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Schulz EC, Yorke BA, Pearson AR, Mehrabi P. Best practices for time-resolved serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2022; 78:14-29. [PMID: 34981758 PMCID: PMC8725164 DOI: 10.1107/s2059798321011621] [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: 08/21/2021] [Accepted: 11/03/2021] [Indexed: 11/10/2022] Open
Abstract
With recent developments in X-ray sources, instrumentation and data-analysis tools, time-resolved crystallographic experiments, which were originally the preserve of a few expert groups, are becoming simpler and can be carried out at more radiation sources, and are thus increasingly accessible to a growing user base. However, these experiments are just that: discrete experiments, not just `data collections'. As such, careful planning and consideration of potential pitfalls is required to enable a successful experiment. Here, some of the key factors that should be considered during the planning and execution of a time-resolved structural study are outlined, with a particular focus on synchrotron-based experiments.
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Affiliation(s)
- Eike C. Schulz
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Briony A. Yorke
- School of Chemistry and Bioscience, University of Bradford, Bradford BD7 1DP, United Kingdom
| | - Arwen R. Pearson
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Pedram Mehrabi
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
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von Stetten D, Giraud T, Carpentier P, Sever F, Terrien M, Dobias F, Juers DH, Flot D, Mueller-Dieckmann C, Leonard GA, de Sanctis D, Royant A. In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:15-26. [PMID: 25615856 PMCID: PMC4304682 DOI: 10.1107/s139900471401517x] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/27/2014] [Indexed: 01/04/2023]
Abstract
The analysis of structural data obtained by X-ray crystallography benefits from information obtained from complementary techniques, especially as applied to the crystals themselves. As a consequence, optical spectroscopies in structural biology have become instrumental in assessing the relevance and context of many crystallographic results. Since the year 2000, it has been possible to record such data adjacent to, or directly on, the Structural Biology Group beamlines of the ESRF. A core laboratory featuring various spectrometers, named the Cryobench, is now in its third version and houses portable devices that can be directly mounted on beamlines. This paper reports the current status of the Cryobench, which is now located on the MAD beamline ID29 and is thus called the ID29S-Cryobench (where S stands for `spectroscopy'). It also reviews the diverse experiments that can be performed at the Cryobench, highlighting the various scientific questions that can be addressed.
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Affiliation(s)
| | - Thierry Giraud
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | - Franc Sever
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Maxime Terrien
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Douglas H. Juers
- Department of Physics, Whitman College, Walla Walla, WA 99362, USA
| | - David Flot
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | | | | | - Antoine Royant
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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Specht A, Bolze F, Omran Z, Nicoud JF, Goeldner M. Photochemical tools to study dynamic biological processes. HFSP JOURNAL 2009; 3:255-64. [PMID: 20119482 PMCID: PMC2799987 DOI: 10.2976/1.3132954] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 04/21/2009] [Indexed: 11/19/2022]
Abstract
Light-responsive biologically active compounds offer the possibility to study the dynamics of biological processes. Phototriggers and photoswitches have been designed, providing the capability to rapidly cause the initiation of wide range of dynamic biological phenomena. We will discuss, in this article, recent developments in the field of light-triggered chemical tools, specially how two-photon excitation, "caged" fluorophores, and the photoregulation of protein activities in combination with time-resolved x-ray techniques should break new grounds in the understanding of dynamic biological processes.
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Affiliation(s)
- Alexandre Specht
- Laboratoire de Conception et Application de Molécules Bioactives, Faculté de Pharmacie, UMR 7199, Université de Strasbourg-CNRS, 74 route du Rhin, F-67401 Illkirch-Graffenstaden Cedex, France
| | - Frédéric Bolze
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213, Université de Strasbourg-CNRS, 74 route du Rhin, F-67401 Illkirch-Graffenstaden Cedex, France
| | - Ziad Omran
- Laboratoire de Conception et Application de Molécules Bioactives, Faculté de Pharmacie, UMR 7199, Université de Strasbourg-CNRS, 74 route du Rhin, F-67401 Illkirch-Graffenstaden Cedex, France
| | - Jean-François Nicoud
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213, Université de Strasbourg-CNRS, 74 route du Rhin, F-67401 Illkirch-Graffenstaden Cedex, France
| | - Maurice Goeldner
- Laboratoire de Conception et Application de Molécules Bioactives, Faculté de Pharmacie, UMR 7199, Université de Strasbourg-CNRS, 74 route du Rhin, F-67401 Illkirch-Graffenstaden Cedex, France
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Specht A, Loudwig S, Peng L, Goeldner M. Complexing photolabile cholinergic ligands with synthetic and biological receptors: a dynamic survey. J INCL PHENOM MACRO 2009. [DOI: 10.1007/s10847-009-9603-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Howard-Jones AR, Adam V, Cowley A, Baldwin JE, Bourgeois D. Cryophotolysis of a caged oxygen compound for use in low temperature biological studies. Photochem Photobiol Sci 2009; 8:1150-6. [PMID: 19639117 DOI: 10.1039/b821516b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mechanistic investigations of biological enzymatic processes require controlled initiation and monitoring of catalytic reactions. A well-known technique to trap and observe reaction intermediates building up along a reaction pathway is the use of low temperature conditions. Here, we report a kinetically competent system for the release of molecular oxygen at cryogenic temperature, using a cobalt-based caged oxygen molecule, (micro-peroxo)(micro-hydroxo)bis[bis(bipyridyl)cobalt(III)] nitrate. Cryophotolysis of this compound was induced using 266 nm laser light and monitored by absorption microspectrophotometry. Furthermore, to verify that photo-fragmentation was accompanied by release of the active caged molecule, the production of dioxygen during cryophotolysis was directly visualized. This work lays the foundations for the use of low temperature reaction triggering as a tool to prolong the lifetime of normally unstable intermediate states in oxygen-dependent enzymes.
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Bourgeois D, Weik M. Kinetic protein crystallography: a tool to watch proteins in action. CRYSTALLOGR REV 2009. [DOI: 10.1080/08893110802604868] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Colletier JP, Weik M. Exploration structurale du paysage conformationnel de l’acétylcholinestérase par cristallographie cinétique. ANNALES PHARMACEUTIQUES FRANÇAISES 2007; 65:108-18. [PMID: 17404544 DOI: 10.1016/s0003-4509(07)90024-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Acetylcholinesterase is a very rapid enzyme, essential in the process of nerve impulse transmission at cholinergic synapses. It is the target of all currently approved anti-Alzheimer drugs and further progress in the modulation of its activity requires structural as well as dynamical information. Exploration of the conformational energy landscape of a protein by means of X-ray crystallography requires the use of experimental tricks, to overcome the inherently static nature of crystallographic structures. Here we report three experimental approaches that allowed to gain structural insight into the dynamics of acetylcholinesterase, which is relevant for structure-based drug design.
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Affiliation(s)
- J-P Colletier
- CEA-CNRS-UJF, Institut de biologie structurale J.-P. Ebel, Umr 5075, Laboratoire de biophysique moléculaire, F 38027 Grenoble.
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Klink BU, Goody RS, Scheidig AJ. A newly designed microspectrofluorometer for kinetic studies on protein crystals in combination with x-ray diffraction. Biophys J 2006; 91:981-92. [PMID: 16698776 PMCID: PMC1563776 DOI: 10.1529/biophysj.105.078931] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a new design for a fluorescence microspectrophotometer for use in kinetic crystallography in combination with x-ray diffraction experiments. The FLUMIX device (Fluorescence spectroscopy to monitor intermediates in x-ray crystallography) is built for 0 degrees fluorescence detection, which has several advantages in comparison to a conventional fluorometer with 90 degrees design. Due to the reduced spatial requirements and the need for only one objective, the system is highly versatile, easy to handle, and can be used for many different applications. In combination with a conventional stereomicroscope, fluorescence measurements or reaction initiation can be performed directly in a hanging drop crystallization setup. The FLUMIX device can be combined with most x-ray sources, normally without the need of a specialized mechanical support. As a biological model system, we have used H-Ras p21 with an artificially introduced photo-labile GTP precursor (caged GTP) and a covalently attached fluorophore (IANBD amide). Using the FLUMIX system, detailed information about the state of photolyzed crystals of the modified H-Ras p21 (p21(mod)) could be obtained. Measurements in combination with a synchrotron beamline showed significant fluorescence changes in p21(mod) crystals even within a few seconds of x-ray exposure at 100 K.
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Affiliation(s)
- Björn U Klink
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Physikalische Biochemie, D-44225 Dortmund, Germany
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Abstract
Crystal structures of protein-ligand complexes provide a detailed view of their spatial arrangement and interactions. In the case of stable, unreactive ligands, such as inhibitors or allosteric regulators, the complexes can be generated by cocrystallization or by soaking the ligand into fully grown crystals. In order to obtain highly occupied stochiometric complexes, the concentration and amount of ligand used needs to be considered. Protein complexes with reactive short-lived species that occur in chemical or binding reactions can be determined using monochromatic X-ray diffraction techniques via kinetic trapping approaches. To this end, the kinetics of the reaction has to be determined in the crystalline state and triggering methods to start the reaction need to be established. To facilitate data interpretation, the experimental conditions are usually chosen such that the peak concentration of the reactive species under investigation is maximized.
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Affiliation(s)
- Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heldelberg, Germany
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Weik M, Vernede X, Royant A, Bourgeois D. Temperature derivative fluorescence spectroscopy as a tool to study dynamical changes in protein crystals. Biophys J 2004; 86:3176-85. [PMID: 15111430 PMCID: PMC1304182 DOI: 10.1016/s0006-3495(04)74365-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Motions through the energy landscape of proteins lead to biological function. At temperatures below a dynamical transition (150-250 K), some of these motions are arrested and the activity of some proteins ceases. Here, we introduce the technique of temperature-derivative fluorescence microspectrophotometry to investigate the dynamical behavior of single protein crystals. The observation of glass transitions in thin films of water/glycerol mixtures allowed us to demonstrate the potential of the technique. Then, protein crystals were investigated, after soaking the samples in a small amount of fluorescein. If the fluorophore resides within the crystal channels, temperature-dependent changes in solvent dynamics can be monitored. Alternatively, if the fluorophore binds to the protein, local dynamical transitions within the biomolecule can be probed directly. A clear dynamical transition was observed at 175 K in the active site of crystalline human butyrylcholinesterase. The results suggest that the dynamics of crystalline proteins is strongly dependent on solvent composition and confinement in the crystal channels. Beyond applications in the field of kinetic crystallography, the highly sensitive temperature-derivative fluorescence microspectrophotometry technique opens the way to many studies on the dynamics of biological nanosamples.
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Affiliation(s)
- Martin Weik
- Laboratoire de Biophysique Moléculaire and Laboratoire de Cristallographie et Cristallogenèse des Protéines, UMR 5075, Institut de Biologie Structurale, 38027 Grenoble, France
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Pelliccioli AP, Wirz J. Photoremovable protecting groups: reaction mechanisms and applications. Photochem Photobiol Sci 2002; 1:441-58. [PMID: 12659154 DOI: 10.1039/b200777k] [Citation(s) in RCA: 538] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photolabile protecting groups enable biochemists to control the release of bioactive compounds in living tissue. 'Caged compounds' (photoactivatable bioagents) have become an important tool to study the events that follow chemical signalling in, e.g., cell biology and the neurosciences. The possibilities are by no means exhausted. Progress will depend on the development of photoremovable protecting groups that satisfy the diverse requirements of new applications--a challenging task for photochemists.
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Affiliation(s)
- Anna Paola Pelliccioli
- Institut für Physikalische Chemie, Universität Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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