1
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Baxter J, Hutchison CD, Fadini A, Maghlaoui K, Cordon-Preciado V, Morgan RML, Agthe M, Horrell S, Tellkamp F, Mehrabi P, Pfeifer Y, Müller-Werkmeister HM, von Stetten D, Pearson AR, van Thor JJ. Power Density Titration of Reversible Photoisomerization of a Fluorescent Protein Chromophore in the Presence of Thermally Driven Barrier Crossing Shown by Quantitative Millisecond Serial Synchrotron X-ray Crystallography. J Am Chem Soc 2024; 146:16394-16403. [PMID: 38848551 PMCID: PMC11191680 DOI: 10.1021/jacs.3c12883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024]
Abstract
We present millisecond quantitative serial X-ray crystallography at 1.7 Å resolution demonstrating precise optical control of reversible population transfer from Trans-Cis and Cis-Trans photoisomerization of a reversibly switchable fluorescent protein, rsKiiro. Quantitative results from the analysis of electron density differences, extrapolated structure factors, and occupancy refinements are shown to correspond to optical measurements of photoinduced population transfer and have sensitivity to a few percent in concentration differences. Millisecond time-resolved concentration differences are precisely and reversibly controlled through intense continuous wave laser illuminations at 405 and 473 nm for the Trans-to-Cis and Cis-to-Trans reactions, respectively, while the X-ray crystallographic measurement and laser illumination of the metastable Trans chromophore conformation causes partial thermally driven reconversion across a 91.5 kJ/mol thermal barrier from which a temperature jump between 112 and 128 K is extracted.
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Affiliation(s)
- James
M. Baxter
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | | | - Alisia Fadini
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - Karim Maghlaoui
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | | | - R. Marc L. Morgan
- Center
for Structural Biology, Imperial College
London, London SW7 2AZ, U.K.
| | - Michael Agthe
- European
Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany
| | - Sam Horrell
- Department
of Physics, Center for Free-Electron Laser Science, Institute for
Nanostructure and Solid State Physics, University
of Hamburg, Hamburg 22607, Germany
| | - Friedjof Tellkamp
- Scientific
Support Unit Machine Physics, Max-Planck-Institute
for Structure and Dynamics of Matter, Hamburg 22761, Germany
| | - Pedram Mehrabi
- Max
Planck Institute for the Structure and Dynamics of Matter, CFEL, Hamburg 22607, Germany
| | - Yannik Pfeifer
- Institute
of Chemistry—Physical Chemistry, University of Potsdam, Potsdam 14469, Germany
| | | | - David von Stetten
- European
Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany
| | - Arwen R. Pearson
- Institute
for Nanostructure and Solid State Physics & The Hamburg Centre
for Ultrafast Imaging, HARBOR, Universität
Hamburg, Hamburg 22607, Germany
| | - Jasper J. van Thor
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
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2
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Khusainov G, Standfuss J, Weinert T. The time revolution in macromolecular crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:020901. [PMID: 38616866 PMCID: PMC11015943 DOI: 10.1063/4.0000247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Macromolecular crystallography has historically provided the atomic structures of proteins fundamental to cellular functions. However, the advent of cryo-electron microscopy for structure determination of large and increasingly smaller and flexible proteins signaled a paradigm shift in structural biology. The extensive structural and sequence data from crystallography and advanced sequencing techniques have been pivotal for training computational models for accurate structure prediction, unveiling the general fold of most proteins. Here, we present a perspective on the rise of time-resolved crystallography as the new frontier of macromolecular structure determination. We trace the evolution from the pioneering time-resolved crystallography methods to modern serial crystallography, highlighting the synergy between rapid detection technologies and state-of-the-art x-ray sources. These innovations are redefining our exploration of protein dynamics, with high-resolution crystallography uniquely positioned to elucidate rapid dynamic processes at ambient temperatures, thus deepening our understanding of protein functionality. We propose that the integration of dynamic structural data with machine learning advancements will unlock predictive capabilities for protein kinetics, revolutionizing dynamics like macromolecular crystallography revolutionized structural biology.
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Affiliation(s)
- Georgii Khusainov
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
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3
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Schmidt D, Hensel D, Petev MV, Khosla M, Brede M, Vadilonga S, Gaal P. WaveGate: a versatile tool for temporal shaping of synchrotron beams. OPTICS EXPRESS 2024; 32:7473-7483. [PMID: 38439426 DOI: 10.1364/oe.515884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/08/2024] [Indexed: 03/06/2024]
Abstract
We present a full performance characterization of a solid state pulse picker for hard x-ray pulses at synchrotrons. The device is called WaveGate. Specifically, we quantify its efficiency (>30 %), timing capabilities (switching times between 100 ns and ms), on-off contrast (>104) and influence on the coherence properties of the incident x-ray beam. In addition, we discuss the implementation of the WaveGate in an optical pump - x-ray probe setup. Even if single pulse selection is performed by external detector gating, the WaveGate drastically increases the efficiency of a measurement. Finally, we introduce advanced timing schemes that can be realized by modulating the time structure of the synchrotron beam.
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4
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Hatcher LE, Warren MR, Skelton JM, Pallipurath AR, Saunders LK, Allan DR, Hathaway P, Crevatin G, Omar D, Williams BH, Coulson BA, Wilson CC, Raithby PR. LED-pump-X-ray-multiprobe crystallography for sub-second timescales. Commun Chem 2022; 5:102. [PMID: 36697958 PMCID: PMC9814726 DOI: 10.1038/s42004-022-00716-1] [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: 01/14/2022] [Accepted: 08/08/2022] [Indexed: 02/01/2023] Open
Abstract
The visualization of chemical processes that occur in the solid-state is key to the design of new functional materials. One of the challenges in these studies is to monitor the processes across a range of timescales in real-time. Here, we present a pump-multiprobe single-crystal X-ray diffraction (SCXRD) technique for studying photoexcited solid-state species with millisecond-to-minute lifetimes. We excite using pulsed LEDs and synchronise to a gated X-ray detector to collect 3D structures with sub-second time resolution while maximising photo-conversion and minimising beam damage. Our implementation provides complete control of the pump-multiprobe sequencing and can access a range of timescales using the same setup. Using LEDs allows variation of the intensity and pulse width and ensures uniform illumination of the crystal, spreading the energy load in time and space. We demonstrate our method by studying the variable-temperature kinetics of photo-activated linkage isomerism in [Pd(Bu4dien)(NO2)][BPh4] single-crystals. We further show that our method extends to following indicative Bragg reflections with a continuous readout Timepix3 detector chip. Our approach is applicable to a range of physical and biological processes that occur on millisecond and slower timescales, which cannot be studied using existing techniques.
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Affiliation(s)
- Lauren E. Hatcher
- grid.7340.00000 0001 2162 1699Department of Chemistry, University of Bath, Bath, UK ,grid.5600.30000 0001 0807 5670School of Chemistry, Cardiff University, Cardiff, UK
| | - Mark R. Warren
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Jonathan M. Skelton
- grid.7340.00000 0001 2162 1699Department of Chemistry, University of Bath, Bath, UK ,grid.5379.80000000121662407Department of Chemistry, University of Manchester, Manchester, UK
| | - Anuradha R. Pallipurath
- grid.7340.00000 0001 2162 1699Department of Chemistry, University of Bath, Bath, UK ,grid.9909.90000 0004 1936 8403School of Chemical and Process Engineering, University of Leeds, Leeds, UK
| | - Lucy K. Saunders
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - David R. Allan
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Paul Hathaway
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Giulio Crevatin
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - David Omar
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Ben H. Williams
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Ben A. Coulson
- grid.5600.30000 0001 0807 5670School of Chemistry, Cardiff University, Cardiff, UK
| | - Chick C. Wilson
- grid.7340.00000 0001 2162 1699Department of Chemistry, University of Bath, Bath, UK
| | - Paul R. Raithby
- grid.7340.00000 0001 2162 1699Department of Chemistry, University of Bath, Bath, UK
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5
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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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6
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Miller MD, Phillips GN. Moving beyond static snapshots: Protein dynamics and the Protein Data Bank. J Biol Chem 2021; 296:100749. [PMID: 33961840 PMCID: PMC8164045 DOI: 10.1016/j.jbc.2021.100749] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 01/02/2023] Open
Abstract
Proteins are the molecular machines of living systems. Their dynamics are an intrinsic part of their evolutionary selection in carrying out their biological functions. Although the dynamics are more difficult to observe than a static, average structure, we are beginning to observe these dynamics and form sound mechanistic connections between structure, dynamics, and function. This progress is highlighted in case studies from myoglobin and adenylate kinase to the ribosome and molecular motors where these molecules are being probed with a multitude of techniques across many timescales. New approaches to time-resolved crystallography are allowing simple “movies” to be taken of proteins in action, and new methods of mapping the variations in cryo-electron microscopy are emerging to reveal a more complete description of life’s machines. The results of these new methods are aided in their dissemination by continual improvements in curation and distribution by the Protein Data Bank and their partners around the world.
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Affiliation(s)
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas, USA; Department of Chemistry, Rice University, Houston, Texas, USA.
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7
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Dejoie C, Tamura N. Pattern-matching indexing of Laue and monochromatic serial crystallography data for applications in materials science. J Appl Crystallogr 2020; 53:824-836. [PMID: 32684897 PMCID: PMC7312145 DOI: 10.1107/s160057672000521x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/13/2020] [Indexed: 11/11/2022] Open
Abstract
Serial crystallography data can be challenging to index, as each frame is processed individually, rather than being processed as a whole like in conventional X-ray single-crystal crystallography. An algorithm has been developed to index still diffraction patterns arising from small-unit-cell samples. The algorithm is based on the matching of reciprocal-lattice vector pairs, as developed for Laue microdiffraction data indexing, combined with three-dimensional pattern matching using a nearest-neighbors approach. As a result, large-bandpass data (e.g. 5-24 keV energy range) and monochromatic data can be processed, the main requirement being prior knowledge of the unit cell. Angles calculated in the vicinity of a few theoretical and experimental reciprocal-lattice vectors are compared, and only vectors with the highest number of common angles are selected as candidates to obtain the orientation matrix. Global matching on the entire pattern is then checked. Four indexing options are available, two for the ranking of the theoretical reciprocal-lattice vectors and two for reducing the number of possible candidates. The algorithm has been used to index several data sets collected under different experimental conditions on a series of model samples. Knowing the crystallographic structure of the sample and using this information to rank the theoretical reflections based on the structure factors helps the indexing of large-bandpass data for the largest-unit-cell samples. For small-bandpass data, shortening the candidate list to determine the orientation matrix should be based on matching pairs of reciprocal-lattice vectors instead of triplet matching.
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Affiliation(s)
- Catherine Dejoie
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Nobumichi Tamura
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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8
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Weinert T, Skopintsev P, James D, Dworkowski F, Panepucci E, Kekilli D, Furrer A, Brünle S, Mous S, Ozerov D, Nogly P, Wang M, Standfuss J. Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography. Science 2020; 365:61-65. [PMID: 31273117 DOI: 10.1126/science.aaw8634] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/11/2019] [Indexed: 11/02/2022]
Abstract
Conformational dynamics are essential for proteins to function. We adapted time-resolved serial crystallography developed at x-ray lasers to visualize protein motions using synchrotrons. We recorded the structural changes in the light-driven proton-pump bacteriorhodopsin over 200 milliseconds in time. The snapshot from the first 5 milliseconds after photoactivation shows structural changes associated with proton release at a quality comparable to that of previous x-ray laser experiments. From 10 to 15 milliseconds onwards, we observe large additional structural rearrangements up to 9 angstroms on the cytoplasmic side. Rotation of leucine-93 and phenylalanine-219 opens a hydrophobic barrier, leading to the formation of a water chain connecting the intracellular aspartic acid-96 with the retinal Schiff base. The formation of this proton wire recharges the membrane pump with a proton for the next cycle.
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Affiliation(s)
- Tobias Weinert
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland.
| | - Petr Skopintsev
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Daniel James
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Florian Dworkowski
- Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Ezequiel Panepucci
- Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Demet Kekilli
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sandra Mous
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zürich, Switzerland
| | - Dmitry Ozerov
- Science IT, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Przemyslaw Nogly
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zürich, Switzerland
| | - Meitian Wang
- Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Jörg Standfuss
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
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9
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Lane TJ, Ratner D. What are the advantages of ghost imaging? Multiplexing for x-ray and electron imaging. OPTICS EXPRESS 2020; 28:5898-5918. [PMID: 32225851 DOI: 10.1364/oe.379503] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/02/2020] [Indexed: 06/10/2023]
Abstract
Ghost imaging, Fourier transform spectroscopy, and the newly developed Hadamard transform crystallography are all examples of multiplexing measurement strategies. Multiplexed experiments are performed by measuring multiple points in space, time, or energy simultaneously. This contrasts to the usual method of systematically scanning single points. How do multiplexed measurements work and when they are advantageous? Here we address these questions with a focus on applications involving x-rays or electrons. We present a quantitative framework for analyzing the expected error and radiation dose of different measurement scheme that enables comparison. We conclude that in very specific situations, multiplexing can offer improvements in resolution and signal-to-noise. If the signal has a sparse representation, these advantages become more general and dramatic, and further less radiation can be used to complete a measurement.
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10
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Zaitsev-Doyle JJ, Puchert A, Pfeifer Y, Yan H, Yorke BA, Müller-Werkmeister HM, Uetrecht C, Rehbein J, Huse N, Pearson AR, Sans M. Synthesis and characterisation of α-carboxynitrobenzyl photocaged l-aspartates for applications in time-resolved structural biology. RSC Adv 2019; 9:8695-8699. [PMID: 35518684 PMCID: PMC9061760 DOI: 10.1039/c9ra00968j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/06/2019] [Indexed: 01/17/2023] Open
Abstract
We report a new synthetic route to a series of α-carboxynitrobenzyl photocaged l-aspartates for application in time-resolved structural biology. The resulting compounds were characterised in terms of UV/Vis absorption properties, aqueous solubility and stability, and photocleavage rates (τ = μs to ms) and quantum yields (φ = 0.05 to 0.14). We report a new synthetic route to a series of α-carboxynitrobenzyl photocaged l-aspartates for application in time-resolved structural biology.![]()
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Affiliation(s)
- John J. Zaitsev-Doyle
- The Hamburg Center for Ultrafast Imaging & Institute for Nanostructure and Solid State Physics
- 22761 Hamburg
- Germany
| | - Anke Puchert
- Department of Physics and Centre for Hybrid Nanostructures
- University of Hamburg
- 22761 Hamburg
- Germany
| | - Yannik Pfeifer
- University of Potsdam
- Institute of Chemistry, Physical Chemistry
- 14476 Potsdam
- Germany
| | - Hao Yan
- Heinrich Pette Institute
- Leibniz Institute for Experimental Virology
- 20251 Hamburg
- Germany
| | | | | | - Charlotte Uetrecht
- Heinrich Pette Institute
- Leibniz Institute for Experimental Virology
- 20251 Hamburg
- Germany
- European XFEL GmbH
| | - Julia Rehbein
- Fachbereich für Chemie und Pharmazie
- Universität Regensburg
- 93053 Regensburg
- Germany
| | - Nils Huse
- The Hamburg Center for Ultrafast Imaging & Institute for Nanostructure and Solid State Physics
- 22761 Hamburg
- Germany
- Department of Physics and Centre for Hybrid Nanostructures
- University of Hamburg
| | - Arwen R. Pearson
- The Hamburg Center for Ultrafast Imaging & Institute for Nanostructure and Solid State Physics
- 22761 Hamburg
- Germany
| | - Marta Sans
- The Hamburg Center for Ultrafast Imaging & Institute for Nanostructure and Solid State Physics
- 22761 Hamburg
- Germany
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11
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Using Spectral Representation to Classify Proteins' Conformational States. Int J Mol Sci 2018; 19:ijms19072089. [PMID: 30021967 PMCID: PMC6073521 DOI: 10.3390/ijms19072089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 11/16/2022] Open
Abstract
Numerous proteins are molecular targets for drug action and hence are important in drug discovery. Structure-based computational drug discovery relies on detailed information regarding protein conformations for subsequent drug screening in silico. There are two key issues in analyzing protein conformations in virtual screening. The first considers the protein’s conformational change in response to physical and chemical conditions. The second is the protein’s atomic resolution reconstruction from X-ray crystallography or nuclear magnetic resonance (NMR) data. In this latter problem, information is needed regarding the sample’s position relative to the source of X-rays. Here, we introduce a new measure for classifying protein conformational states using spectral representation and Wigner’s D-functions. Predictions based on the new measure are in good agreement with conformational states of proteins. These results could also be applied to improve conformational alignment of the snapshots given by protein crystallography.
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12
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Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons. Nat Commun 2017; 8:542. [PMID: 28912485 PMCID: PMC5599499 DOI: 10.1038/s41467-017-00630-4] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/14/2017] [Indexed: 12/24/2022] Open
Abstract
Historically, room-temperature structure determination was succeeded by cryo-crystallography to mitigate radiation damage. Here, we demonstrate that serial millisecond crystallography at a synchrotron beamline equipped with high-viscosity injector and high frame-rate detector allows typical crystallographic experiments to be performed at room-temperature. Using a crystal scanning approach, we determine the high-resolution structure of the radiation sensitive molybdenum storage protein, demonstrate soaking of the drug colchicine into tubulin and native sulfur phasing of the human G protein-coupled adenosine receptor. Serial crystallographic data for molecular replacement already converges in 1,000–10,000 diffraction patterns, which we collected in 3 to maximally 82 minutes. Compared with serial data we collected at a free-electron laser, the synchrotron data are of slightly lower resolution, however fewer diffraction patterns are needed for de novo phasing. Overall, the data we collected by room-temperature serial crystallography are of comparable quality to cryo-crystallographic data and can be routinely collected at synchrotrons. Serial crystallography was developed for protein crystal data collection with X-ray free-electron lasers. Here the authors present several examples which show that serial crystallography using high-viscosity injectors can also be routinely employed for room-temperature data collection at synchrotrons.
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13
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Helliwell JR. New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences. Biosci Rep 2017; 37:BSR20170204. [PMID: 28572170 PMCID: PMC6434086 DOI: 10.1042/bsr20170204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022] Open
Abstract
Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography's role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.
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14
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A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun 2017; 8:15123. [PMID: 28436492 PMCID: PMC5413968 DOI: 10.1038/ncomms15123] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/03/2017] [Indexed: 12/02/2022] Open
Abstract
In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous (‘weak' or ‘noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state—even from inaccurate maps—by subtracting a proportion of the confounding ‘ground state'; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches. Building a ligand into a weak region of an electron density map of a protein is a subjective process. Here, the authors present a new method to obtain a clear electron density for a bound ligand based on multi-crystal experiments and 3D background correction.
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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.
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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
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Palamini M, Canciani A, Forneris F. Identifying and Visualizing Macromolecular Flexibility in Structural Biology. Front Mol Biosci 2016; 3:47. [PMID: 27668215 PMCID: PMC5016524 DOI: 10.3389/fmolb.2016.00047] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/22/2016] [Indexed: 12/29/2022] Open
Abstract
Structural biology comprises a variety of tools to obtain atomic resolution data for the investigation of macromolecules. Conventional structural methodologies including crystallography, NMR and electron microscopy often do not provide sufficient details concerning flexibility and dynamics, even though these aspects are critical for the physiological functions of the systems under investigation. However, the increasing complexity of the molecules studied by structural biology (including large macromolecular assemblies, integral membrane proteins, intrinsically disordered systems, and folding intermediates) continuously demands in-depth analyses of the roles of flexibility and conformational specificity involved in interactions with ligands and inhibitors. The intrinsic difficulties in capturing often subtle but critical molecular motions in biological systems have restrained the investigation of flexible molecules into a small niche of structural biology. Introduction of massive technological developments over the recent years, which include time-resolved studies, solution X-ray scattering, and new detectors for cryo-electron microscopy, have pushed the limits of structural investigation of flexible systems far beyond traditional approaches of NMR analysis. By integrating these modern methods with powerful biophysical and computational approaches such as generation of ensembles of molecular models and selective particle picking in electron microscopy, more feasible investigations of dynamic systems are now possible. Using some prominent examples from recent literature, we review how current structural biology methods can contribute useful data to accurately visualize flexibility in macromolecular structures and understand its important roles in regulation of biological processes.
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Affiliation(s)
| | | | - Federico Forneris
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of PaviaPavia, Italy
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17
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Beddard GS, Yorke BA. Pump-Probe Spectroscopy Using the Hadamard Transform. APPLIED SPECTROSCOPY 2016; 70:1292-1299. [PMID: 27340218 DOI: 10.1177/0003702816653927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/20/2015] [Indexed: 06/06/2023]
Abstract
A new method of performing pump-probe experiments is proposed and experimentally demonstrated by a proof of concept on the millisecond scale. The idea behind this method is to measure the total probe intensity arising from several time points as a group, instead of measuring each time separately. These measurements are multiplexes that are then transformed into the true signal via multiplication with a binary Hadamard S matrix. Each group of probe pulses is determined by using the pattern of a row of the Hadamard S matrix and the experiment is completed by rotating this pattern by one step for each sample excitation until the original pattern is again produced. Thus to measure n time points, n excitation events are needed and n probe patterns each taken from the n × n S matrix. The time resolution is determined by the shortest time between the probe pulses. In principle, this method could be used over all timescales, instead of the conventional pump-probe method which uses delay lines for picosecond and faster time resolution, or fast detectors and oscilloscopes on longer timescales. This new method is particularly suitable for situations where the probe intensity is weak and/or the detector is noisy. When the detector is noisy, there is in principle a signal to noise advantage over conventional pump-probe methods.
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19
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Levantino M, Yorke BA, Monteiro DC, Cammarata M, Pearson AR. Using synchrotrons and XFELs for time-resolved X-ray crystallography and solution scattering experiments on biomolecules. Curr Opin Struct Biol 2015; 35:41-8. [PMID: 26342489 DOI: 10.1016/j.sbi.2015.07.017] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 07/27/2015] [Accepted: 07/31/2015] [Indexed: 11/17/2022]
Abstract
Time-resolved structural information is key to understand the mechanism of biological processes, such as catalysis and signalling. Recent developments in X-ray sources as well as data collection and analysis methods are making routine time-resolved X-ray crystallography and solution scattering experiments a real possibility for structural biologists. Here we review the information that can be obtained from these techniques and discuss the considerations that must be taken into account when designing a time-resolved experiment.
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Affiliation(s)
- Matteo Levantino
- Department of Physics and Chemistry, University of Palermo, Palermo 90128, Italy
| | - Briony A Yorke
- Hamburg Centre for Ultrafast Imaging & Institute of Nanostructure and Solid State Physics, University of Hamburg, Hamburg 22607, Germany
| | - Diana Cf Monteiro
- Astbury Centre for Structural Molecular Biology & School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Marco Cammarata
- Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1, Rennes 35042, France
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging & Institute of Nanostructure and Solid State Physics, University of Hamburg, Hamburg 22607, Germany.
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20
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Dejoie C, Smeets S, Baerlocher C, Tamura N, Pattison P, Abela R, McCusker LB. Serial snapshot crystallography for materials science with SwissFEL. IUCRJ 2015; 2:361-70. [PMID: 25995845 PMCID: PMC4420546 DOI: 10.1107/s2052252515006740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/03/2015] [Indexed: 06/04/2023]
Abstract
New opportunities for studying (sub)microcrystalline materials with small unit cells, both organic and inorganic, will open up when the X-ray free electron laser (XFEL) presently being constructed in Switzerland (SwissFEL) comes online in 2017. Our synchrotron-based experiments mimicking the 4%-energy-bandpass mode of the SwissFEL beam show that it will be possible to record a diffraction pattern of up to 10 randomly oriented crystals in a single snapshot, to index the resulting reflections, and to extract their intensities reliably. The crystals are destroyed with each XFEL pulse, but by combining snapshots from several sets of crystals, a complete set of data can be assembled, and crystal structures of materials that are difficult to analyze otherwise will become accessible. Even with a single shot, at least a partial analysis of the crystal structure will be possible, and with 10-50 femtosecond pulses, this offers tantalizing possibilities for time-resolved studies.
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Affiliation(s)
- Catherine Dejoie
- Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich, 8093, Switzerland
| | - Stef Smeets
- Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich, 8093, Switzerland
| | - Christian Baerlocher
- Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich, 8093, Switzerland
| | - Nobumichi Tamura
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Philip Pattison
- Swiss-Norwegian Beamlines, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble, 38042, France
- Laboratory of Crystallography, EPFL, Rte de la Sorge, Lausanne, 1015, Switzerland
| | - Rafael Abela
- SwissFEL, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Lynne B. McCusker
- Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich, 8093, Switzerland
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Helliwell JR, Mitchell EP. Synchrotron radiation macromolecular crystallography: science and spin-offs. IUCRJ 2015; 2:283-91. [PMID: 25866664 PMCID: PMC4392420 DOI: 10.1107/s205225251402795x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 12/22/2014] [Indexed: 05/11/2023]
Abstract
A current overview of synchrotron radiation (SR) in macromolecular crystallography (MX) instrumentation, methods and applications is presented. Automation has been and remains a central development in the last decade, as have the rise of remote access and of industrial service provision. Results include a high number of Protein Data Bank depositions, with an increasing emphasis on the successful use of microcrystals. One future emphasis involves pushing the frontiers of using higher and lower photon energies. With the advent of X-ray free-electron lasers, closely linked to SR developments, the use of ever smaller samples such as nanocrystals, nanoclusters and single molecules is anticipated, as well as the opening up of femtosecond time-resolved diffraction structural studies. At SR sources, a very high-throughput assessment for the best crystal samples and the ability to tackle just a few micron and sub-micron crystals will become widespread. With higher speeds and larger detectors, diffraction data volumes are becoming long-term storage and archiving issues; the implications for today and the future are discussed. Together with the rise of the storage ring to its current pre-eminence in MX data provision, the growing tendency of central facility sites to offer other centralized facilities complementary to crystallography, such as cryo-electron microscopy and NMR, is a welcome development.
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Affiliation(s)
- John R. Helliwell
- School of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, England
| | - Edward P. Mitchell
- ESRF, 71 avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Staffordshire ST5 5BG, England
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Yorke BA, Beddard GS, Owen RL, Pearson AR. Erratum: Corrigendum: Time-resolved crystallography using the Hadamard transform. Nat Methods 2015. [DOI: 10.1038/nmeth0215-160e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Helliwell JR, Brink A, Kaenket S, Starkey VL, Tanley SWM. X-ray diffraction in temporally and spatially resolved biomolecular science. Faraday Discuss 2015; 177:429-41. [PMID: 25605312 DOI: 10.1039/c4fd00166d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Time-resolved Laue protein crystallography at the European Synchrotron Radiation Facility (ESRF) opened up the field of sub-nanosecond protein crystal structure analyses. There are a limited number of such time-resolved studies in the literature. Why is this? The X-ray laser now gives us femtosecond (fs) duration pulses, typically 10 fs up to ∼50 fs. Their use is attractive for the fastest time-resolved protein crystallography studies. It has been proposed that single molecules could even be studied with the advantage of being able to measure X-ray diffraction from a 'crystal lattice free' single molecule, with or without temporal resolved structural changes. This is altogether very challenging R&D. So as to assist this effort we have undertaken studies of metal clusters that bind to proteins, both 'fresh' and after repeated X-ray irradiation to assess their X-ray-photo-dynamics, namely Ta6Br12, K2PtI6 and K2PtBr6 bound to a test protein, hen egg white lysozyme. These metal complexes have the major advantage of being very recognisable shapes (pseudo spherical or octahedral) and thereby offer a start to (probably very difficult) single molecule electron density map interpretations, both static and dynamic. A further approach is to investigate the X-ray laser beam diffraction strength of a well scattering nano-cluster; an example from nature being the iron containing ferritin. Electron crystallography and single particle electron microscopy imaging offers alternatives to X-ray structural studies; our structural studies of crustacyanin, a 320 kDa protein carotenoid complex, can be extended either by electron based techniques or with the X-ray laser representing a fascinating range of options. General outlook remarks concerning X-ray, electron and neutron macromolecular crystallography as well as 'NMR crystallography' conclude the article.
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