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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.
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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
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2
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Huang CY, Aumonier S, Olieric V, Wang M. Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals. Acta Crystallogr D Struct Biol 2024; 80:620-628. [PMID: 39052318 DOI: 10.1107/s2059798324006697] [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: 04/17/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
Advances in structural biology have relied heavily on synchrotron cryo-crystallography and cryogenic electron microscopy to elucidate biological processes and for drug discovery. However, disparities between cryogenic and room-temperature (RT) crystal structures pose challenges. Here, Cryo2RT, a high-throughput RT data-collection method from cryo-cooled crystals that leverages the cryo-crystallography workflow, is introduced. Tested on endothiapepsin crystals with four soaked fragments, thaumatin and SARS-CoV-2 3CLpro, Cryo2RT reveals unique ligand-binding poses, offers a comparable throughput to cryo-crystallography and eases the exploration of structural dynamics at various temperatures.
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Affiliation(s)
- Chia Ying Huang
- Swiss Light Source, Center for Photon Science, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Sylvain Aumonier
- Swiss Light Source, Center for Photon Science, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Center for Photon Science, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Meitian Wang
- Swiss Light Source, Center for Photon Science, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
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3
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Henkel A, Oberthür D. A snapshot love story: what serial crystallography has done and will do for us. Acta Crystallogr D Struct Biol 2024; 80:563-579. [PMID: 38984902 PMCID: PMC11301758 DOI: 10.1107/s2059798324005588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024] Open
Abstract
Serial crystallography, born from groundbreaking experiments at the Linac Coherent Light Source in 2009, has evolved into a pivotal technique in structural biology. Initially pioneered at X-ray free-electron laser facilities, it has now expanded to synchrotron-radiation facilities globally, with dedicated experimental stations enhancing its accessibility. This review gives an overview of current developments in serial crystallography, emphasizing recent results in time-resolved crystallography, and discussing challenges and shortcomings.
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Affiliation(s)
- Alessandra Henkel
- Center for Free-Electron Laser Science CFELDeutsches Elektronen-Synchrotron DESYNotkestr. 8522607HamburgGermany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFELDeutsches Elektronen-Synchrotron DESYNotkestr. 8522607HamburgGermany
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4
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Huang CY, Metz A, Lange R, Artico N, Potot C, Hazemann J, Müller M, Dos Santos M, Chambovey A, Ritz D, Eris D, Meyer S, Bourquin G, Sharpe M, Mac Sweeney A. Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket. Acta Crystallogr D Struct Biol 2024; 80:123-136. [PMID: 38289714 PMCID: PMC10836397 DOI: 10.1107/s2059798324000329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate-binding pocket. Of 631 soaked fragments, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (three hits) or at crystal-packing interfaces (two hits). Notably, two fragments with a pose that was sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. The structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography.
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Affiliation(s)
- Chia Ying Huang
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Alexander Metz
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Roland Lange
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Nadia Artico
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Céline Potot
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | - Manon Müller
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | | | - Daniel Ritz
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Deniz Eris
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Solange Meyer
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | - May Sharpe
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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5
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Carrillo M, Mason TJ, Karpik A, Martiel I, Kepa MW, McAuley KE, Beale JH, Padeste C. Micro-structured polymer fixed targets for serial crystallography at synchrotrons and XFELs. IUCRJ 2023; 10:678-693. [PMID: 37727961 PMCID: PMC10619457 DOI: 10.1107/s2052252523007595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023]
Abstract
Fixed targets are a popular form of sample-delivery system used in serial crystallography at synchrotron and X-ray free-electron laser sources. They offer a wide range of sample-preparation options and are generally easy to use. The supports are typically made from silicon, quartz or polymer. Of these, currently, only silicon offers the ability to perform an aperture-aligned data collection where crystals are loaded into cavities in precise locations and sequentially rastered through, in step with the X-ray pulses. The polymer-based fixed targets have lacked the precision fabrication to enable this data-collection strategy and have been limited to directed-raster scans with crystals randomly distributed across the polymer surface. Here, the fabrication and first results from a new polymer-based fixed target, the micro-structured polymer fixed targets (MISP chips), are presented. MISP chips, like those made from silicon, have a precise array of cavities and fiducial markers. They consist of a structured polymer membrane and a stabilization frame. Crystals can be loaded into the cavities and the excess crystallization solution removed through apertures at their base. The fiducial markers allow for a rapid calculation of the aperture locations. The chips have a low X-ray background and, since they are optically transparent, also allow for an a priori analysis of crystal locations. This location mapping could, ultimately, optimize hit rates towards 100%. A black version of the MISP chip was produced to reduce light contamination for optical-pump/X-ray probe experiments. A study of the loading properties of the chips reveals that these types of fixed targets are best optimized for crystals of the order of 25 µm, but quality data can be collected from crystals as small as 5 µm. With the development of these chips, it has been proved that polymer-based fixed targets can be made with the precision required for aperture-alignment-based data-collection strategies. Further work can now be directed towards more cost-effective mass fabrication to make their use more sustainable for serial crystallography facilities and users.
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Affiliation(s)
- Melissa Carrillo
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002 Basel, Switzerland
- Swiss Nanoscience Institute, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Thomas J. Mason
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Agnieszka Karpik
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
- Institute of Polymer Nanotechnology (INKA), FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Engineering, Klosterzelgstrasse 2, 5210 Windisch, Switzerland
| | - Isabelle Martiel
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Michal W. Kepa
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | | | - John H. Beale
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Celestino Padeste
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
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Steiner RA. Introduction to the virtual thematic issue on room-temperature biological crystallography. IUCRJ 2023; 10:248-250. [PMID: 37000491 PMCID: PMC10161770 DOI: 10.1107/s2052252523002968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Room-temperature biological crystallography has seen a resergence in recent years and a collection of articles recently published in IUCrJ, Acta Cryst. D Structural Biology and Acta Cryst. F Structural Biology Communications, have been collected together to produce a virtual special issue at https://journals.iucr.org/special_issues/2022/RT/.
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Affiliation(s)
- Roberto A. Steiner
- King’s College London, New Hunt’s House - Guy’s Campus, London SE1 1UL, United Kingdom
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/B, Padova, 35131, Italy
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7
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Steiner RA. Introduction to the virtual thematic issue on room-temperature biological crystallography. Acta Crystallogr F Struct Biol Commun 2023; 79:79-81. [PMID: 37013862 PMCID: PMC10071831 DOI: 10.1107/s2053230x23002935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Room-temperature biological crystallography has seen a resergence in recent years and a collection of articles recently published in IUCrJ, Acta Cryst. D Structural Biology and Acta Cryst. F Structural Biology Communications, have been collected together to produce a virtual special issue at https://journals.iucr.org/special_issues/2022/RT/.
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Affiliation(s)
- Roberto A. Steiner
- King’s College London, New Hunt’s House - Guy’s Campus, London SE1 1UL, United Kingdom
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/B, Padova, 35131, Italy
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8
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Helliwell JR. Relating protein crystal structure to ligand-binding thermodynamics. Acta Crystallogr F Struct Biol Commun 2022; 78:403-407. [PMID: 36458619 PMCID: PMC9716570 DOI: 10.1107/s2053230x22011244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
An important interface between biophysical chemistry and biological crystal structures involves whether it is possible to relate experimental calorimetry measurements of protein ligand binding to 3D structures. This has proved to be challenging. The probes of the structure of matter, namely X-rays, neutrons and electrons, have challenges of one type or another in their use. This article focuses on saccharide binding to lectins as a theme, yet after 25 years or so it is still a work in progress to connect 3D structure to binding energies. Whilst this study involved one type of protein (lectins) and one class of ligand (monosaccharides), i.e. it was specific, it was of general importance, as measured for instance by its wide impact. The impetus for writing this update now, as a Scientific Comment, is that a breakthrough in neutron crystal structure determinations of saccharide-bound lectins has been achieved. It is suggested here that this new research from neutron protein crystallography could improve, i.e. reduce, the errors in the estimated binding energies.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom,Correspondence e-mail:
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