1
|
Foos N, Florial JB, Eymery M, Sinoir J, Felisaz F, Oscarsson M, Beteva A, Bowler MW, Nurizzo D, Papp G, Soler-Lopez M, Nanao M, Basu S, McCarthy AA. In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry. IUCRJ 2024; 11:780-791. [PMID: 39008358 PMCID: PMC11364034 DOI: 10.1107/s2052252524005785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024]
Abstract
The advent of serial crystallography has rejuvenated and popularized room-temperature X-ray crystal structure determination. Structures determined at physiological temperature reveal protein flexibility and dynamics. In addition, challenging samples (e.g. large complexes, membrane proteins and viruses) form fragile crystals that are often difficult to harvest for cryo-crystallography. Moreover, a typical serial crystallography experiment requires a large number of microcrystals, mainly achievable through batch crystallization. Many medically relevant samples are expressed in mammalian cell lines, producing a meager quantity of protein that is incompatible with batch crystallization. This can limit the scope of serial crystallography approaches. Direct in situ data collection from a 96-well crystallization plate enables not only the identification of the best diffracting crystallization condition but also the possibility for structure determination under ambient conditions. Here, we describe an in situ serial crystallography (iSX) approach, facilitating direct measurement from crystallization plates mounted on a rapidly exchangeable universal plate holder deployed at a microfocus beamline, ID23-2, at the European Synchrotron Radiation Facility. We applied our iSX approach on a challenging project, autotaxin, a therapeutic target expressed in a stable human cell line, to determine the structure in the lowest-symmetry P1 space group at 3.0 Å resolution. Our in situ data collection strategy provided a complete dataset for structure determination while screening various crystallization conditions. Our data analysis reveals that the iSX approach is highly efficient at a microfocus beamline, improving throughput and demonstrating how crystallization plates can be routinely used as an alternative method of presenting samples for serial crystallography experiments at synchrotrons.
Collapse
Affiliation(s)
- Nicolas Foos
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Jean-Baptise Florial
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Mathias Eymery
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Jeremy Sinoir
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Franck Felisaz
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Marcus Oscarsson
- European Synchrotron Radiation Facility71 Avenue des Martyrs38042GrenobleFrance
| | - Antonia Beteva
- European Synchrotron Radiation Facility71 Avenue des Martyrs38042GrenobleFrance
| | - Matthew W. Bowler
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Didier Nurizzo
- European Synchrotron Radiation Facility71 Avenue des Martyrs38042GrenobleFrance
| | - Gergely Papp
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | | | - Max Nanao
- European Synchrotron Radiation Facility71 Avenue des Martyrs38042GrenobleFrance
| | - Shibom Basu
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Andrew A. McCarthy
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| |
Collapse
|
2
|
Thompson AJ, Sanchez-Weatherby J, Williams LJ, Mikolajek H, Sandy J, Worrall JAR, Hough MA. Efficient in situ screening of and data collection from microcrystals in crystallization plates. Acta Crystallogr D Struct Biol 2024; 80:279-288. [PMID: 38488731 PMCID: PMC10994175 DOI: 10.1107/s2059798324001955] [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: 12/15/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024] Open
Abstract
A considerable bottleneck in serial crystallography at XFEL and synchrotron sources is the efficient production of large quantities of homogenous, well diffracting microcrystals. Efficient high-throughput screening of batch-grown microcrystals and the determination of ground-state structures from different conditions is thus of considerable value in the early stages of a project. Here, a highly sample-efficient methodology to measure serial crystallography data from microcrystals by raster scanning within standard in situ 96-well crystallization plates is described. Structures were determined from very small quantities of microcrystal suspension and the results were compared with those from other sample-delivery methods. The analysis of a two-dimensional batch crystallization screen using this method is also described as a useful guide for further optimization and the selection of appropriate conditions for scaling up microcrystallization.
Collapse
Affiliation(s)
- Amy J. Thompson
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Juan Sanchez-Weatherby
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Lewis J. Williams
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Halina Mikolajek
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James Sandy
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Jonathan A. R. Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Michael A. Hough
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| |
Collapse
|
3
|
Gildea RJ, Beilsten-Edmands J, Axford D, Horrell S, Aller P, Sandy J, Sanchez-Weatherby J, Owen CD, Lukacik P, Strain-Damerell C, Owen RL, Walsh MA, Winter G. xia2.multiplex: a multi-crystal data-analysis pipeline. Acta Crystallogr D Struct Biol 2022; 78:752-769. [PMID: 35647922 PMCID: PMC9159281 DOI: 10.1107/s2059798322004399] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/25/2022] [Indexed: 11/11/2022] Open
Abstract
In macromolecular crystallography, radiation damage limits the amount of data that can be collected from a single crystal. It is often necessary to merge data sets from multiple crystals; for example, small-wedge data collections from micro-crystals, in situ room-temperature data collections and data collection from membrane proteins in lipidic mesophases. Whilst the indexing and integration of individual data sets may be relatively straightforward with existing software, merging multiple data sets from small wedges presents new challenges. The identification of a consensus symmetry can be problematic, particularly in the presence of a potential indexing ambiguity. Furthermore, the presence of non-isomorphous or poor-quality data sets may reduce the overall quality of the final merged data set. To facilitate and help to optimize the scaling and merging of multiple data sets, a new program, xia2.multiplex, has been developed which takes data sets individually integrated with DIALS and performs symmetry analysis, scaling and merging of multi-crystal data sets. xia2.multiplex also performs analysis of various pathologies that typically affect multi-crystal data sets, including non-isomorphism, radiation damage and preferential orientation. After the description of a number of use cases, the benefit of xia2.multiplex is demonstrated within a wider autoprocessing framework in facilitating a multi-crystal experiment collected as part of in situ room-temperature fragment-screening experiments on the SARS-CoV-2 main protease.
Collapse
Affiliation(s)
- Richard J. Gildea
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James Beilsten-Edmands
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Danny Axford
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Sam Horrell
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Pierre Aller
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James Sandy
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Juan Sanchez-Weatherby
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - C. David Owen
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Petra Lukacik
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Claire Strain-Damerell
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Robin L. Owen
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Martin A. Walsh
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Graeme Winter
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| |
Collapse
|
4
|
Okumura H, Sakai N, Murakami H, Mizuno N, Nakamura Y, Ueno G, Masunaga T, Kawamura T, Baba S, Hasegawa K, Yamamoto M, Kumasaka T. In situ crystal data-collection and ligand-screening system at SPring-8. Acta Crystallogr F Struct Biol Commun 2022; 78:241-251. [PMID: 35647681 PMCID: PMC9158660 DOI: 10.1107/s2053230x22005283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
An in situ X-ray diffraction measurement system using a crystallization plate has been constructed at the SPring-8 protein crystallography beamline. Utilizing small-wedge measurements and incorporating a liquid dispenser to prepare protein–ligand complex crystals, this system will make ligand screening possible. In situ diffraction data collection using crystallization plates has been utilized for macromolecules to evaluate crystal quality without requiring additional sample treatment such as cryocooling. Although it is difficult to collect complete data sets using this technique due to the mechanical limitation of crystal rotation, recent advances in methods for data collection from multiple crystals have overcome this issue. At SPring-8, an in situ diffraction measurement system was constructed consisting of a goniometer for a plate, an articulated robot and plate storage. Using this system, complete data sets were obtained utilizing the small-wedge measurement method. Combining this system with an acoustic liquid handler to prepare protein–ligand complex crystals by applying fragment compounds to trypsin crystals for in situ soaking, binding was confirmed for seven out of eight compounds. These results show that the system functioned properly to collect complete data for structural analysis and to expand the capability for ligand screening in combination with a liquid dispenser.
Collapse
|
5
|
Kong H, Li M, Xu Q, Zhou H, Yu F, Wang Q. Implementation of level-2 biosafety for a macromolecular crystallography beamline at SSRF. AMERICAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING 2021; 11:529-536. [PMID: 35003890 PMCID: PMC8727877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
Macromolecular crystallography is commonly used to determine the structure of biological macromolecules. Currently the beamlines at synchrotron radiation facilities play an important role in macromolecular crystallography, and have produced an enormous number of molecular structures to help solve scientific questions and support applications. Structure information makes significant contributions to the virus-related research as well. However, it is mandatory to be protected the operators under a compatible biosafety infrastructure when a pathological agent is set up in a beamline. Here a level-2 biosafety protection for a macromolecular crystallography beamline at Shanghai Synchrotron Radiation Facility (SSRF) is introduced. To fulfill the biosafety in a radioactive environment, a dedicated design is implemented. Since the beamline will be opened to the external users from nationwide research units, the management process and experimental method are also drawn up.
Collapse
Affiliation(s)
- Huating Kong
- Shanghai Advanced Research Institute, Chinese Academy of SciencesShanghai 201204, China
| | - Minjun Li
- Shanghai Advanced Research Institute, Chinese Academy of SciencesShanghai 201204, China
| | - Qin Xu
- Shanghai Advanced Research Institute, Chinese Academy of SciencesShanghai 201204, China
- University of Chinese Academy of SciencesBeijing 100049, China
| | - Huan Zhou
- Shanghai Advanced Research Institute, Chinese Academy of SciencesShanghai 201204, China
| | - Feng Yu
- Shanghai Advanced Research Institute, Chinese Academy of SciencesShanghai 201204, China
| | - Qisheng Wang
- Shanghai Advanced Research Institute, Chinese Academy of SciencesShanghai 201204, China
- Shanghai Institute of Applied Physics, Chinese Academy of SciencesShanghai 201800, China
| |
Collapse
|
6
|
Sui S, Mulichak A, Kulathila R, McGee J, Filiatreault D, Saha S, Cohen A, Song J, Hung H, Selway J, Kirby C, Shrestha OK, Weihofen W, Fodor M, Xu M, Chopra R, Perry SL. A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening. J Appl Crystallogr 2021; 54:1034-1046. [PMID: 34429718 PMCID: PMC8366422 DOI: 10.1107/s1600576721004155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/18/2021] [Indexed: 11/10/2022] Open
Abstract
A novel capillary-based microfluidic strategy to accelerate the process of small-molecule-compound screening by room-temperature X-ray crystallography using protein crystals is reported. The ultra-thin microfluidic devices are composed of a UV-curable polymer, patterned by cleanroom photolithography, and have nine capillary channels per chip. The chip was designed for ease of sample manipulation, sample stability and minimal X-ray background. 3D-printed frames and cassettes conforming to SBS standards are used to house the capillary chips, providing additional mechanical stability and compatibility with automated liquid- and sample-handling robotics. These devices enable an innovative in situ crystal-soaking screening workflow, akin to high-throughput compound screening, such that quantitative electron density maps sufficient to determine weak binding events are efficiently obtained. This work paves the way for adopting a room-temperature microfluidics-based sample delivery method at synchrotron sources to facilitate high-throughput protein-crystallography-based screening of compounds at high concentration with the aim of discovering novel binding events in an automated manner.
Collapse
Affiliation(s)
- Shuo Sui
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Anne Mulichak
- IMCA-CAT, Argonne National Laboratory, Lemont, IL, USA
| | | | - Joshua McGee
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | | | - Sarthak Saha
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Aina Cohen
- Macromolecular Crystallography Group, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | - Jinhu Song
- Macromolecular Crystallography Group, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | | | - Jonathan Selway
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Christina Kirby
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Om K. Shrestha
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Michelle Fodor
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Mei Xu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Rajiv Chopra
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Sarah L. Perry
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| |
Collapse
|
7
|
A comprehensive approach to X-ray crystallography for drug discovery at a synchrotron facility - The example of Diamond Light Source. DRUG DISCOVERY TODAY. TECHNOLOGIES 2020; 37:83-92. [PMID: 34895658 DOI: 10.1016/j.ddtec.2020.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/30/2020] [Accepted: 10/29/2020] [Indexed: 11/21/2022]
Abstract
A detailed understanding of the interactions between drugs and their targets is crucial to develop the best possible therapeutic agents. Structure-based drug design relies on the availability of high-resolution structures obtained primarily through X-ray crystallography. Collecting and analysing quickly a large quantity of structural data is crucial to accelerate drug discovery pipelines. Researchers from academia and industry can access the highly automated macromolecular crystallography (MX) beamlines of Diamond Light Source, the UK national synchrotron, to rapidly collect diffraction data from large numbers of crystals. With seven beamlines dedicated to MX, Diamond offers bespoke solutions for a wide variety of user requirements. Working in synergy with state-of-the-art laboratories and other life science instruments to provide an integrated offering, the MX beamlines provide innovative and multidisciplinary approaches to the determination of structures of new pharmacological targets as well as the efficient study of protein-ligand complexes.
Collapse
|
8
|
Birch J, Cheruvara H, Gamage N, Harrison PJ, Lithgo R, Quigley A. Changes in Membrane Protein Structural Biology. BIOLOGY 2020; 9:E401. [PMID: 33207666 PMCID: PMC7696871 DOI: 10.3390/biology9110401] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022]
Abstract
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome.
Collapse
Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Harish Cheruvara
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadisha Gamage
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Peter J. Harrison
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Ryan Lithgo
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, Leicestershire, UK
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| |
Collapse
|
9
|
Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
Collapse
|
10
|
Ren Z, Wang C, Shin H, Bandara S, Kumarapperuma I, Ren MY, Kang W, Yang X. An automated platform for in situ serial crystallography at room temperature. IUCRJ 2020; 7:1009-1018. [PMID: 33209315 PMCID: PMC7642789 DOI: 10.1107/s2052252520011288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Direct observation of functional motions in protein structures is highly desirable for understanding how these nanomachineries of life operate at the molecular level. Because cryogenic temperatures are non-physiological and may prohibit or even alter protein structural dynamics, it is necessary to develop robust X-ray diffraction methods that enable routine data collection at room temperature. We recently reported a crystal-on-crystal device to facilitate in situ diffraction of protein crystals at room temperature devoid of any sample manipulation. Here an automated serial crystallography platform based on this crystal-on-crystal technology is presented. A hardware and software prototype has been implemented, and protocols have been established that allow users to image, recognize and rank hundreds to thousands of protein crystals grown on a chip in optical scanning mode prior to serial introduction of these crystals to an X-ray beam in a programmable and high-throughput manner. This platform has been tested extensively using fragile protein crystals. We demonstrate that with affordable sample consumption, this in situ serial crystallography technology could give rise to room-temperature protein structures of higher resolution and superior map quality for those protein crystals that encounter difficulties during freezing. This serial data collection platform is compatible with both monochromatic oscillation and Laue methods for X-ray diffraction and presents a widely applicable approach for static and dynamic crystallographic studies at room temperature.
Collapse
Affiliation(s)
- Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
- Renz Research, Inc., Westmont, IL 60559, USA
| | - Cong Wang
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Heewhan Shin
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Sepalika Bandara
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Indika Kumarapperuma
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Michael Y. Ren
- A. James Clark School of Engineering, University of Maryland, College Park, MD 20742, USA
| | - Weijia Kang
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| |
Collapse
|
11
|
Lawrence JM, Orlans J, Evans G, Orville AM, Foadi J, Aller P. High-throughput in situ experimental phasing. Acta Crystallogr D Struct Biol 2020; 76:790-801. [PMID: 32744261 PMCID: PMC7397491 DOI: 10.1107/s2059798320009109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/03/2020] [Indexed: 11/10/2022] Open
Abstract
In this article, a new approach to experimental phasing for macromolecular crystallography (MX) at synchrotrons is introduced and described for the first time. It makes use of automated robotics applied to a multi-crystal framework in which human intervention is reduced to a minimum. Hundreds of samples are automatically soaked in heavy-atom solutions, using a Labcyte Inc. Echo 550 Liquid Handler, in a highly controlled and optimized fashion in order to generate derivatized and isomorphous crystals. Partial data sets obtained on MX beamlines using an in situ setup for data collection are processed with the aim of producing good-quality anomalous signal leading to successful experimental phasing.
Collapse
Affiliation(s)
- Joshua M. Lawrence
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Julien Orlans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- UMR0203, Biologie Fonctionnelle, Insectes et Interactions (BF2i); Institut National des Sciences Appliquées de Lyon (INSA Lyon); Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Lyon (Univ Lyon), F-69621 Villeurbanne, France
| | - Gwyndaf Evans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - James Foadi
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| |
Collapse
|
12
|
Beilsten-Edmands J, Winter G, Gildea R, Parkhurst J, Waterman D, Evans G. Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling. Acta Crystallogr D Struct Biol 2020; 76:385-399. [PMID: 32254063 PMCID: PMC7137103 DOI: 10.1107/s2059798320003198] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/08/2020] [Indexed: 11/29/2022] Open
Abstract
In processing X-ray diffraction data, the intensities obtained from integration of the diffraction images must be corrected for experimental effects in order to place all intensities on a common scale both within and between data collections. Scaling corrects for effects such as changes in sample illumination, absorption and, to some extent, global radiation damage that cause the measured intensities of symmetry-equivalent observations to differ throughout a data set. This necessarily requires a prior evaluation of the point-group symmetry of the crystal. This paper describes and evaluates the scaling algorithms implemented within the DIALS data-processing package and demonstrates the effectiveness and key features of the implementation on example macromolecular crystallographic rotation data. In particular, the scaling algorithms enable new workflows for the scaling of multi-crystal or multi-sweep data sets, providing the analysis required to support current trends towards collecting data from ever-smaller samples. In addition, the implementation of a free-set validation method is discussed, which allows the quantification of the suitability of scaling-model and algorithm choices.
Collapse
Affiliation(s)
- James Beilsten-Edmands
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Graeme Winter
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Richard Gildea
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James Parkhurst
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - David Waterman
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| |
Collapse
|
13
|
Duyvesteyn HME, Ren J, Walter TS, Fry EE, Stuart DI. Glutathione facilitates enterovirus assembly by binding at a druggable pocket. Commun Biol 2020; 3:9. [PMID: 31909201 PMCID: PMC6941975 DOI: 10.1038/s42003-019-0722-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/02/2019] [Indexed: 01/05/2023] Open
Abstract
Enteroviruses cause a range of human and animal diseases, some life-threatening, but there remain no licenced anti-enterovirus drugs. However, a benzene-sulfonamide derivative and related compounds have been shown recently to block infection of a range of enteroviruses by binding the capsid at a positively-charged surface depression conserved across many enteroviruses. It has also been established that glutathione is essential for the assembly of many enteroviruses, interacting with the capsid proteins to facilitate the formation of the pentameric assembly intermediate, although the mechanism is unknown. Here we show, by high resolution structure analyses of enterovirus F3, that reduced glutathione binds to the same interprotomer pocket as the benzene-sulfonamide derivative. Bound glutathione makes strong interactions with adjacent protomers, thereby explaining the underlying biological role of this druggable binding pocket and delineating the pharmacophore for potential antivirals.
Collapse
Affiliation(s)
- Helen M. E. Duyvesteyn
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE UK
| | - Jingshan Ren
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN UK
| | - Thomas S. Walter
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN UK
| | - Elizabeth E. Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN UK
| | - David I. Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE UK
| |
Collapse
|
14
|
Huang CY, Olieric V, Caffrey M, Wang M. In Meso In Situ Serial X-Ray Crystallography (IMISX): A Protocol for Membrane Protein Structure Determination at the Swiss Light Source. Methods Mol Biol 2020; 2127:293-319. [PMID: 32112330 DOI: 10.1007/978-1-0716-0373-4_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The lipid cubic phases (LCP) have enabled the determination of many important high-resolution structures of membrane proteins such as G-protein-coupled receptors, photosensitive proteins, enzymes, channels, and transporters. However, harvesting the crystals from the glass or plastic plates in which crystals grow is challenging. The in meso in situ serial X-ray crystallography (IMISX) method uses thin plastic windowed plates that minimize LCP crystal manipulation. The method, which is compatible with high-throughput in situ measurements, allows systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without direct crystal harvesting. In this chapter, we describe an IMISX protocol for in situ serial X-ray data collection of LCP-grown crystals at both cryogenic and room temperatures which includes the crystallization setup, sample delivery, automated serial diffraction data collection, and experimental phasing. We also detail how the IMISX method was applied successfully for the structure determination of two novel targets-the undecaprenyl-pyrophosphate phosphatase BacA and the chemokine G-protein-coupled receptor CCR2A.
Collapse
Affiliation(s)
- Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland.
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Martin Caffrey
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| |
Collapse
|
15
|
Polikarpov M, Bourenkov G, Snigireva I, Snigirev A, Zimmermann S, Csanko K, Brockhauser S, Schneider TR. Visualization of protein crystals by high-energy phase-contrast X-ray imaging. Acta Crystallogr D Struct Biol 2019; 75:947-958. [PMID: 31692469 PMCID: PMC6834075 DOI: 10.1107/s2059798319011379] [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: 04/09/2019] [Accepted: 08/13/2019] [Indexed: 12/05/2022] Open
Abstract
For the extraction of the best possible X-ray diffraction data from macromolecular crystals, accurate positioning of the crystals with respect to the X-ray beam is crucial. In addition, information about the shape and internal defects of crystals allows the optimization of data-collection strategies. Here, it is demonstrated that the X-ray beam available on the macromolecular crystallography beamline P14 at the high-brilliance synchrotron-radiation source PETRA III at DESY, Hamburg, Germany can be used for high-energy phase-contrast microtomography of protein crystals mounted in an optically opaque lipidic cubic phase matrix. Three-dimensional tomograms have been obtained at X-ray doses that are substantially smaller and on time scales that are substantially shorter than those used for diffraction-scanning approaches that display protein crystals at micrometre resolution. Adding a compound refractive lens as an objective to the imaging setup, two-dimensional imaging at sub-micrometre resolution has been achieved. All experiments were performed on a standard macromolecular crystallography beamline and are compatible with standard diffraction data-collection workflows and apparatus. Phase-contrast X-ray imaging of macromolecular crystals could find wide application at existing and upcoming low-emittance synchrotron-radiation sources.
Collapse
Affiliation(s)
- Maxim Polikarpov
- European Molecular Biology Laboratory, Hamburg Unit c/o DESY, Building 25A, Notkestrasse 85, 22607 Hamburg, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Unit c/o DESY, Building 25A, Notkestrasse 85, 22607 Hamburg, Germany
| | - Irina Snigireva
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043 Grenoble, France
| | - Anatoly Snigirev
- X-ray Optics and Physical Materials Science Laboratory, Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236041, Russian Federation
| | - Sophie Zimmermann
- European Molecular Biology Laboratory, Hamburg Unit c/o DESY, Building 25A, Notkestrasse 85, 22607 Hamburg, Germany
- BASF SE, Pfalzgrafenstrasse 1, 67061 Ludwigshafen, Germany
| | - Krisztian Csanko
- Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Sandor Brockhauser
- Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Thomas R. Schneider
- European Molecular Biology Laboratory, Hamburg Unit c/o DESY, Building 25A, Notkestrasse 85, 22607 Hamburg, Germany
| |
Collapse
|
16
|
Abstract
Until recently X-ray crystallography has been the standard technique for virus structure determinations. Available X-ray sources have continuously improved over the decades, leading to the realization of X-ray free-electron lasers (XFELs). They provide high-intensity femtosecond X-ray pulses, which allow for new kinds of experiments by making use of the diffraction-before-destruction principle. By overcoming classical dose constraints, they at least in principle allow researchers to perform X-ray virus structure determination for single particles at room temperature. Simultaneously, the availability of XFELs led to the development of the method of serial femtosecond crystallography, where a crystal structure is determined from the measurement of hundreds to thousands of microcrystals. In the case of virus crystallography this method does not require freezing of the crystals and allows researchers to perform experiments under non-equilibrium conditions (e.g., by laser-induced temperature jumps or rapid chemical mixing), which is currently not possible with electron microscopy.
Collapse
Affiliation(s)
- A. Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - M.O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Ebrahim A, Moreno-Chicano T, Appleby MV, Chaplin AK, Beale JH, Sherrell DA, Duyvesteyn HME, Owada S, Tono K, Sugimoto H, Strange RW, Worrall JAR, Axford D, Owen RL, Hough MA. Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins. IUCRJ 2019; 6:543-551. [PMID: 31316799 PMCID: PMC6608622 DOI: 10.1107/s2052252519003956] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/22/2019] [Indexed: 05/18/2023]
Abstract
An approach is demonstrated to obtain, in a sample- and time-efficient manner, multiple dose-resolved crystal structures from room-temperature protein microcrystals using identical fixed-target supports at both synchrotrons and X-ray free-electron lasers (XFELs). This approach allows direct comparison of dose-resolved serial synchrotron and damage-free XFEL serial femtosecond crystallography structures of radiation-sensitive proteins. Specifically, serial synchrotron structures of a heme peroxidase enzyme reveal that X-ray induced changes occur at far lower doses than those at which diffraction quality is compromised (the Garman limit), consistent with previous studies on the reduction of heme proteins by low X-ray doses. In these structures, a functionally relevant bond length is shown to vary rapidly as a function of absorbed dose, with all room-temperature synchrotron structures exhibiting linear deformation of the active site compared with the XFEL structure. It is demonstrated that extrapolation of dose-dependent synchrotron structures to zero dose can closely approximate the damage-free XFEL structure. This approach is widely applicable to any protein where the crystal structure is altered by the synchrotron X-ray beam and provides a solution to the urgent requirement to determine intact structures of such proteins in a high-throughput and accessible manner.
Collapse
Affiliation(s)
- Ali Ebrahim
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Tadeo Moreno-Chicano
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Martin V. Appleby
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Amanda K. Chaplin
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - John H. Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Helen M. E. Duyvesteyn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
- Division of Structural Biology (STRUBI), The Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Hiroshi Sugimoto
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Jonathan A. R. Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| |
Collapse
|
19
|
Stuart DI, Ren J, Wang X, Rao Z, Fry EE. Hepatitis A Virus Capsid Structure. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a031807. [PMID: 30037986 DOI: 10.1101/cshperspect.a031807] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Hepatitis A virus (HAV) has been enigmatic, evading detailed structural analysis for many years. Its recently determined high-resolution structure revealed an angular surface without the indentations often characteristic of receptor-binding sites. The viral protein 1 (VP1) β-barrel shows no sign of a pocket factor and the amino terminus of VP2 displays a "domain swap" across the pentamer interface, as in a subset of mammalian picornaviruses and insect picorna-like viruses. Structure-based phylogeny confirms this placement. These differences suggest an uncoating mechanism distinct from that of enteroviruses. An empty capsid structure reveals internal differences in VP0 and the VP1 amino terminus connected with particle maturation. An HAV/Fab complex structure, in which the antigen-binding fragment (Fab) appears to act as a receptor-mimic, clarifies some historical epitope mapping data, but some remain difficult to reconcile. We still have little idea of the structural features of enveloped HAV particles.
Collapse
Affiliation(s)
- David I Stuart
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Jingshan Ren
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Xiangxi Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Zihe Rao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China.,Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Elizabeth E Fry
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| |
Collapse
|
20
|
Suzuki Y, Torii K, Inaka K, Fujiwara T, Tanaka H, Arai Y. A novel handling-free method of mounting single protein crystals for synchrotron structure analyses at room temperature. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:054101. [PMID: 31153273 DOI: 10.1063/1.5070122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
We have developed a handling-free mounting method for X-ray crystallography of protein crystals at room temperatures-the glass capillary method. In this method, crystals were nucleated and grown on the capillary walls, and then, growth solutions were gently removed. The procedures for collecting data on the crystals were conducted by simply setting the capillary on the goniometer of a synchrotron beamline without touching the crystals. Crystal quality was characterized using mosaicity, resolution at I/σ(I) = 2, I/σ(I) at resolution = 2.0 Å, Rmerge, and completeness. Wilson plots were also used to characterize the quality of crystals. In particular, all samples showed very low mosaicity; the handling-free method successfully retained their low mosaicity and effectively maintained the crystal quality.
Collapse
Affiliation(s)
- Yoshihisa Suzuki
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima, Tokushima 770-8506, Japan
| | - Kumi Torii
- Faculty of Engineering, Tokushima University, 2-1 Minamijosanjima, Tokushima 770-8506, Japan
| | - Koji Inaka
- Maruwa Foods and Biosciences, Inc., 170-1 Tsutsui-cho, Yamatokoriyama, Nara 639-1123, Japan
| | - Takahisa Fujiwara
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima, Tokushima 770-8506, Japan
| | - Hiroaki Tanaka
- Confocal Science Inc., Hayakawa 2nd Building 7F, 2-12-2 Iwamoto-cho, Chiyoda-ku, Tokyo 101-0032, Japan
| | - Yasutomo Arai
- Japan Aerospace Exploration Agency (JAXA), 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| |
Collapse
|
21
|
Basu S, Finke A, Vera L, Wang M, Olieric V. Making routine native SAD a reality: lessons from beamline X06DA at the Swiss Light Source. Acta Crystallogr D Struct Biol 2019; 75:262-271. [PMID: 30950397 PMCID: PMC6450063 DOI: 10.1107/s2059798319003103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/01/2019] [Indexed: 01/19/2023] Open
Abstract
Native single-wavelength anomalous dispersion (SAD) is the most attractive de novo phasing method in macromolecular crystallography, as it directly utilizes intrinsic anomalous scattering from native crystals. However, the success of such an experiment depends on accurate measurements of the reflection intensities and therefore on careful data-collection protocols. Here, the low-dose, multiple-orientation data-collection protocol for native SAD phasing developed at beamline X06DA (PXIII) at the Swiss Light Source is reviewed, and its usage over the last four years on conventional crystals (>50 µm) is reported. Being experimentally very simple and fast, this method has gained popularity and has delivered 45 de novo structures to date (13 of which have been published). Native SAD is currently the primary choice for experimental phasing among X06DA users. The method can address challenging cases: here, native SAD phasing performed on a streptavidin-biotin crystal with P21 symmetry and a low Bijvoet ratio of 0.6% is highlighted. The use of intrinsic anomalous signals as sequence markers for model building and the assignment of ions is also briefly described.
Collapse
Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Aaron Finke
- MacCHESS, Cornell University, Ithaca, New York, USA
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| |
Collapse
|
22
|
Winter G, Gildea RJ, Paterson NG, Beale J, Gerstel M, Axford D, Vollmar M, McAuley KE, Owen RL, Flaig R, Ashton AW, Hall DR. How best to use photons. Acta Crystallogr D Struct Biol 2019; 75:242-261. [PMID: 30950396 PMCID: PMC6450062 DOI: 10.1107/s2059798319003528] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/13/2019] [Indexed: 11/10/2022] Open
Abstract
Strategies for collecting X-ray diffraction data have evolved alongside beamline hardware and detector developments. The traditional approaches for diffraction data collection have emphasised collecting data from noisy integrating detectors (i.e. film, image plates and CCD detectors). With fast pixel array detectors on stable beamlines, the limiting factor becomes the sample lifetime, and the question becomes one of how to expend the photons that your sample can diffract, i.e. as a smaller number of stronger measurements or a larger number of weaker data. This parameter space is explored via experiment and synthetic data treatment and advice is derived on how best to use the equipment on a modern beamline. Suggestions are also made on how to acquire data in a conservative manner if very little is known about the sample lifetime.
Collapse
Affiliation(s)
- Graeme Winter
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Richard J. Gildea
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Neil G. Paterson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - John Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Markus Gerstel
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Melanie Vollmar
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Katherine E. McAuley
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Ralf Flaig
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Alun W. Ashton
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - David R. Hall
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Sanchez-Weatherby J, Sandy J, Mikolajek H, Lobley CMC, Mazzorana M, Kelly J, Preece G, Littlewood R, Sørensen TLM. VMXi: a fully automated, fully remote, high-flux in situ macromolecular crystallography beamline. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:291-301. [PMID: 30655497 PMCID: PMC6337891 DOI: 10.1107/s1600577518015114] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 10/26/2018] [Indexed: 05/04/2023]
Abstract
VMXi is a new high-flux microfocus macromolecular crystallography beamline at Diamond Light Source. The beamline, dedicated to fully automated and fully remote data collection of macromolecular crystals in situ, allows rapid screening of hundreds of crystallization plates from multiple user groups. Its main purpose is to give fast feedback at the complex stages of crystallization and crystal optimization, but it also enables data collection of small and delicate samples that are particularly difficult to harvest using conventional cryo-methods, crystals grown in the lipidic cubic phase, and allows for multi-crystal data collections in drug discovery programs. The beamline is equipped with two monochromators: one with a narrow band-pass and fine energy resolution (optimal for regular oscillation experiments), and one with a wide band-pass and a high photon flux (optimal for fast screening). The beamline has a state-of-the-art detector and custom goniometry that allows fast data collection. This paper describes the beamline design, current status and future plans.
Collapse
Affiliation(s)
- Juan Sanchez-Weatherby
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK
| | - James Sandy
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK
| | - Halina Mikolajek
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK
| | - Carina M. C. Lobley
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK
| | - Marco Mazzorana
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK
| | - Jon Kelly
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK
| | - Geoff Preece
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK
| | - Rich Littlewood
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK
| | - Thomas L.-M. Sørensen
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| |
Collapse
|
25
|
Structural biology and structure–function relationships of membrane proteins. Biochem Soc Trans 2018; 47:47-61. [DOI: 10.1042/bst20180269] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 01/02/2023]
Abstract
Abstract
The study of structure–function relationships of membrane proteins (MPs) has been one of the major goals in the field of structural biology. Many Noble Prizes regarding remarkable accomplishments in MP structure determination and biochemistry have been awarded over the last few decades. Mutations or improper folding of these proteins are associated with numerous serious illnesses. Therefore, as important drug targets, the study of their primary sequence and three-dimensional fold, combined with cell-based assays, provides vital information about their structure–function relationships. Today, this information is vital to drug discovery and medicine. In the last two decades, many have been the technical advances and breakthroughs in the field of MP structural biology that have contributed to an exponential growth in the number of unique MP structures in the Protein Data Bank. Nevertheless, given the medical importance and many unanswered questions, it will never be an excess of MP structures, regardless of the method used. Owing to the extension of the field, in this brief review, we will only focus on structure–function relationships of the three most significant pharmaceutical classes: G protein-coupled receptors, ion channels and transporters.
Collapse
|
26
|
Gao Y, Xu W, Shi W, Soares A, Jakoncic J, Myers S, Martins B, Skinner J, Liu Q, Bernstein H, McSweeney S, Nazaretski E, Fuchs MR. High-speed raster-scanning synchrotron serial microcrystallography with a high-precision piezo-scanner. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1362-1370. [PMID: 30179174 PMCID: PMC6140394 DOI: 10.1107/s1600577518010354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/18/2018] [Indexed: 05/06/2023]
Abstract
The Frontier Microfocus Macromolecular Crystallography (FMX) beamline at the National Synchrotron Light Source II with its 1 µm beam size and photon flux of 3 × 1012 photons s-1 at a photon energy of 12.66 keV has reached unprecedented dose rates for a structural biology beamline. The high dose rate presents a great advantage for serial microcrystallography in cutting measurement time from hours to minutes. To provide the instrumentation basis for such measurements at the full flux of the FMX beamline, a high-speed, high-precision goniometer based on a unique XYZ piezo positioner has been designed and constructed. The piezo-based goniometer is able to achieve sub-100 nm raster-scanning precision at over 10 grid-linepairs s-1 frequency for fly scans of a 200 µm-wide raster. The performance of the scanner in both laboratory and serial crystallography measurements up to the maximum frame rate of 750 Hz of the Eiger 16M's 4M region-of-interest mode has been verified in this work. This unprecedented experimental speed significantly reduces serial-crystallography data collection time at synchrotrons, allowing utilization of the full brightness of the emerging synchrotron radiation facilities.
Collapse
Affiliation(s)
- Yuan Gao
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Weihe Xu
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wuxian Shi
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
- Case Center for Synchrotron Biosciences, Case Western Reserve University, OH 44106, USA
| | - Alexei Soares
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jean Jakoncic
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Stuart Myers
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Bruno Martins
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - John Skinner
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Qun Liu
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Herbert Bernstein
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
- School of Chemistry and Materials Science, Rochester Institute of Technology, NY 14623, USA
| | - Sean McSweeney
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Evgeny Nazaretski
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Martin R. Fuchs
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| |
Collapse
|
27
|
Ren Z, Ayhan M, Bandara S, Bowatte K, Kumarapperuma I, Gunawardana S, Shin H, Wang C, Zeng X, Yang X. Crystal-on-crystal chips for in situ serial diffraction at room temperature. LAB ON A CHIP 2018; 18:2246-2256. [PMID: 29952383 PMCID: PMC6057835 DOI: 10.1039/c8lc00489g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Recent developments in serial crystallography at X-ray free electron lasers (XFELs) and synchrotrons have been driven by two scientific goals in structural biology - first, static structure determination from nano or microcrystals of membrane proteins and large complexes that are difficult for conventional cryocrystallography, and second, direct observations of transient structural species in biochemical reactions at near atomic resolution. Since room-temperature diffraction experiments naturally demand a large quantity of purified protein, sample economy is critically important for all steps of serial crystallography from crystallization, crystal delivery to data collection. Here we report the development and applications of "crystal-on-crystal" devices to facilitate large-scale in situ serial diffraction experiments on protein crystals of all sizes - large, small, or microscopic. We show that the monocrystalline quartz as a substrate material prevents vapor loss during crystallization and significantly reduces background X-ray scattering. These devices can be readily adopted at XFEL and synchrotron beamlines, which enable efficient delivery of hundreds to millions of crystals to the X-ray beam, with an overall protein consumption per dataset comparable to that of cryocrystallography.
Collapse
Affiliation(s)
- Zhong Ren
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
- Renz Research, Inc., Westmont, IL 60559, USA
- Corresponding authors: and
| | - Medine Ayhan
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Sepalika Bandara
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kalinga Bowatte
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Indika Kumarapperuma
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Semini Gunawardana
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Heewhan Shin
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Cong Wang
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Xiaoli Zeng
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Xiaojing Yang
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, The University of Illinois at Chicago, Chicago, IL 60607, USA
- Corresponding authors: and
| |
Collapse
|
28
|
Banerjee S, Montaville P, Chavas LMG, Ramaswamy S. The New Era of Microcrystallography. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0086-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
29
|
McCarthy AA, Barrett R, Beteva A, Caserotto H, Dobias F, Felisaz F, Giraud T, Guijarro M, Janocha R, Khadrouche A, Lentini M, Leonard GA, Lopez Marrero M, Malbet-Monaco S, McSweeney S, Nurizzo D, Papp G, Rossi C, Sinoir J, Sorez C, Surr J, Svensson O, Zander U, Cipriani F, Theveneau P, Mueller-Dieckmann C. ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1249-1260. [PMID: 29979188 PMCID: PMC6038607 DOI: 10.1107/s1600577518007166] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/13/2018] [Indexed: 05/05/2023]
Abstract
ID30B is an undulator-based high-intensity, energy-tuneable (6.0-20 keV) and variable-focus (20-200 µm in diameter) macromolecular crystallography (MX) beamline at the ESRF. It was the last of the ESRF Structural Biology Group's beamlines to be constructed and commissioned as part of the ESRF's Phase I Upgrade Program and has been in user operation since June 2015. Both a modified microdiffractometer (MD2S) incorporating an in situ plate screening capability and a new flexible sample changer (the FlexHCD) were specifically developed for ID30B. Here, the authors provide the current beamline characteristics and detail how different types of MX experiments can be performed on ID30B (http://www.esrf.eu/id30b).
Collapse
Affiliation(s)
- Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Ray Barrett
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Antonia Beteva
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Hugo Caserotto
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Franck Felisaz
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Matias Guijarro
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Robert Janocha
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Akim Khadrouche
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Mario Lentini
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Marcos Lopez Marrero
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | | | - Sean McSweeney
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Gergely Papp
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Christopher Rossi
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Jeremy Sinoir
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Clement Sorez
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - John Surr
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - Ulrich Zander
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Florent Cipriani
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France
| | - Pascal Theveneau
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | | |
Collapse
|
30
|
Birch J, Axford D, Foadi J, Meyer A, Eckhardt A, Thielmann Y, Moraes I. The fine art of integral membrane protein crystallisation. Methods 2018; 147:150-162. [PMID: 29778646 DOI: 10.1016/j.ymeth.2018.05.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/13/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022] Open
Abstract
Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral membrane proteins has proven to be far from trivial, hence they are underrepresented in the protein data bank. Low expression levels, insolubility and instability are just a few of the many hurdles one faces when studying these proteins. X-ray crystallography has been the most used method to determine atomic structures of membrane proteins. However, the production of high quality membrane protein crystals is always very challenging, often seen more as art than a rational experiment. Here we review valuable approaches, methods and techniques to successful membrane protein crystallisation.
Collapse
Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK
| | - James Foadi
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Arne Meyer
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Annette Eckhardt
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Yvonne Thielmann
- Max Planck Institute of Biophysics, Molecular Membrane Biology, Max-von-Laue-Strasse 3, 60438 Frankfurt, Germany
| | - Isabel Moraes
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK; Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK; National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
| |
Collapse
|
31
|
Grimes JM, Hall DR, Ashton AW, Evans G, Owen RL, Wagner A, McAuley KE, von Delft F, Orville AM, Sorensen T, Walsh MA, Ginn HM, Stuart DI. Where is crystallography going? Acta Crystallogr D Struct Biol 2018; 74:152-166. [PMID: 29533241 PMCID: PMC5947779 DOI: 10.1107/s2059798317016709] [Citation(s) in RCA: 42] [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: 09/17/2017] [Accepted: 11/20/2017] [Indexed: 11/28/2022] Open
Abstract
Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and cryo-crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments. In addition, X-ray free-electron lasers offer to capture fragments of reciprocal space without radiation damage, and open up the subpicosecond regime of protein dynamics and activity. But electrons have recently stolen the limelight: so is X-ray crystallography in rude health, or will imaging methods, especially single-particle electron microscopy, render it obsolete for the most interesting biology, whilst electron diffraction enables structure determination from even the smallest crystals? We will lay out some information to help you decide.
Collapse
Affiliation(s)
- Jonathan M. Grimes
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
| | - David R. Hall
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Alun W. Ashton
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Gwyndaf Evans
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Robin L. Owen
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Armin Wagner
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Katherine E. McAuley
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Frank von Delft
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Allen M. Orville
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Thomas Sorensen
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Martin A. Walsh
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Helen M. Ginn
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
| | - David I. Stuart
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
| |
Collapse
|
32
|
High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions. Nat Protoc 2018; 13:260-292. [PMID: 29300389 DOI: 10.1038/nprot.2017.135] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein crystallography has significantly advanced in recent years, with in situ data collection, in which crystals are placed in the X-ray beam within their growth medium, being a major point of focus. In situ methods eliminate the need to harvest crystals, a previously unavoidable drawback, particularly for often small membrane-protein crystals. Here, we present a protocol for the high-throughput in situ X-ray screening of and data collection from soluble and membrane-protein crystals at room temperature (20-25°C) and under cryogenic conditions. The Mylar in situ method uses Mylar-based film sandwich plates that are inexpensive, easy to make, and compatible with automated imaging, and that show very low background scattering. They support crystallization in microbatch and vapor-diffusion modes, as well as in lipidic cubic phases (LCPs). A set of 3D-printed holders for differently sized patches of Mylar sandwich films makes the method robust and versatile, allows for storage and shipping of crystals, and enables automated mounting at synchrotrons, as well as goniometer-based screening and data collection. The protocol covers preparation of in situ plates and setup of crystallization trials; 3D printing and assembly of holders; opening of plates, isolation of film patches containing crystals, and loading them onto holders; basic screening and data-collection guidelines; and unloading of holders, as well as reuse and recycling of them. In situ plates are prepared and assembled in 1 h; holders are 3D-printed and assembled in ≤90 min; and an in situ plate is opened, and a film patch containing crystals is isolated and loaded onto a holder in 5 min.
Collapse
|
33
|
Burton CG, Axford D, Edwards AMJ, Gildea RJ, Morris RH, Newton MI, Orville AM, Prince M, Topham PD, Docker PT. An acoustic on-chip goniometer for room temperature macromolecular crystallography. LAB ON A CHIP 2017; 17:4225-4230. [PMID: 29124258 DOI: 10.1039/c7lc00812k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This paper describes the design, development and successful use of an on-chip goniometer for room-temperature macromolecular crystallography via acoustically induced rotations. We present for the first time a low cost, rate-tunable, acoustic actuator for gradual in-fluid sample reorientation about varying axes and its utilisation for protein structure determination on a synchrotron beamline. The device enables the efficient collection of diffraction data via a rotation method from a sample within a surface confined droplet. This method facilitates efficient macromolecular structural data acquisition in fluid environments for dynamical studies.
Collapse
Affiliation(s)
- C G Burton
- Aston Institute of Material Research, Aston University, Birmingham B4 7ET, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Papp G, Rossi C, Janocha R, Sorez C, Lopez-Marrero M, Astruc A, McCarthy A, Belrhali H, Bowler MW, Cipriani F. Towards a compact and precise sample holder for macromolecular crystallography. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:829-840. [PMID: 28994412 PMCID: PMC5633908 DOI: 10.1107/s2059798317013742] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022]
Abstract
Most of the sample holders currently used in macromolecular crystallography offer limited storage density and poor initial crystal-positioning precision upon mounting on a goniometer. This has now become a limiting factor at high-throughput beamlines, where data collection can be performed in a matter of seconds. Furthermore, this lack of precision limits the potential benefits emerging from automated harvesting systems that could provide crystal-position information which would further enhance alignment at beamlines. This situation provided the motivation for the development of a compact and precise sample holder with corresponding pucks, handling tools and robotic transfer protocols. The development process included four main phases: design, prototype manufacture, testing with a robotic sample changer and validation under real conditions on a beamline. Two sample-holder designs are proposed: NewPin and miniSPINE. They share the same robot gripper and allow the storage of 36 sample holders in uni-puck footprint-style pucks, which represents 252 samples in a dry-shipping dewar commonly used in the field. The pucks are identified with human- and machine-readable codes, as well as with radio-frequency identification (RFID) tags. NewPin offers a crystal-repositioning precision of up to 10 µm but requires a specific goniometer socket. The storage density could reach 64 samples using a special puck designed for fully robotic handling. miniSPINE is less precise but uses a goniometer mount compatible with the current SPINE standard. miniSPINE is proposed for the first implementation of the new standard, since it is easier to integrate at beamlines. An upgraded version of the SPINE sample holder with a corresponding puck named SPINEplus is also proposed in order to offer a homogenous and interoperable system. The project involved several European synchrotrons and industrial companies in the fields of consumables and sample-changer robotics. Manual handling of miniSPINE was tested at different institutes using evaluation kits, and pilot beamlines are being equipped with compatible robotics for large-scale evaluation. A companion paper describes a new sample changer FlexED8 (Papp et al., 2017, Acta Cryst., D73, 841-851).
Collapse
Affiliation(s)
- Gergely Papp
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Christopher Rossi
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Robert Janocha
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Clement Sorez
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Marcos Lopez-Marrero
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Anthony Astruc
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Andrew McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Hassan Belrhali
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Florent Cipriani
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| |
Collapse
|
35
|
Šrajer V, Schmidt M. Watching Proteins Function with Time-resolved X-ray Crystallography. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2017; 50:373001. [PMID: 29353938 PMCID: PMC5771432 DOI: 10.1088/1361-6463/aa7d32] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron X-ray sources. An expansive database of more than 100,000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al., 2005a; Schmidt 2008; Neutze and Moffat, 2012; Šrajer 2014). In this approach, short and intense X-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron X-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard X-rays (XFELs; 5-20 keV), which provide exceptionally intense, femtosecond X-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al., 2014; Barends et al., 2015; Pande et al., 2016). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline challenges and further developments necessary to broaden the application of these methods to many important proteins and enzymes of biomedical relevance.
Collapse
Affiliation(s)
- Vukica Šrajer
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, IL, USA
| |
Collapse
|
36
|
Mylona A, Carr S, Aller P, Moraes I, Treisman R, Evans G, Foadi J. A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software. CRYSTALS 2017; 7:242. [PMID: 29456874 PMCID: PMC5813789 DOI: 10.3390/cryst7080242] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present article describes how to use the computer program BLEND to help assemble complete datasets for the solution of macromolecular structures, starting from partial or complete datasets, derived from data collection from multiple crystals. The program is demonstrated on more than two hundred X-ray diffraction datasets obtained from 50 crystals of a complex formed between the SRF transcription factor, its cognate DNA, and a peptide from the SRF cofactor MRTF-A. This structure is currently in the process of being fully solved. While full details of the structure are not yet available, the repeated application of BLEND on data from this structure, as they have become available, has made it possible to produce electron density maps clear enough to visualise the potential location of MRTF sequences.
Collapse
Affiliation(s)
- Anastasia Mylona
- Signalling and Transcription Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Pierre Aller
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Isabel Moraes
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Richard Treisman
- Signalling and Transcription Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - James Foadi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| |
Collapse
|
37
|
Roedig P, Ginn HM, Pakendorf T, Sutton G, Harlos K, Walter TS, Meyer J, Fischer P, Duman R, Vartiainen I, Reime B, Warmer M, Brewster AS, Young ID, Michels-Clark T, Sauter NK, Kotecha A, Kelly J, Rowlands DJ, Sikorsky M, Nelson S, Damiani DS, Alonso-Mori R, Ren J, Fry EE, David C, Stuart DI, Wagner A, Meents A. High-speed fixed-target serial virus crystallography. Nat Methods 2017; 14:805-810. [PMID: 28628129 PMCID: PMC5588887 DOI: 10.1038/nmeth.4335] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/15/2017] [Indexed: 12/19/2022]
Abstract
We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.
Collapse
Affiliation(s)
- Philip Roedig
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Helen M. Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Tim Pakendorf
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Geoff Sutton
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Thomas S. Walter
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jan Meyer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Pontus Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Ramona Duman
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Ismo Vartiainen
- Institute of Photonics, University of Eastern Finland, Joensuu, Finland
| | - Bernd Reime
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Martin Warmer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - James Kelly
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- The Pirbright Institute, Pirbright, United Kingdom
| | - David J. Rowlands
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Marcin Sikorsky
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Silke Nelson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Daniel S. Damiani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jingshan Ren
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elizabeth E. Fry
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - David I. Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Armin Wagner
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Alke Meents
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Center for Free Electron Laser Science (CFEL), Hamburg, Germany
| |
Collapse
|
38
|
On the state of crystallography at the dawn of the electron microscopy revolution. Curr Opin Struct Biol 2017; 46:95-101. [PMID: 28686957 PMCID: PMC5689515 DOI: 10.1016/j.sbi.2017.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/05/2017] [Accepted: 06/11/2017] [Indexed: 12/20/2022]
Abstract
While protein crystallography has, for many years, been the most used method for structural analysis of macromolecular complexes, remarkable recent advances in high-resolution electron cryo-microscopy led to suggestions that 'the revolution will not be crystallised'. Here we highlight the current success rate, speed and ease of modern crystallographic structure determination and some recent triumphs of both 'classical' crystallography and the use of X-ray free electron lasers. We also outline fundamental differences between structure determination using X-ray crystallography and electron microscopy. We suggest that crystallography will continue to co-exist with electron microscopy as part of an integrated array of methods, allowing structural biologists to focus on fundamental biological questions rather than being constrained by the methods available.
Collapse
|
39
|
Locating and Visualizing Crystals for X-Ray Diffraction Experiments. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1607:143-164. [PMID: 28573572 DOI: 10.1007/978-1-4939-7000-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Macromolecular crystallography has advanced from using macroscopic crystals, which might be >1 mm on a side, to crystals that are essentially invisible to the naked eye, or even under a standard laboratory microscope. As crystallography requires recognizing crystals when they are produced, and then placing them in an X-ray, electron, or neutron beam, this provides challenges, particularly in the case of advanced X-ray sources, where beams have very small cross sections and crystals may be vanishingly small. Methods for visualizing crystals are reviewed here, and examples of different types of cases are presented, including: standard crystals, crystals grown in mesophase, in situ crystallography, and crystals grown for X-ray Free Electron Laser or Micro Electron Diffraction experiments. As most techniques have limitations, it is desirable to have a range of complementary techniques available to identify and locate crystals. Ideally, a given technique should not cause sample damage, but sometimes it is necessary to use techniques where damage can only be minimized. For extreme circumstances, the act of probing location may be coincident with collecting X-ray diffraction data. Future challenges and directions are also discussed.
Collapse
|
40
|
Kotecha A, Wang Q, Dong X, Ilca SL, Ondiviela M, Zihe R, Seago J, Charleston B, Fry EE, Abrescia NGA, Springer TA, Huiskonen JT, Stuart DI. Rules of engagement between αvβ6 integrin and foot-and-mouth disease virus. Nat Commun 2017; 8:15408. [PMID: 28534487 PMCID: PMC5457520 DOI: 10.1038/ncomms15408] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/26/2017] [Indexed: 11/21/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) mediates cell entry by attachment to an integrin receptor, generally αvβ6, via a conserved arginine-glycine-aspartic acid (RGD) motif in the exposed, antigenic, GH loop of capsid protein VP1. Infection can also occur in tissue culture adapted virus in the absence of integrin via acquired basic mutations interacting with heparin sulphate (HS); this virus is attenuated in natural infections. HS interaction has been visualized at a conserved site in two serotypes suggesting a propensity for sulfated-sugar binding. Here we determined the interaction between αvβ6 and two tissue culture adapted FMDV strains by cryo-electron microscopy. In the preferred mode of engagement, the fully open form of the integrin, hitherto unseen at high resolution, attaches to an extended GH loop via interactions with the RGD motif plus downstream hydrophobic residues. In addition, an N-linked sugar of the integrin attaches to the previously identified HS binding site, suggesting a functional role.
Collapse
Affiliation(s)
- Abhay Kotecha
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Quan Wang
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianchi Dong
- Program in Cellular and Molecular Medicine and Division of Hematology, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Serban L. Ilca
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Marina Ondiviela
- Structural Biology Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Spain
| | - Rao Zihe
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | | | | | - Elizabeth E. Fry
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Nicola G. A. Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Timothy A. Springer
- Program in Cellular and Molecular Medicine and Division of Hematology, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Juha T. Huiskonen
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - David I. Stuart
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
- Diamond Light Sources, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| |
Collapse
|
41
|
Abstract
Prompted by methodological advances in measurements with X-ray free electron lasers, it was realized in the last two years that traditional (or conventional) methods for data collection from crystals of macromolecular specimens can be complemented by synchrotron measurements on microcrystals that would individually not suffice for a complete data set. Measuring, processing, and merging many partial data sets of this kind requires new techniques which have since been implemented at several third-generation synchrotron facilities, and are described here. Among these, we particularly focus on the possibility of in situ measurements combined with in meso crystal preparations and data analysis with the XDS package and auxiliary programs.
Collapse
Affiliation(s)
- Kay Diederichs
- Department of Biology, Universität Konstanz, Box 647, D-78457, Konstanz, Germany.
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| |
Collapse
|
42
|
Abstract
Membrane proteins are crucial components of cellular membranes and are responsible for a variety of physiological functions. The advent of new tools and technologies for structural biology of membrane proteins has led to a significant increase in the number of structures deposited to the Protein Data Bank during the past decade. This new knowledge has expanded our fundamental understanding of their mechanism of function and contributed to the drug-design efforts. In this chapter we discuss current approaches for membrane protein expression, solubilization, crystallization, and data collection. Additionally, we describe the protein quality-control assays that are often instrumental as a guideline for a shorter path toward the structure.
Collapse
Affiliation(s)
- Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Enrique E Abola
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA.
| |
Collapse
|
43
|
Russi S, González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H. Conformational variation of proteins at room temperature is not dominated by radiation damage. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:73-82. [PMID: 28009548 PMCID: PMC5182021 DOI: 10.1107/s1600577516017343] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/28/2016] [Indexed: 05/09/2023]
Abstract
Protein crystallography data collection at synchrotrons is routinely carried out at cryogenic temperatures to mitigate radiation damage. Although damage still takes place at 100 K and below, the immobilization of free radicals increases the lifetime of the crystals by approximately 100-fold. Recent studies have shown that flash-cooling decreases the heterogeneity of the conformational ensemble and can hide important functional mechanisms from observation. These discoveries have motivated increasing numbers of experiments to be carried out at room temperature. However, the trade-offs between increased risk of radiation damage and increased observation of alternative conformations at room temperature relative to cryogenic temperature have not been examined. A considerable amount of effort has previously been spent studying radiation damage at cryo-temperatures, but the relevance of these studies to room temperature diffraction is not well understood. Here, the effects of radiation damage on the conformational landscapes of three different proteins (T. danielli thaumatin, hen egg-white lysozyme and human cyclophilin A) at room (278 K) and cryogenic (100 K) temperatures are investigated. Increasingly damaged datasets were collected at each temperature, up to a maximum dose of the order of 107 Gy at 100 K and 105 Gy at 278 K. Although it was not possible to discern a clear trend between damage and multiple conformations at either temperature, it was observed that disorder, monitored by B-factor-dependent crystallographic order parameters, increased with higher absorbed dose for the three proteins at 100 K. At 278 K, however, the total increase in this disorder was only statistically significant for thaumatin. A correlation between specific radiation damage affecting side chains and the amount of disorder was not observed. This analysis suggests that elevated conformational heterogeneity in crystal structures at room temperature is observed despite radiation damage, and not as a result thereof.
Collapse
Affiliation(s)
- Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ana González
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Lillian R. Kenner
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
| | - Daniel A. Keedy
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
| | - Henry van den Bedem
- Bioscience Department, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| |
Collapse
|
44
|
Bruno AE, Soares AS, Owen RL, Snell EH. The use of haptic interfaces and web services in crystallography: an application for a 'screen to beam' interface. J Appl Crystallogr 2016; 49:2082-2090. [PMID: 27980513 PMCID: PMC5139995 DOI: 10.1107/s160057671601431x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/08/2016] [Indexed: 11/10/2022] Open
Abstract
Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. The work presented here illustrates the application of a haptic interface to crystallization screening in order to provide a natural means for visualizing and selecting results. By linking this to a cloud-based database and web-based application program interface, the same application shifts the approach from 'point and click' to 'touch and share', where results can be selected, annotated and discussed collaboratively. In the crystallographic application, given a suitable crystallization plate, beamline and robotic end effector, the resulting information can be used to close the loop between screening and X-ray analysis, allowing a direct and efficient 'screen to beam' approach. The application is not limited to the area of crystallization screening; 'touch and share' can be used by any information-rich scientific analysis and geographically distributed collaboration.
Collapse
Affiliation(s)
- Andrew E. Bruno
- Center for Computational Research, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Alexei S. Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973, USA
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 ODE, UK
| | - Edward H. Snell
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Department of Structural Biology, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| |
Collapse
|
45
|
Broecker J, Klingel V, Ou WL, Balo AR, Kissick D, Ogata CM, Kuo A, Ernst OP. A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals. CRYSTAL GROWTH & DESIGN 2016; 16:6318-6326. [PMID: 28261000 PMCID: PMC5328415 DOI: 10.1021/acs.cgd.6b00950] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/30/2016] [Indexed: 05/20/2023]
Abstract
In recent years, in situ data collection has been a major focus of progress in protein crystallography. Here, we introduce the Mylar in situ method using Mylar-based sandwich plates that are inexpensive, easy to make and handle, and show significantly less background scattering than other setups. A variety of cognate holders for patches of Mylar in situ sandwich films corresponding to one or more wells makes the method robust and versatile, allows for storage and shipping of entire wells, and enables automated crystal imaging, screening, and goniometer-based X-ray diffraction data-collection at room temperature and under cryogenic conditions for soluble and membrane-protein crystals grown in or transferred to these plates. We validated the Mylar in situ method using crystals of the water-soluble proteins hen egg-white lysozyme and sperm whale myoglobin as well as the 7-transmembrane protein bacteriorhodopsin from Haloquadratum walsbyi. In conjunction with current developments at synchrotrons, this approach promises high-resolution structural studies of membrane proteins to become faster and more routine.
Collapse
Affiliation(s)
- Jana Broecker
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- E-mail:
| | - Viviane Klingel
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Wei-Lin Ou
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Aidin R. Balo
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David
J. Kissick
- GM/CA
at Advanced Photon Source, Argonne National
Laboratory, Lemont, Illinois 60439, United States
| | - Craig M. Ogata
- GM/CA
at Advanced Photon Source, Argonne National
Laboratory, Lemont, Illinois 60439, United States
| | - Anling Kuo
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Oliver P. Ernst
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- E-mail:
| |
Collapse
|
46
|
Schubert R, Kapis S, Gicquel Y, Bourenkov G, Schneider TR, Heymann M, Betzel C, Perbandt M. A multicrystal diffraction data-collection approach for studying structural dynamics with millisecond temporal resolution. IUCRJ 2016; 3:393-401. [PMID: 27840678 PMCID: PMC5094441 DOI: 10.1107/s2052252516016304] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/13/2016] [Indexed: 05/20/2023]
Abstract
Many biochemical processes take place on timescales ranging from femto-seconds to seconds. Accordingly, any time-resolved experiment must be matched to the speed of the structural changes of interest. Therefore, the timescale of interest defines the requirements of the X-ray source, instrumentation and data-collection strategy. In this study, a minimalistic approach for in situ crystallization is presented that requires only a few microlitres of sample solution containing a few hundred crystals. It is demonstrated that complete diffraction data sets, merged from multiple crystals, can be recorded within only a few minutes of beamtime and allow high-resolution structural information of high quality to be obtained with a temporal resolution of 40 ms. Global and site-specific radiation damage can be avoided by limiting the maximal dose per crystal to 400 kGy. Moreover, analysis of the data collected at higher doses allows the time-resolved observation of site-specific radiation damage. Therefore, our approach is well suited to observe structural changes and possibly enzymatic reactions in the low-millisecond regime.
Collapse
Affiliation(s)
- Robin Schubert
- University of Hamburg c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging c/o DESY, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Svetlana Kapis
- University of Hamburg c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Yannig Gicquel
- Center for Free Electron Laser Science c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | | | - Michael Heymann
- Center for Free Electron Laser Science c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian Betzel
- University of Hamburg c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Markus Perbandt
- University of Hamburg c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging c/o DESY, Luruper Chaussee 149, 22761 Hamburg, Germany
| |
Collapse
|
47
|
Sui S, Wang Y, Kolewe KW, Srajer V, Henning R, Schiffman JD, Dimitrakopoulos C, Perry SL. Graphene-based microfluidics for serial crystallography. LAB ON A CHIP 2016; 16:3082-96. [PMID: 27241728 PMCID: PMC4970872 DOI: 10.1039/c6lc00451b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Microfluidic strategies to enable the growth and subsequent serial crystallographic analysis of micro-crystals have the potential to facilitate both structural characterization and dynamic structural studies of protein targets that have been resistant to single-crystal strategies. However, adapting microfluidic crystallization platforms for micro-crystallography requires a dramatic decrease in the overall device thickness. We report a robust strategy for the straightforward incorporation of single-layer graphene into ultra-thin microfluidic devices. This architecture allows for a total material thickness of only ∼1 μm, facilitating on-chip X-ray diffraction analysis while creating a sample environment that is stable against significant water loss over several weeks. We demonstrate excellent signal-to-noise in our X-ray diffraction measurements using a 1.5 μs polychromatic X-ray exposure, and validate our approach via on-chip structure determination using hen egg white lysozyme (HEWL) as a model system. Although this work is focused on the use of graphene for protein crystallography, we anticipate that this technology should find utility in a wide range of both X-ray and other lab on a chip applications.
Collapse
Affiliation(s)
- Shuo Sui
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Yuxi Wang
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Kristopher W Kolewe
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Vukica Srajer
- BioCARS Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL 60439, USA
| | - Robert Henning
- BioCARS Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL 60439, USA
| | - Jessica D Schiffman
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Christos Dimitrakopoulos
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Sarah L Perry
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| |
Collapse
|
48
|
Owen RL, Juanhuix J, Fuchs M. Current advances in synchrotron radiation instrumentation for MX experiments. Arch Biochem Biophys 2016; 602:21-31. [PMID: 27046341 PMCID: PMC5505570 DOI: 10.1016/j.abb.2016.03.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 11/15/2022]
Abstract
Following pioneering work 40 years ago, synchrotron beamlines dedicated to macromolecular crystallography (MX) have improved in almost every aspect as instrumentation has evolved. Beam sizes and crystal dimensions are now on the single micron scale while data can be collected from proteins with molecular weights over 10 MDa and from crystals with unit cell dimensions over 1000 Å. Furthermore it is possible to collect a complete data set in seconds, and obtain the resulting structure in minutes. The impact of MX synchrotron beamlines and their evolution is reflected in their scientific output, and MX is now the method of choice for a variety of aims from ligand binding to structure determination of membrane proteins, viruses and ribosomes, resulting in a much deeper understanding of the machinery of life. A main driving force of beamline evolution have been advances in almost every aspect of the instrumentation comprising a synchrotron beamline. In this review we aim to provide an overview of the current status of instrumentation at modern MX experiments. The most critical optical components are discussed, as are aspects of endstation design, sample delivery, visualisation and positioning, the sample environment, beam shaping, detectors and data acquisition and processing.
Collapse
Affiliation(s)
- Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Jordi Juanhuix
- Alba Synchrotron, Carrer de la llum 2-26, Cerdanyola, 08192, Spain.
| | - Martin Fuchs
- National Synchrotron Light Source II, Brookhaven National Lab, Upton, NY, 11973, USA.
| |
Collapse
|
49
|
Roedig P, Duman R, Sanchez-Weatherby J, Vartiainen I, Burkhardt A, Warmer M, David C, Wagner A, Meents A. Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering. J Appl Crystallogr 2016; 49:968-975. [PMID: 27275143 PMCID: PMC4886986 DOI: 10.1107/s1600576716006348] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/14/2016] [Indexed: 11/25/2022] Open
Abstract
Recent success at X-ray free-electron lasers has led to serial crystallography experiments staging a comeback at synchrotron sources as well. With crystal lifetimes typically in the millisecond range and the latest-generation detector technologies with high framing rates up to 1 kHz, fast sample exchange has become the bottleneck for such experiments. A micro-patterned chip has been developed from single-crystalline silicon, which acts as a sample holder for up to several thousand microcrystals at a very low background level. The crystals can be easily loaded onto the chip and excess mother liquor can be efficiently removed. Dehydration of the crystals is prevented by keeping them in a stream of humidified air during data collection. Further sealing of the sample holder, for example with Kapton, is not required. Room-temperature data collection from insulin crystals loaded onto the chip proves the applicability of the chip for macromolecular crystallography. Subsequent structure refinements reveal no radiation-damage-induced structural changes for insulin crystals up to a dose of 565.6 kGy, even though the total diffraction power of the crystals has on average decreased to 19.1% of its initial value for the same dose. A decay of the diffracting power by half is observed for a dose of D1/2 = 147.5 ± 19.1 kGy, which is about 1/300 of the dose before crystals show a similar decay at cryogenic temperatures.
Collapse
Affiliation(s)
- Philip Roedig
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, Hamburg 22607, Germany
| | - Ramona Duman
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Juan Sanchez-Weatherby
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | | | - Anja Burkhardt
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, Hamburg 22607, Germany
| | - Martin Warmer
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, Hamburg 22607, Germany
| | | | - Armin Wagner
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Alke Meents
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, Hamburg 22607, Germany
| |
Collapse
|
50
|
Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature. Sci Rep 2016; 6:25558. [PMID: 27150272 PMCID: PMC4858681 DOI: 10.1038/srep25558] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/18/2016] [Indexed: 12/27/2022] Open
Abstract
Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.
Collapse
|