr Opin Struct Biol 2020; 63:18-25. [PMID: 32305785 DOI: 10.1016/j.sbi.2020.03.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/22/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023]
Abstract
G protein-coupled receptors (GPCRs) constitute the largest superfamily of membrane proteins that are involved in regulation of sensory and physiological processes and implicated in many diseases. The last decade revolutionized the GPCR field by unraveling multiple high-resolution structures of many different receptors in complexes with various ligands and signaling partners. A complete understanding of the complex nature of GPCR function is, however, impossible to attain without combining static structural snapshots with information about GPCR dynamics obtained by complementary spectroscopic techniques. As illustrated in this review, structure and dynamics studies are now paving the way for understanding important questions of GPCR biology such as partial and biased agonism, allostery, oligomerization, and other fundamental aspects of GPCR signaling.
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24
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Viscosity-adjustable grease matrices for serial nanocrystallography. Sci Rep 2020; 10:1371. [PMID: 31992735 PMCID: PMC6987181 DOI: 10.1038/s41598-020-57675-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/30/2019] [Indexed: 11/26/2022] Open
Abstract
Serial femtosecond crystallography (SFX) has enabled determination of room temperature structures of proteins with minimum radiation damage. A highly viscous grease matrix acting as a crystal carrier for serial sample loading at a low flow rate of ~0.5 μl min−1 was introduced into the beam path of X-ray free-electron laser. This matrix makes it possible to determine the protein structure with a sample consumption of less than 1 mg of the protein. The viscosity of the matrix is an important factor in maintaining a continuous and stable sample column from a nozzle of a high viscosity micro-extrusion injector for serial sample loading. Using conventional commercial grease (an oil-based, viscous agent) with insufficient control of viscosity in a matrix often gives an unexpectedly low viscosity, providing an unstable sample stream, with effects such as curling of the stream. Adjustment of the grease viscosity is extremely difficult since the commercial grease contains unknown compounds, which may act as unexpected inhibitors of proteins. This study introduces two novel grease matrix carriers comprising known compounds with a viscosity higher than that of conventional greases, to determine the proteinase K structure from nano-/microcrystals.
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25
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Gustavsson M. New insights into the structure and function of chemokine receptor:chemokine complexes from an experimental perspective. J Leukoc Biol 2020; 107:1115-1122. [DOI: 10.1002/jlb.2mr1219-288r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022] Open
Affiliation(s)
- Martin Gustavsson
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
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26
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Nam KH. Shortening injection matrix for serial crystallography. Sci Rep 2020; 10:107. [PMID: 31919476 PMCID: PMC6952439 DOI: 10.1038/s41598-019-56135-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/06/2019] [Indexed: 11/11/2022] Open
Abstract
Serial crystallography allows crystal structures to be determined at room temperature through the steady delivery of crystals to the X-ray interaction point. Viscous delivery media are advantageous because they afford efficient sample delivery from an injector or syringe at a low flow rate. Hydrophobic delivery media, such as lipidic cubic phase (LCP) or grease, provide a stable injection stream and are widely used. The development of new hydrophobic delivery materials can expand opportunities for future SX studies with various samples. Here, I introduce fat-based shortening as a delivery medium for SX experiments. This material is commercially available at low cost and is straightforward to handle because its phase (i.e., solid or liquid) can be controlled by temperature. Shortening was extruded from a syringe needle in a stable injection stream even below 200 nl/min. X-ray exposed shortening produced several background scattering rings, which have similar or lower intensities than those of LCP and contribute negligibly to data processing. Serial millisecond crystallography was performed using two shortening delivery media, and the room temperature crystal structures of lysozyme and glucose isomerase were successfully determined at resolutions of 1.5–2.0 Å. Therefore, shortening can be used as a sample delivery medium in SX experiments.
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Affiliation(s)
- Ki Hyun Nam
- Division of Biotechnology, Korea University, Seoul, Republic of Korea. .,Institute of Life Science and Natural Resources, Korea University, Seoul, Republic of Korea. .,Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea.
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27
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Shimazu Y, Tono K, Tanaka T, Yamanaka Y, Nakane T, Mori C, Terakado Kimura K, Fujiwara T, Sugahara M, Tanaka R, Doak RB, Shimamura T, Iwata S, Nango E, Yabashi M. High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure. J Appl Crystallogr 2019; 52:1280-1288. [PMID: 31798359 PMCID: PMC6878880 DOI: 10.1107/s1600576719012846] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 09/16/2019] [Indexed: 11/21/2022] Open
Abstract
A sample-injection device has been developed at SPring-8 Angstrom Compact Free-Electron Laser (SACLA) for serial femtosecond crystallography (SFX) at atmospheric pressure. Microcrystals embedded in a highly viscous carrier are stably delivered from a capillary nozzle with the aid of a coaxial gas flow and a suction device. The cartridge-type sample reservoir is easily replaceable and facilitates sample reloading or exchange. The reservoir is positioned in a cooling jacket with a temperature-regulated water flow, which is useful to prevent drastic changes in the sample temperature during data collection. This work demonstrates that the injector successfully worked in SFX of the human A2A adenosine receptor complexed with an antagonist, ZM241385, in lipidic cubic phase and for hen egg-white lysozyme microcrystals in a grease carrier. The injection device has also been applied to many kinds of proteins, not only for static structural analyses but also for dynamics studies using pump-probe techniques.
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Affiliation(s)
- Yoshiaki Shimazu
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yasuaki Yamanaka
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Chihiro Mori
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kanako Terakado Kimura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takaaki Fujiwara
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - R. Bruce Doak
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Tatsuro Shimamura
- 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, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 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, Hyogo 679-5148, Japan
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28
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Ishchenko A, Stauch B, Han GW, Batyuk A, Shiriaeva A, Li C, Zatsepin N, Weierstall U, Liu W, Nango E, Nakane T, Tanaka R, Tono K, Joti Y, Iwata S, Moraes I, Gati C, Cherezov V. Toward G protein-coupled receptor structure-based drug design using X-ray lasers. IUCRJ 2019; 6:1106-1119. [PMID: 31709066 PMCID: PMC6830214 DOI: 10.1107/s2052252519013137] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β2-adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.
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Affiliation(s)
- Andrii Ishchenko
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Benjamin Stauch
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Gye Won Han
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Anna Shiriaeva
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Cornelius Gati
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Vadim Cherezov
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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29
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Andersson R, Safari C, Båth P, Bosman R, Shilova A, Dahl P, Ghosh S, Dunge A, Kjeldsen-Jensen R, Nan J, Shoeman RL, Kloos M, Doak RB, Mueller U, Neutze R, Brändén G. Well-based crystallization of lipidic cubic phase microcrystals for serial X-ray crystallography experiments. Acta Crystallogr D Struct Biol 2019; 75:937-946. [PMID: 31588925 PMCID: PMC6779076 DOI: 10.1107/s2059798319012695] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022] Open
Abstract
Serial crystallography is having an increasing impact on structural biology. This emerging technique opens up new possibilities for studying protein structures at room temperature and investigating structural dynamics using time-resolved X-ray diffraction. A limitation of the method is the intrinsic need for large quantities of well ordered micrometre-sized crystals. Here, a method is presented to screen for conditions that produce microcrystals of membrane proteins in the lipidic cubic phase using a well-based crystallization approach. A key advantage over earlier approaches is that the progress of crystal formation can be easily monitored without interrupting the crystallization process. In addition, the protocol can be scaled up to efficiently produce large quantities of crystals for serial crystallography experiments. Using the well-based crystallization methodology, novel conditions for the growth of showers of microcrystals of three different membrane proteins have been developed. Diffraction data are also presented from the first user serial crystallography experiment performed at MAX IV Laboratory.
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Affiliation(s)
- Rebecka Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | | | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Andreas Dunge
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, SE-431 50 Gothenburg, Sweden
| | - Rasmus Kjeldsen-Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus, Denmark
| | - Jie Nan
- MAX IV Laboratory, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Robert L. Shoeman
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Marco Kloos
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - R. Bruce Doak
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Uwe Mueller
- MAX IV Laboratory, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
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30
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Morris RH, Dye ER, Axford D, Newton MI, Beale JH, Docker PT. Non-Contact Universal Sample Presentation for Room Temperature Macromolecular Crystallography Using Acoustic Levitation. Sci Rep 2019; 9:12431. [PMID: 31455801 PMCID: PMC6712007 DOI: 10.1038/s41598-019-48612-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/24/2019] [Indexed: 11/18/2022] Open
Abstract
Macromolecular Crystallography is a powerful and valuable technique to assess protein structures. Samples are commonly cryogenically cooled to minimise radiation damage effects from the X-ray beam, but low temperatures hinder normal protein functions and this procedure can introduce structural artefacts. Previous experiments utilising acoustic levitation for beamline science have focused on Langevin horns which deliver significant power to the confined droplet and are complex to set up accurately. In this work, the low power, portable TinyLev acoustic levitation system is used in combination with an approach to dispense and contain droplets, free of physical sample support to aid protein crystallography experiments. This method facilitates efficient X-ray data acquisition in ambient conditions compatible with dynamic studies. Levitated samples remain free of interference from fixed sample mounts, receive negligible heating, do not suffer significant evaporation and since the system occupies a small volume, can be readily installed at other light sources.
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Affiliation(s)
- R H Morris
- School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK.
| | - E R Dye
- School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - D Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, OX11 0DE, UK
| | - M I Newton
- School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - J H Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, OX11 0DE, UK
| | - P T Docker
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, OX11 0DE, UK
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31
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Standfuss J. Membrane protein dynamics studied by X-ray lasers – or why only time will tell. Curr Opin Struct Biol 2019; 57:63-71. [DOI: 10.1016/j.sbi.2019.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/05/2023]
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32
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Nass Kovacs G, Colletier JP, Grünbein ML, Yang Y, Stensitzki T, Batyuk A, Carbajo S, Doak RB, Ehrenberg D, Foucar L, Gasper R, Gorel A, Hilpert M, Kloos M, Koglin JE, Reinstein J, Roome CM, Schlesinger R, Seaberg M, Shoeman RL, Stricker M, Boutet S, Haacke S, Heberle J, Heyne K, Domratcheva T, Barends TRM, Schlichting I. Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin. Nat Commun 2019; 10:3177. [PMID: 31320619 PMCID: PMC6639342 DOI: 10.1038/s41467-019-10758-0] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/28/2019] [Indexed: 11/10/2022] Open
Abstract
Bacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption is isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were used to identify a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multiphoton effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins. Bacteriorhodopsin (bR) is a light-driven proton pump. Here the authors combine time-resolved crystallography at a free-electron laser, ultrafast spectroscopy and quantum chemistry to study the structural changes following multiphoton photoexcitation of bR and find that they occur within 300 fs not only in the light-absorbing chromophore but also in the surrounding protein.
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Affiliation(s)
- Gabriela Nass Kovacs
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Jacques-Philippe Colletier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Marie Luise Grünbein
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Yang Yang
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Till Stensitzki
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Alexander Batyuk
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Sergio Carbajo
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - R Bruce Doak
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - David Ehrenberg
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Lutz Foucar
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Raphael Gasper
- Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Alexander Gorel
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Mario Hilpert
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Marco Kloos
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Jason E Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Jochen Reinstein
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Christopher M Roome
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Ramona Schlesinger
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Matthew Seaberg
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Robert L Shoeman
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Miriam Stricker
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Stefan Haacke
- Université de Strasbourg-CNRS, UMR 7504, IPCMS, 23 Rue du Loess, 67034, Strasbourg, France
| | - Joachim Heberle
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Karsten Heyne
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Tatiana Domratcheva
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany.
| | - Thomas R M Barends
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Ilme Schlichting
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany.
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Mishin A, Gusach A, Luginina A, Marin E, Borshchevskiy V, Cherezov V. An outlook on using serial femtosecond crystallography in drug discovery. Expert Opin Drug Discov 2019; 14:933-945. [PMID: 31184514 DOI: 10.1080/17460441.2019.1626822] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: X-ray crystallography has made important contributions to modern drug development but its application to many important drug targets has been extremely challenging. The recent emergence of X-ray free electron lasers (XFELs) and advancements in serial femtosecond crystallography (SFX) have offered new opportunities to overcome limitations of traditional crystallography to accelerate the structure-based drug discovery (SBDD) process. Areas covered: In this review, the authors describe the general principles of X-ray generation and the main properties of XFEL beams, outline details of SFX data collection and processing, and summarize the progress in the development of associated instrumentation for sample delivery and X-ray detection. An overview of the SFX applications to various important drug targets such as membrane proteins is also provided. Expert opinion: While SFX has already made clear advancements toward the understanding of the structure and dynamics of several major drug targets, its robust application in SBDD still needs further developments of new high-throughput techniques for sample production, automation of crystal delivery and data collection, as well as for processing and storage of large amounts of data. The expansion of the available XFEL beamtime is a key to the success of SFX in SBDD.
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Affiliation(s)
- Alexey Mishin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Anastasiia Gusach
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Aleksandra Luginina
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Egor Marin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Valentin Borshchevskiy
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Vadim Cherezov
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia.,b Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California , Los Angeles , CA , USA
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34
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Kwan TOC, Reis R, Siligardi G, Hussain R, Cheruvara H, Moraes I. Selection of Biophysical Methods for Characterisation of Membrane Proteins. Int J Mol Sci 2019; 20:E2605. [PMID: 31137900 PMCID: PMC6566885 DOI: 10.3390/ijms20102605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 02/01/2023] Open
Abstract
Over the years, there have been many developments and advances in the field of integral membrane protein research. As important pharmaceutical targets, it is paramount to understand the mechanisms of action that govern their structure-function relationships. However, the study of integral membrane proteins is still incredibly challenging, mostly due to their low expression and instability once extracted from the native biological membrane. Nevertheless, milligrams of pure, stable, and functional protein are always required for biochemical and structural studies. Many modern biophysical tools are available today that provide critical information regarding to the characterisation and behaviour of integral membrane proteins in solution. These biophysical approaches play an important role in both basic research and in early-stage drug discovery processes. In this review, it is not our objective to present a comprehensive list of all existing biophysical methods, but a selection of the most useful and easily applied to basic integral membrane protein research.
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Affiliation(s)
- Tristan O C Kwan
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
| | - Rosana Reis
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Harish Cheruvara
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
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35
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Stauch B, Johansson LC, McCorvy JD, Patel N, Han GW, Huang XP, Gati C, Batyuk A, Slocum ST, Ishchenko A, Brehm W, White TA, Michaelian N, Madsen C, Zhu L, Grant TD, Grandner JM, Shiriaeva A, Olsen RHJ, Tribo AR, Yous S, Stevens RC, Weierstall U, Katritch V, Roth BL, Liu W, Cherezov V. Structural basis of ligand recognition at the human MT 1 melatonin receptor. Nature 2019; 569:284-288. [PMID: 31019306 PMCID: PMC6696938 DOI: 10.1038/s41586-019-1141-3] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 03/25/2019] [Indexed: 11/08/2022]
Abstract
Melatonin (N-acetyl-5-methoxytryptamine) is a neurohormone that maintains circadian rhythms1 by synchronization to environmental cues and is involved in diverse physiological processes2 such as the regulation of blood pressure and core body temperature, oncogenesis, and immune function3. Melatonin is formed in the pineal gland in a light-regulated manner4 by enzymatic conversion from 5-hydroxytryptamine (5-HT or serotonin), and modulates sleep and wakefulness5 by activating two high-affinity G-protein-coupled receptors, type 1A (MT1) and type 1B (MT2)3,6. Shift work, travel, and ubiquitous artificial lighting can disrupt natural circadian rhythms; as a result, sleep disorders affect a substantial population in modern society and pose a considerable economic burden7. Over-the-counter melatonin is widely used to alleviate jet lag and as a safer alternative to benzodiazepines and other sleeping aids8,9, and is one of the most popular supplements in the United States10. Here, we present high-resolution room-temperature X-ray free electron laser (XFEL) structures of MT1 in complex with four agonists: the insomnia drug ramelteon11, two melatonin analogues, and the mixed melatonin-serotonin antidepressant agomelatine12,13. The structure of MT2 is described in an accompanying paper14. Although the MT1 and 5-HT receptors have similar endogenous ligands, and agomelatine acts on both receptors, the receptors differ markedly in the structure and composition of their ligand pockets; in MT1, access to the ligand pocket is tightly sealed from solvent by extracellular loop 2, leaving only a narrow channel between transmembrane helices IV and V that connects it to the lipid bilayer. The binding site is extremely compact, and ligands interact with MT1 mainly by strong aromatic stacking with Phe179 and auxiliary hydrogen bonds with Asn162 and Gln181. Our structures provide an unexpected example of atypical ligand entry for a non-lipid receptor, lay the molecular foundation of ligand recognition by melatonin receptors, and will facilitate the design of future tool compounds and therapeutic agents, while their comparison to 5-HT receptors yields insights into the evolution and polypharmacology of G-protein-coupled receptors.
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MESH Headings
- Acetamides/chemistry
- Acetamides/metabolism
- Amino Acid Sequence
- Antidepressive Agents/chemistry
- Antidepressive Agents/metabolism
- Crystallization
- Electrons
- Humans
- Indenes/chemistry
- Indenes/metabolism
- Lasers
- Ligands
- Melatonin/analogs & derivatives
- Melatonin/chemistry
- Models, Molecular
- Molecular Docking Simulation
- Mutation
- Receptor, Melatonin, MT1/agonists
- Receptor, Melatonin, MT1/chemistry
- Receptor, Melatonin, MT1/genetics
- Receptor, Melatonin, MT1/metabolism
- Receptor, Serotonin, 5-HT2C/chemistry
- Structure-Activity Relationship
- Substrate Specificity
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Affiliation(s)
- Benjamin Stauch
- Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Linda C Johansson
- Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - John D McCorvy
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nilkanth Patel
- Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Gye Won Han
- Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cornelius Gati
- SLAC National Accelerator Laboratory, Bioscience Division, Menlo Park, CA, USA
- Stanford University, Department of Structural Biology, Stanford, CA, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Samuel T Slocum
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrii Ishchenko
- Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
| | - Nairie Michaelian
- Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Caleb Madsen
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Lan Zhu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Thomas D Grant
- Hauptman-Woodward Institute, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jessica M Grandner
- Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Anna Shiriaeva
- Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Reid H J Olsen
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra R Tribo
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Saïd Yous
- Univ Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, France
| | - Raymond C Stevens
- Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Vsevolod Katritch
- Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Wei Liu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Vadim Cherezov
- Bridge Institute,USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
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36
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Abstract
Over the past six decades, steadily increasing progress in the application of the principles and techniques of the physical sciences to the study of biological systems has led to remarkable insights into the molecular basis of life. Of particular significance has been the way in which the determination of the structures and dynamical properties of proteins and nucleic acids has so often led directly to a profound understanding of the nature and mechanism of their functional roles. The increasing number and power of experimental and theoretical techniques that can be applied successfully to living systems is now ushering in a new era of structural biology that is leading to fundamentally new information about the maintenance of health, the origins of disease, and the development of effective strategies for therapeutic intervention. This article provides a brief overview of some of the most powerful biophysical methods in use today, along with references that provide more detailed information about recent applications of each of them. In addition, this article acts as an introduction to four authoritative reviews in this volume. The first shows the ways that a multiplicity of biophysical methods can be combined with computational techniques to define the architectures of complex biological systems, such as those involving weak interactions within ensembles of molecular components. The second illustrates one aspect of this general approach by describing how recent advances in mass spectrometry, particularly in combination with other techniques, can generate fundamentally new insights into the properties of membrane proteins and their functional interactions with lipid molecules. The third reviewdemonstrates the increasing power of rapidly evolving diffraction techniques, employing the very short bursts of X-rays of extremely high intensity that are now accessible as a result of the construction of free-electron lasers, in particular to carry out time-resolved studies of biochemical reactions. The fourth describes in detail the application of such approaches to probe the mechanism of the light-induced changes associated with bacteriorhodopsin's ability to convert light energy into chemical energy.
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Affiliation(s)
- Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
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37
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Nam KH. Sample Delivery Media for Serial Crystallography. Int J Mol Sci 2019; 20:E1094. [PMID: 30836596 PMCID: PMC6429298 DOI: 10.3390/ijms20051094] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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38
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Polyacrylamide injection matrix for serial femtosecond crystallography. Sci Rep 2019; 9:2525. [PMID: 30792457 PMCID: PMC6385504 DOI: 10.1038/s41598-019-39020-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/11/2019] [Indexed: 01/09/2023] Open
Abstract
Serial femtosecond crystallography (SFX) provides opportunities to observe the dynamics of macromolecules without causing radiation damage at room temperature. Although SFX provides a biologically more reliable crystal structure than provided by the existing synchrotron sources, there are limitations due to the consumption of many crystal samples. A viscous medium as a carrier matrix reduces the flow rate of the crystal sample from the injector, thereby dramatically reducing sample consumption. However, the currently available media cannot be applied to specific crystal samples owing to reactions between the viscous medium and crystal sample. The discovery and characterisation of a new delivery medium for SFX can further expand its use. Herein, we report the preparation of a polyacrylamide (PAM) injection matrix to determine the crystal structure with an X-ray free-electron laser. We obtained 11,936 and 22,213 indexed images using 0.5 mg lysozyme and 1.0 mg thermolysin, respectively. We determined the crystal structures of lysozyme and thermolysin delivered in PAM at 1.7 Å and 1.8 Å resolutions. The maximum background scattering from PAM was lower than monoolein, a commonly used viscous medium. Our results show that PAM can be used as a sample delivery media in SFX studies.
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39
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Keedy DA. Journey to the center of the protein: allostery from multitemperature multiconformer X-ray crystallography. Acta Crystallogr D Struct Biol 2019; 75:123-137. [PMID: 30821702 PMCID: PMC6400254 DOI: 10.1107/s2059798318017941] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 12/19/2018] [Indexed: 02/08/2023] Open
Abstract
Proteins inherently fluctuate between conformations to perform functions in the cell. For example, they sample product-binding, transition-state-stabilizing and product-release states during catalysis, and they integrate signals from remote regions of the structure for allosteric regulation. However, there is a lack of understanding of how these dynamic processes occur at the basic atomic level. This gap can be at least partially addressed by combining variable-temperature (instead of traditional cryogenic temperature) X-ray crystallography with algorithms for modeling alternative conformations based on electron-density maps, in an approach called multitemperature multiconformer X-ray crystallography (MMX). Here, the use of MMX to reveal alternative conformations at different sites in a protein structure and to estimate the degree of energetic coupling between them is discussed. These insights can suggest testable hypotheses about allosteric mechanisms. Temperature is an easily manipulated experimental parameter, so the MMX approach is widely applicable to any protein that yields well diffracting crystals. Moreover, the general principles of MMX are extensible to other perturbations such as pH, pressure, ligand concentration etc. Future work will explore strategies for leveraging X-ray data across such perturbation series to more quantitatively measure how different parts of a protein structure are coupled to each other, and the consequences thereof for allostery and other aspects of protein function.
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Affiliation(s)
- Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, USA
- Department of Chemistry and Biochemistry, City College of New York, New York, USA
- PhD Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, USA
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40
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Grünbein ML, Nass Kovacs G. Sample delivery for serial crystallography at free-electron lasers and synchrotrons. Acta Crystallogr D Struct Biol 2019; 75:178-191. [PMID: 30821706 PMCID: PMC6400261 DOI: 10.1107/s205979831801567x] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/05/2018] [Indexed: 12/21/2022] Open
Abstract
The high peak brilliance and femtosecond pulse duration of X-ray free-electron lasers (XFELs) provide new scientific opportunities for experiments in physics, chemistry and biology. In structural biology, one of the major applications is serial femtosecond crystallography. The intense XFEL pulse results in the destruction of any exposed microcrystal, making serial data collection mandatory. This requires a high-throughput serial approach to sample delivery. To this end, a number of such sample-delivery techniques have been developed, some of which have been ported to synchrotron sources, where they allow convenient low-dose data collection at room temperature. Here, the current sample-delivery techniques used at XFEL and synchrotron sources are reviewed, with an emphasis on liquid injection and high-viscosity extrusion, including their application for time-resolved experiments. The challenges associated with sample delivery at megahertz repetition-rate XFELs are also outlined.
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Affiliation(s)
- Marie Luise Grünbein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Gabriela Nass Kovacs
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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41
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Audet M, White KL, Breton B, Zarzycka B, Han GW, Lu Y, Gati C, Batyuk A, Popov P, Velasquez J, Manahan D, Hu H, Weierstall U, Liu W, Shui W, Katritch V, Cherezov V, Hanson MA, Stevens RC. Crystal structure of misoprostol bound to the labor inducer prostaglandin E 2 receptor. Nat Chem Biol 2019; 15:11-17. [PMID: 30510194 PMCID: PMC6289721 DOI: 10.1038/s41589-018-0160-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/05/2018] [Indexed: 01/07/2023]
Abstract
Misoprostol is a life-saving drug in many developing countries for women at risk of post-partum hemorrhaging owing to its affordability, stability, ease of administration and clinical efficacy. However, misoprostol lacks receptor and tissue selectivities, and thus its use is accompanied by a number of serious side effects. The development of pharmacological agents combining the advantages of misoprostol with improved selectivity is hindered by the absence of atomic details of misoprostol action in labor induction. Here, we present the 2.5 Å resolution crystal structure of misoprostol free-acid form bound to the myometrium labor-inducing prostaglandin E2 receptor 3 (EP3). The active state structure reveals a completely enclosed binding pocket containing a structured water molecule that coordinates misoprostol's ring structure. Modeling of selective agonists in the EP3 structure reveals rationales for selectivity. These findings will provide the basis for the next generation of uterotonic drugs that will be suitable for administration in low resource settings.
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Affiliation(s)
- Martin Audet
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Kate L. White
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Billy Breton
- Domain Therapeutics NA Inc., Frederick-Banting Road, Montreal H4S 1Z9, Canada
| | - Barbara Zarzycka
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Gye Won Han
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Yan Lu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Cornelius Gati
- Linac Coherent Light Source, SLAC, National Accelerator Laboratory, Menlo Park, California 94025, USA,Stanford University, Department of Structural Biology, Palo Alto, California 94305, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC, National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Petr Popov
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA,Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Jeffrey Velasquez
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - David Manahan
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Hao Hu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Uwe Weierstall
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Vsevolod Katritch
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA,Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Vadim Cherezov
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA,Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | | | - Raymond C. Stevens
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA,Correspondence:
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42
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Yun JH, Li X, Park JH, Wang Y, Ohki M, Jin Z, Lee W, Park SY, Hu H, Li C, Zatsepin N, Hunter MS, Sierra RG, Koralek J, Yoon CH, Cho HS, Weierstall U, Tang L, Liu H, Lee W. Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency. J Biol Chem 2018; 294:794-804. [PMID: 30455349 DOI: 10.1074/jbc.ra118.004038] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/12/2018] [Indexed: 11/06/2022] Open
Abstract
Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate because of a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 Å, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all-trans retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main and side chains as well as of chloride and water molecules because of temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.
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Affiliation(s)
- Ji-Hye Yun
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Xuanxuan Li
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China.,Department of Engineering Physics, Tsinghua University, Beijing 100086, China
| | - Jae-Hyun Park
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Yang Wang
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China
| | - Mio Ohki
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Zeyu Jin
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Wonbin Lee
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Hao Hu
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Chufeng Li
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Nadia Zatsepin
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Jake Koralek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Hyun-Soo Cho
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, South Korea
| | - Uwe Weierstall
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Leihan Tang
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China,
| | - Weontae Lee
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea,
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43
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Botha S, Baitan D, Jungnickel KEJ, Oberthür D, Schmidt C, Stern S, Wiedorn MO, Perbandt M, Chapman HN, Betzel C. De novo protein structure determination by heavy-atom soaking in lipidic cubic phase and SIRAS phasing using serial synchrotron crystallography. IUCRJ 2018; 5:524-530. [PMID: 30224955 PMCID: PMC6126645 DOI: 10.1107/s2052252518009223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/26/2018] [Indexed: 05/30/2023]
Abstract
During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application of experimental phasing to serial crystallography data has remained a challenging task owing to the inherent inaccuracy of the diffraction data. Here, a particularly gentle method for incorporating heavy atoms into micrometre-sized crystals utilizing lipidic cubic phase (LCP) as a carrier medium is reported. Soaking in LCP prior to data collection offers a new, efficient and gentle approach for preparing heavy-atom-derivative crystals directly before diffraction data collection using serial crystallography methods. This approach supports effective phasing by utilizing a reasonably low number of diffraction patterns. Using synchrotron radiation and exploiting the anomalous scattering signal of mercury for single isomorphous replacement with anomalous scattering (SIRAS) phasing resulted in high-quality electron-density maps that were sufficient for building a complete structural model of proteinase K at 1.9 Å resolution using automatic model-building tools.
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Affiliation(s)
- S. Botha
- Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
- Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - D. Baitan
- Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
- Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
- Xtal Concepts GmbH, Marlowring 19, 22525 Hamburg, Germany
| | - K. E. J. Jungnickel
- Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
| | - D. Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - C. Schmidt
- Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
- Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
| | - S. Stern
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - M. O. Wiedorn
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - M. Perbandt
- Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
- Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - H. N. Chapman
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - C. Betzel
- Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
- Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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44
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Huang CY, Olieric V, Howe N, Warshamanage R, Weinert T, Panepucci E, Vogeley L, Basu S, Diederichs K, Caffrey M, Wang M. In situ serial crystallography for rapid de novo membrane protein structure determination. Commun Biol 2018; 1:124. [PMID: 30272004 PMCID: PMC6123769 DOI: 10.1038/s42003-018-0123-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/19/2018] [Indexed: 11/30/2022] Open
Abstract
De novo membrane protein structure determination is often limited by the availability of large crystals and the difficulties in obtaining accurate diffraction data for experimental phasing. Here we present a method that combines in situ serial crystallography with de novo phasing for fast, efficient membrane protein structure determination. The method enables systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without the need for direct crystal harvesting. The requisite data quality for experimental phasing is achieved by accumulating diffraction signals from isomorphous crystals identified post-data collection. The method works in all experimental phasing scenarios and is particularly attractive with fragile, weakly diffracting microcrystals. The automated serial data collection approach can be readily adopted at most microfocus macromolecular crystallography beamlines.
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Affiliation(s)
- Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Nicole Howe
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | | | - Tobias Weinert
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Ezequiel Panepucci
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Lutz Vogeley
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Shibom Basu
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Kay Diederichs
- Fachbereich Biologie, Universität Konstanz, M647, D-78457, Konstanz, Germany
| | - Martin Caffrey
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland.
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland.
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45
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Abstract
G protein-coupled receptors (GPCRs) represent a large superfamily of membrane proteins that mediate cell signaling and regulate a variety of physiological processes in the human body. Structure-function studies of this superfamily were enabled a decade ago by multiple breakthroughs in technology that included receptor stabilization, crystallization in a membrane environment, and microcrystallography. The recent emergence of X-ray free-electron lasers (XFELs) has further accelerated structural studies of GPCRs and other challenging proteins by overcoming radiation damage and providing access to high-resolution structures and dynamics using micrometer-sized crystals. Here, we summarize key technology advancements and major milestones of GPCR research using XFELs and provide a brief outlook on future developments in the field.
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Affiliation(s)
- Benjamin Stauch
- Department of Chemistry and Bridge Institute, University of Southern California, Los Angeles, California 90089, USA; ,
| | - Vadim Cherezov
- Department of Chemistry and Bridge Institute, University of Southern California, Los Angeles, California 90089, USA; ,
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46
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Ishchenko A, Gati C, Cherezov V. Structural biology of G protein-coupled receptors: new opportunities from XFELs and cryoEM. Curr Opin Struct Biol 2018; 51:44-52. [PMID: 29554543 DOI: 10.1016/j.sbi.2018.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 01/14/2023]
Abstract
G protein-coupled receptors mediate cell signaling and regulate the majority of sensory and physiological processes in the human body. Recent breakthroughs in cryo-electron microscopy and X-ray free electron lasers have accelerated structural studies of difficult-to-crystallize receptors and their signaling complexes, and have opened up new opportunities in understanding conformational dynamics and visualizing the process of receptor activation with unprecedented spatial and temporal resolution. Here, we summarize major milestones and challenges associated with the application of these techniques and outline future directions in their development with a focus on membrane protein structural biology.
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Affiliation(s)
- Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Cornelius Gati
- SLAC National Accelerator Laboratory, Bioscience Division, Menlo Park, CA 94025, USA; Stanford University, Department of Structural Biology, Stanford, CA 94305, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia.
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47
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Schieferstein JM, Pawate AS, Varel MJ, Guha S, Astrauskaite I, Gennis RB, Kenis PJA. X-ray transparent microfluidic platforms for membrane protein crystallization with microseeds. LAB ON A CHIP 2018; 18:944-954. [PMID: 29469138 PMCID: PMC5849577 DOI: 10.1039/c7lc01141e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Crystallization of membrane proteins is a critical step for uncovering atomic resolution 3-D structures and elucidating structure-function relationships. Microseeding, the process of transferring sub-microscopic crystal nuclei from initial screens into new crystallization experiments, is an effective, yet underutilized approach to grow crystals suitable for X-ray crystallography. Here, we report simplified methods for crystallization of membrane proteins that utilize microseeding in X-ray transparent microfluidic chips. First, a microfluidic method for introduction of microseed dilutions into metastable crystallization experiments is demonstrated for photoactive yellow protein and cytochrome bo3 oxidase. As microseed concentration decreased, the number of crystals decreased while the average size increased. Second, we demonstrate a microfluidic chip for microseed screening, where many crystallization conditions were formulated on-chip prior to mixing with microseeds. Crystallization composition, crystal size, and diffraction data were collected and mapped on phase diagrams, which revealed that crystals of similar diffraction quality and size typically grow in distinct regions of the phase diagram.
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Affiliation(s)
- Jeremy M Schieferstein
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, USA.
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48
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Park J, Kim S, Kim S, Nam KH. Multifarious injection chamber for molecular structure study (MICOSS) system: development and application for serial femtosecond crystallography at Pohang Accelerator Laboratory X-ray Free-Electron Laser. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:323-328. [PMID: 29488909 DOI: 10.1107/s160057751800022x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/04/2018] [Indexed: 06/08/2023]
Abstract
The multifarious injection chamber for molecular structure study (MICOSS) experimental system has been developed at the Pohang Accelerator Laboratory X-ray Free-Electron Laser for conducting serial femtosecond crystallography. This system comprises several instruments such as a dedicated sample chamber, sample injectors, sample environment diagnostic system and detector stage for convenient distance manipulation. Serial femtosecond crystallography experiments of lysozyme crystals have been conducted successfully. The diffraction peaks have reached to ∼1.8 Å resolution at the photon energy of 9.785 keV.
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Affiliation(s)
- Jaehyun Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Seonghan Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sangsoo Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Ki Hyun Nam
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
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49
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Lee DB, Kim JM, Seok JH, Lee JH, Jo JD, Mun JY, Conrad C, Coe J, Nelson G, Hogue B, White TA, Zatsepin N, Weierstall U, Barty A, Chapman H, Fromme P, Spence J, Chung MS, Oh CH, Kim KH. Supersaturation-controlled microcrystallization and visualization analysis for serial femtosecond crystallography. Sci Rep 2018; 8:2541. [PMID: 29416086 PMCID: PMC5803221 DOI: 10.1038/s41598-018-20899-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/23/2018] [Indexed: 11/09/2022] Open
Abstract
Time-resolved serial femtosecond crystallography with X-ray free electron laser (XFEL) holds the potential to view fast reactions occurring at near-physiological temperature. However, production and characterization of homogeneous micron-sized protein crystals at high density remain a bottleneck, due to the lack of the necessary equipments in ordinary laboratories. We describe here supersaturation-controlled microcrystallization and visualization and analysis tools that can be easily used in any laboratory. The microcrystallization conditions of the influenza virus hemagglutinin were initially obtained with low reproducibility, which was improved by employing a rapid evaporation of hanging drops. Supersaturation-controlled microcrystallization was then developed in a vapor diffusion mode, where supersaturation was induced by evaporation in hanging drops sequentially for durations ranging from 30 sec to 3 min, depending on the protein. It was applied successfully to the microcrystal formation of lysozyme, ferritin and hemagglutinin with high density. Moreover, visualization and analysis tools were developed to characterize the microcrystals observed by light microscopy. The size and density distributions of microcrystals analyzed by the tools were found to be consistent with the results of manual analysis, further validated by high-resolution microscopic analyses. Our supersaturation-controlled microcrystallization and visualization and analysis tools will provide universal access to successful XFEL studies.
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Affiliation(s)
- Dan Bi Lee
- Department of Biotechnology & Bioinformatics, Korea University, Sejong, Korea
| | - Jong-Min Kim
- Department of Electronics & Information Engineering, Korea University, Sejong, Korea
| | - Jong Hyeon Seok
- Department of Biotechnology & Bioinformatics, Korea University, Sejong, Korea
| | - Ji-Hye Lee
- Department of Biotechnology & Bioinformatics, Korea University, Sejong, Korea
| | - Jae Deok Jo
- Department of Biotechnology & Bioinformatics, Korea University, Sejong, Korea
| | - Ji Young Mun
- Department of Structure and Function of Neural Network, Korea Brain Research Institute, Daegu, Korea
| | - Chelsie Conrad
- Department of Chemistry, Arizona State University, Tempe, Arizona, USA
| | - Jesse Coe
- Department of Chemistry, Arizona State University, Tempe, Arizona, USA
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Brenda Hogue
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Petra Fromme
- Department of Chemistry, Arizona State University, Tempe, Arizona, USA
| | - John Spence
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Mi Sook Chung
- Department of Food and Nutrition, Duksung Women's University, Seoul, Korea
| | - Chang-Hyun Oh
- Department of Electronics & Information Engineering, Korea University, Sejong, Korea.
| | - Kyung Hyun Kim
- Department of Biotechnology & Bioinformatics, Korea University, Sejong, Korea.
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50
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Kimura F, Kimura T. Magnetically textured powders—an alternative to single-crystal and powder X-ray diffraction methods. CrystEngComm 2018. [DOI: 10.1039/c7ce01305a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Structure determination of materials in their crystalline phase aids in the understanding and design of their functions.
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Affiliation(s)
- Fumiko Kimura
- Division of Forestry and Biomaterials
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Tsunehisa Kimura
- Division of Forestry and Biomaterials
- Kyoto University
- Kyoto 606-8502
- Japan
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