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Mendez D, Holton JM, Lyubimov AY, Hollatz S, Mathews II, Cichosz A, Martirosyan V, Zeng T, Stofer R, Liu R, Song J, McPhillips S, Soltis M, Cohen AE. Deep residual networks for crystallography trained on synthetic data. Acta Crystallogr D Struct Biol 2024; 80:26-43. [PMID: 38164955 PMCID: PMC10833344 DOI: 10.1107/s2059798323010586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024] Open
Abstract
The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.
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Affiliation(s)
- Derek Mendez
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - James M. Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, UC San Francisco, San Francisco, CA 94158, USA
| | - Artem Y. Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sabine Hollatz
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Irimpan I. Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aleksander Cichosz
- Department of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Vardan Martirosyan
- Department of Mathematics, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Teo Zeng
- Department of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ryan Stofer
- Department of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ruobin Liu
- Department of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Scott McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mike Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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2
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Henning RW, Kosheleva I, Šrajer V, Kim IS, Zoellner E, Ranganathan R. BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:014301. [PMID: 38304444 PMCID: PMC10834067 DOI: 10.1063/4.0000238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024]
Abstract
A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods-UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.
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Affiliation(s)
- Robert W. Henning
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Irina Kosheleva
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Vukica Šrajer
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - In-Sik Kim
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Eric Zoellner
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rama Ranganathan
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
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3
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Wu D, Wang L, Li W, Li X. Identifying a New Target for BtOBP8: Discovery of a Small Amino Ketone Molecule Containing Benzothiazole Fragments. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:17635-17645. [PMID: 37651643 DOI: 10.1021/acs.jafc.3c02594] [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: 09/02/2023]
Abstract
Insects rely on odorant-binding proteins (OBPs) for chemical perception, making OBPs a promising target for studying attractants and repellents of pests, such as Bemisia tabaci. However, no reports have reported using B. tabaci OBPs (BtOBPs) as pesticide screening targets. To fill this gap, we obtained BtOBP8 through prokaryotic expression and purification. Then, we confirmed its identity using western blotting and mass spectrometry. Next, we used the sitting drop and hanging drop methods to screen its crystal conditions. Using microscale thermophoresis and isothermal titration calorimetry, we identified the highest affinity ligand, 3l, from 30 compounds. Furthermore, point mutation techniques identified Val119 as a key amino acid residue in binding 31 to BtOBP8. Finally, we tested the bioactivity of B. tabaci Mediterranean and found that 3l more effectively inhibits the bioactivity of B. tabaci MED than imidacloprid. This study presents a new approach for developing green insecticides specific to B. tabaci MED by targeting OBPs. Conclusively, identifying and targeting specific OBPs can create more targeted and effective pest control strategies without relying on toxic chemicals.
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Affiliation(s)
- Danxia Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Li Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Wei Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Xiangyang Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China
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4
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Gu KK, Liu Z, Narayanasamy SR, Shelby ML, Chan N, Coleman MA, Frank M, Kuhl TL. All polymer microfluidic chips-A fixed target sample delivery workhorse for serial crystallography. BIOMICROFLUIDICS 2023; 17:051302. [PMID: 37840537 PMCID: PMC10576627 DOI: 10.1063/5.0167164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]
Abstract
The development of x-ray free electron laser (XFEL) light sources and serial crystallography methodologies has led to a revolution in protein crystallography, enabling the determination of previously unobtainable protein structures and near-atomic resolution of otherwise poorly diffracting protein crystals. However, to utilize XFEL sources efficiently demands the continuous, rapid delivery of a large number of difficult-to-handle microcrystals to the x-ray beam. A recently developed fixed-target system, in which crystals of interest are enclosed within a sample holder, which is rastered through the x-ray beam, is discussed in detail in this Perspective. The fixed target is easy to use, maintains sample hydration, and can be readily modified to allow a broad range of sample types and different beamline requirements. Recent innovations demonstrate the potential of such microfluidic-based fixed targets to be an all-around "workhorse" for serial crystallography measurements. This Perspective will summarize recent advancements in microfluidic fixed targets for serial crystallography, examine needs for future development, and guide users in designing, choosing, and utilizing a fixed-target sample delivery device for their system.
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Affiliation(s)
- Kevin K. Gu
- Department of Chemical Engineering, University of California at Davis, Davis, California 95616, USA
| | - Zhongrui Liu
- Department of Chemical Engineering, University of California at Davis, Davis, California 95616, USA
| | - Sankar Raju Narayanasamy
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Megan L. Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Nicholas Chan
- Department of Chemical Engineering, University of California at Davis, Davis, California 95616, USA
| | | | | | - Tonya L. Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, California 95616, USA
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5
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Besaw JE, Miller RJD. Addressing high excitation conditions in time-resolved X-ray diffraction experiments and issues of biological relevance. Curr Opin Struct Biol 2023; 81:102624. [PMID: 37331203 DOI: 10.1016/j.sbi.2023.102624] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023]
Abstract
One of the most important fundamental questions connecting chemistry to biology is how chemistry scales in complexity up to biological systems where there are innumerable possible pathways and competing processes. With the development of ultrabright electron and x-ray sources, it has been possible to literally light up atomic motions to directly observe the reduction in dimensionality in the barrier crossing region to a few key reaction modes. How do these chemical processes further couple to the surrounding protein or macromolecular assembly to drive biological functions? Optical methods to trigger photoactive biological processes are needed to probe this issue on the relevant timescales. However, the excitation conditions have been in the highly nonlinear regime, which questions the biological relevance of the observed structural dynamics.
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Affiliation(s)
- Jessica E Besaw
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - R J Dwayne Miller
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
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6
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Skaist Mehlman T, Biel JT, Azeem SM, Nelson ER, Hossain S, Dunnett L, Paterson NG, Douangamath A, Talon R, Axford D, Orins H, von Delft F, Keedy DA. Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B. eLife 2023; 12:84632. [PMID: 36881464 PMCID: PMC9991056 DOI: 10.7554/elife.84632] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/12/2023] [Indexed: 03/08/2023] Open
Abstract
Much of our current understanding of how small-molecule ligands interact with proteins stems from X-ray crystal structures determined at cryogenic (cryo) temperature. For proteins alone, room-temperature (RT) crystallography can reveal previously hidden, biologically relevant alternate conformations. However, less is understood about how RT crystallography may impact the conformational landscapes of protein-ligand complexes. Previously, we showed that small-molecule fragments cluster in putative allosteric sites using a cryo crystallographic screen of the therapeutic target PTP1B (Keedy et al., 2018). Here, we have performed two RT crystallographic screens of PTP1B using many of the same fragments, representing the largest RT crystallographic screens of a diverse library of ligands to date, and enabling a direct interrogation of the effect of data collection temperature on protein-ligand interactions. We show that at RT, fewer ligands bind, and often more weakly - but with a variety of temperature-dependent differences, including unique binding poses, changes in solvation, new binding sites, and distinct protein allosteric conformational responses. Overall, this work suggests that the vast body of existing cryo-temperature protein-ligand structures may provide an incomplete picture, and highlights the potential of RT crystallography to help complete this picture by revealing distinct conformational modes of protein-ligand systems. Our results may inspire future use of RT crystallography to interrogate the roles of protein-ligand conformational ensembles in biological function.
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Affiliation(s)
- Tamar Skaist Mehlman
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
- PhD Program in Biochemistry, CUNY Graduate CenterNew YorkUnited States
| | - Justin T Biel
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Syeda Maryam Azeem
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | | | - Sakib Hossain
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | - Louise Dunnett
- Diamond Light SourceDidcotUnited Kingdom
- Research Complex at Harwell, Harwell Science and Innovation CampusDidcotUnited Kingdom
| | | | - Alice Douangamath
- Diamond Light SourceDidcotUnited Kingdom
- Research Complex at Harwell, Harwell Science and Innovation CampusDidcotUnited Kingdom
| | | | | | - Helen Orins
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | - Frank von Delft
- Diamond Light SourceDidcotUnited Kingdom
- Research Complex at Harwell, Harwell Science and Innovation CampusDidcotUnited Kingdom
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Department of Biochemistry, University of JohannesburgJohannesburgSouth Africa
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
- Department of Chemistry and Biochemistry, City College of New YorkNew YorkUnited States
- PhD Programs in Biochemistry, Biology, and Chemistry, CUNY Graduate CenterNew YorkUnited States
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7
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Mehrabi P, Schulz EC. Sample Preparation for Time-Resolved Serial Crystallography: Practical Considerations. Methods Mol Biol 2023; 2652:361-379. [PMID: 37093487 DOI: 10.1007/978-1-0716-3147-8_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Time-resolved serial crystallography is an emerging method to elucidate the structure-function relationship of biomolecular systems at up to atomic resolution. However, to make this demanding method a success, a number of experimental requirements have to be met. In this chapter, we summarize general guidelines and protocols towards performing time-resolved crystallography experiments, with a particular emphasis on sample requirements and preparation but also a brief excursion into reaction initiation.
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Affiliation(s)
- Pedram Mehrabi
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany.
- Max Planck Institute for Structure and Dynamics of Matter, Hamburg, Germany.
| | - Eike C Schulz
- Max Planck Institute for Structure and Dynamics of Matter, Hamburg, Germany.
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
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8
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Thorne RE. Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization. Acta Crystallogr D Struct Biol 2023; 79:78-94. [PMID: 36601809 PMCID: PMC9815097 DOI: 10.1107/s2059798322011652] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/04/2022] [Indexed: 01/05/2023] Open
Abstract
For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein-solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54, e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.
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Affiliation(s)
- Robert E. Thorne
- Physics Department, Cornell University, Ithaca, NY 14853, USA
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
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9
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Aquaporin Gating: A New Twist to Unravel Permeation through Water Channels. Int J Mol Sci 2022; 23:ijms232012317. [PMID: 36293170 PMCID: PMC9604103 DOI: 10.3390/ijms232012317] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/17/2022] Open
Abstract
Aquaporins (AQPs) are small transmembrane tetrameric proteins that facilitate water, solute and gas exchange. Their presence has been extensively reported in the biological membranes of almost all living organisms. Although their discovery is much more recent than ion transport systems, different biophysical approaches have contributed to confirm that permeation through each monomer is consistent with closed and open states, introducing the term gating mechanism into the field. The study of AQPs in their native membrane or overexpressed in heterologous systems have experimentally demonstrated that water membrane permeability can be reversibly modified in response to specific modulators. For some regulation mechanisms, such as pH changes, evidence for gating is also supported by high-resolution structures of the water channel in different configurations as well as molecular dynamics simulation. Both experimental and simulation approaches sustain that the rearrangement of conserved residues contributes to occlude the cavity of the channel restricting water permeation. Interestingly, specific charged and conserved residues are present in the environment of the pore and, thus, the tetrameric structure can be subjected to alter the positions of these charges to sustain gating. Thus, is it possible to explore whether the displacement of these charges (gating current) leads to conformational changes? To our knowledge, this question has not yet been addressed at all. In this review, we intend to analyze the suitability of this proposal for the first time.
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Vasireddi R, Gardais A, Chavas LMG. Manufacturing of Ultra-Thin X-ray-Compatible COC Microfluidic Devices for Optimal In Situ Macromolecular Crystallography Experiments. MICROMACHINES 2022; 13:1365. [PMID: 36014287 PMCID: PMC9416059 DOI: 10.3390/mi13081365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Cyclic-olefin-copolymer (COC)-based microfluidic devices are increasingly becoming the center of highly valuable research for in situ X-ray measurements due to their compatibility with X-rays, biological compounds, chemical resistance, optical properties, low cost, and simplified handling. COC microfluidic devices present potential solutions to challenging biological applications such as protein binding, folding, nucleation, growth kinetics, and structural changes. In recent years, the techniques applied to manufacturing and handling these devices have capitalized on enormous progress toward small-scale sample probing. Here, we describe the new and innovative design aspects, fabrication, and experimental implementation of low-cost and micron-sized X-ray-compatible microfluidic sample environments that address diffusion-based crystal formation for crystallographic characterization. The devices appear fully compatible with crystal growth and subsequent X-ray diffraction experiments, resulting in remarkably low background data recording. The results highlighted in this research demonstrate how the engineered microfluidic devices allow the recording of accurate crystallographic data at room temperature and structure determination at high resolution.
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Affiliation(s)
| | - Antonin Gardais
- Synchrotron SOLEIL, L’Orme des Merisier, Saint-Aubin, 91192 Gif-sur-Yvette, France
| | - Leonard M. G. Chavas
- Department of Applied Physics, Nagoya University, Nagoya 464-8603, Japan
- Synchrotron Radiation Research Center, Nagoya University, Nagoya 464-8603, Japan
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11
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Through Diffusion Measurements of Molecules to a Numerical Model for Protein Crystallization in Viscous Polyethylene Glycol Solution. CRYSTALS 2022. [DOI: 10.3390/cryst12070881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Protein crystallography has become a popular method for biochemists, but obtaining high-quality protein crystals for precise structural analysis and larger ones for neutron analysis requires further technical progress. Many studies have noted the importance of solvent viscosity for the probability of crystal nucleation and for mass transportation; therefore, in this paper, we have reported on experimental results and simulation studies regarding the use of viscous polyethylene glycol (PEG) solvents for protein crystals. We investigated the diffusion rates of proteins, peptides, and small molecules in viscous PEG solvents using fluorescence correlation spectroscopy. In high-molecular-weight PEG solutions (molecular weights: 10,000 and 20,000), solute diffusion showed deviations, with a faster diffusion than that estimated by the Stokes–Einstein equation. We showed that the extent of the deviation depends on the difference between the molecular sizes of the solute and PEG solvent, and succeeded in creating equations to predict diffusion coefficients in viscous PEG solutions. Using these equations, we have developed a new numerical model of 1D diffusion processes of proteins and precipitants in a counter-diffusion chamber during crystallization processes. Examples of the application of anomalous diffusion in counter-diffusion crystallization are shown by the growth of lysozyme crystals.
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12
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Liu C, Li Z, Liu Z, Yang S, Wang Q, Chai Z. Understanding the P-Loop Conformation in the Determination of Inhibitor Selectivity Toward the Hepatocellular Carcinoma-Associated Dark Kinase STK17B. Front Mol Biosci 2022; 9:901603. [PMID: 35620482 PMCID: PMC9127184 DOI: 10.3389/fmolb.2022.901603] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/22/2022] [Indexed: 12/26/2022] Open
Abstract
As a member of the death-associated protein kinase family of serine/threonine kinases, the STK17B has been associated with diverse diseases such as hepatocellular carcinoma. However, the conformational dynamics of the phosphate-binding loop (P-loop) in the determination of inhibitor selectivity profile to the STK17B are less understood. Here, a multi-microsecond length molecular dynamics (MD) simulation of STK17B in the three different states (ligand-free, ADP-bound, and ligand-bound states) was carried out to uncover the conformational plasticity of the P-loop. Together with the analyses of principal component analysis, cross-correlation and generalized correlation motions, secondary structural analysis, and community network analysis, the conformational dynamics of the P-loop in the different states were revealed, in which the P-loop flipped into the ADP-binding site upon the inhibitor binding and interacted with the inhibitor and the C-lobe, strengthened the communication between the N- and C-lobes. These resulting interactions contributed to inhibitor selectivity profile to the STK17B. Our results may advance our understanding of kinase inhibitor selectivity and offer possible implications for the design of highly selective inhibitors for other protein kinases.
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Affiliation(s)
- Chang Liu
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University (Navy Medical University), Shanghai, China
| | - Zhizhen Li
- Department of Biliary Surgery I, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University (Navy Medical University), Shanghai, China
| | - Zonghan Liu
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University (Navy Medical University), Shanghai, China
| | - Shiye Yang
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University (Navy Medical University), Shanghai, China
| | - Qing Wang
- Oncology Department, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University (Navy Medical University), Shanghai, China
- Department of Hepatic Surgery, Shanghai Geriatric Center, Shanghai, China
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13
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Selikhanov G, Fufina T, Guenther S, Meents A, Gabdulkhakov A, Vasilieva L. X-ray structure of the Rhodobacter sphaeroides reaction center with an M197 Phe→His substitution clarifies the properties of the mutant complex. IUCRJ 2022; 9:261-271. [PMID: 35371503 PMCID: PMC8895020 DOI: 10.1107/s2052252521013178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
The first steps of the global process of photosynthesis take place in specialized membrane pigment-protein complexes called photosynthetic reaction centers (RCs). The RC of the photosynthetic purple bacterium Rhodobacter sphaeroides, a relatively simple analog of the more complexly organized photosystem II in plants, algae and cyanobacteria, serves as a convenient model for studying pigment-protein interactions that affect photochemical processes. In bacterial RCs the bacteriochlorophyll (BChl) dimer P serves as the primary electron donor, and its redox potential is a critical factor in the efficient functioning of the RC. It has previously been shown that the replacement of Phe M197 by His strongly affects the oxidation potential of P (E m P/P+), increasing its value by 125 mV, as well as increasing the thermal stability of RC and its stability in response to external pressure. The crystal structures of F(M197)H RC at high resolution obtained using various techniques presented in this report clarify the optical and electrochemical properties of the primary electron donor and the increased resistance of the mutant complex to denaturation. The electron-density maps are consistent with the donation of a hydrogen bond from the imidazole group of His M197 to the C2-acetyl carbonyl group of BChl PB. The formation of this hydrogen bond leads to a considerable out-of-plane rotation of the acetyl carbonyl group and results in a 1.2 Å shift of the O atom of this group relative to the wild-type structure. Besides, the distance between BChl PA and PB in the area of pyrrole ring I was found to be increased by up to 0.17 Å. These structural changes are discussed in association with the spectral properties of BChl dimer P. The electron-density maps strongly suggest that the imidazole group of His M197 accepts another hydrogen bond from the nearest water molecule, which in turn appears to form two more hydrogen bonds to Asn M195 and Asp L155. As a result of the F(M197)H mutation, BChl PB finds itself connected to the extensive hydrogen-bonding network that pre-existed in wild-type RC. Dissimilarities in the two hydrogen-bonding networks near the M197 and L168 sites may account for the different changes of the E m P/P+ in F(M197)H and H(L168)F RCs. The involvement of His M197 in the hydrogen-bonding network also appears to be related to stabilization of the F(M197)H RC structure. Analysis of the experimental data presented here and of the data available in the literature points to the fact that the hydrogen-bonding networks in the vicinity of BChl dimer P may play an important role in fine-tuning the redox properties of the primary electron donor.
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Affiliation(s)
- Georgii Selikhanov
- Group of Structural Studies of Macromolecular Complexes, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino 142290, Moscow Region, Russian Federation
- Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, Pushchino 142290, Moscow Region, Russian Federation
| | - Tatiana Fufina
- Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, Pushchino 142290, Moscow Region, Russian Federation
| | - Sebastian Guenther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Azat Gabdulkhakov
- Group of Structural Studies of Macromolecular Complexes, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino 142290, Moscow Region, Russian Federation
| | - Lyudmila Vasilieva
- Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, Pushchino 142290, Moscow Region, Russian Federation
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14
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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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15
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Axford D, Judge PJ, Bada Juarez JF, Kwan TOC, Birch J, Vinals J, Watts A, Moraes I. Two states of a light-sensitive membrane protein captured at room temperature using thin-film sample mounts. Acta Crystallogr D Struct Biol 2022; 78:52-58. [PMID: 34981761 PMCID: PMC8725165 DOI: 10.1107/s2059798321011220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/26/2021] [Indexed: 11/25/2022] Open
Abstract
Room-temperature diffraction methods are highly desirable for dynamic studies of biological macromolecules, since they allow high-resolution structural data to be collected as proteins undergo conformational changes. For crystals grown in lipidic cubic phase (LCP), an extruder is commonly used to pass a stream of microcrystals through the X-ray beam; however, the sample quantities required for this method may be difficult to produce for many membrane proteins. A more sample-efficient environment was created using two layers of low X-ray transmittance polymer films to mount crystals of the archaerhodopsin-3 (AR3) photoreceptor and room-temperature diffraction data were acquired. By using transparent and opaque polymer films, two structures, one corresponding to the desensitized, dark-adapted (DA) state and the other to the ground or light-adapted (LA) state, were solved to better than 1.9 Å resolution. All of the key structural features of AR3 were resolved, including the retinal chromophore, which is present as the 13-cis isomer in the DA state and as the all-trans isomer in the LA state. The film-sandwich sample environment enables diffraction data to be recorded at room temperature in both illuminated and dark conditions, which more closely approximate those in vivo. This simple approach is applicable to a wide range of membrane proteins crystallized in LCP and light-sensitive samples in general at synchrotron and laboratory X-ray sources.
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Affiliation(s)
- Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Peter J. Judge
- Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Juan F. Bada Juarez
- Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Tristan O. C. Kwan
- National Physical Laboratory, Hampton Road, Teddington, London, United Kingdom
| | - James Birch
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Javier Vinals
- Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Anthony Watts
- Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington, London, United Kingdom
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16
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Grünbein ML, Kovacs GN, Kloos M, Gorel A, Doak RB, Shoeman RL, Barends TRM, Schlichting I. Crystallographic Studies of Rhodopsins: Structure and Dynamics. Methods Mol Biol 2022; 2501:147-168. [PMID: 35857227 DOI: 10.1007/978-1-0716-2329-9_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Crystal structures have provided detailed insight in the architecture of rhodopsin photoreceptors. Of particular interest are the protein-chromophore interactions that govern the light-induced retinal isomerization and ultimately induce the large structural changes important for the various biological functions of the family. The reaction intermediates occurring along the rhodopsin photocycle have vastly differing lifetimes, from hundreds of femtoseconds to milliseconds. Detailed insight at high spatial and temporal resolution can be obtained by time-resolved crystallography using pump-probe approaches at X-ray free-electron lasers. Alternatively, cryotrapping approaches can be used. Both the approaches are described, including illumination and sample delivery. The importance of appropriate photoexcitation avoiding multiphoton absorption is stressed.
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Affiliation(s)
| | | | - Marco Kloos
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Alexander Gorel
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - R Bruce Doak
- Max Planck Institute for Medical Research, Heidelberg, Germany
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17
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Martiel I, Beale JH, Karpik A, Huang CY, Vera L, Olieric N, Wranik M, Tsai CJ, Mühle J, Aurelius O, John J, Högbom M, Wang M, Marsh M, Padeste C. Versatile microporous polymer-based supports for serial macromolecular crystallography. Acta Crystallogr D Struct Biol 2021; 77:1153-1167. [PMID: 34473086 PMCID: PMC8411977 DOI: 10.1107/s2059798321007324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 07/15/2021] [Indexed: 11/10/2022] Open
Abstract
Serial data collection has emerged as a major tool for data collection at state-of-the-art light sources, such as microfocus beamlines at synchrotrons and X-ray free-electron lasers. Challenging targets, characterized by small crystal sizes, weak diffraction and stringent dose limits, benefit most from these methods. Here, the use of a thin support made of a polymer-based membrane for performing serial data collection or screening experiments is demonstrated. It is shown that these supports are suitable for a wide range of protein crystals suspended in liquids. The supports have also proved to be applicable to challenging cases such as membrane proteins growing in the sponge phase. The sample-deposition method is simple and robust, as well as flexible and adaptable to a variety of cases. It results in an optimally thin specimen providing low background while maintaining minute amounts of mother liquor around the crystals. The 2 × 2 mm area enables the deposition of up to several microlitres of liquid. Imaging and visualization of the crystals are straightforward on the highly transparent membrane. Thanks to their affordable fabrication, these supports have the potential to become an attractive option for serial experiments at synchrotrons and free-electron lasers.
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Affiliation(s)
- Isabelle Martiel
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - John H. Beale
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Agnieszka Karpik
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
- Institute of Polymer Nanotechnology (INKA), FHNW University of Applied Sciences and Arts Northwestern Switzerland, 5210 Windisch, Switzerland
| | - Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Laura Vera
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Natacha Olieric
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Maximilian Wranik
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Ching-Ju Tsai
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Jonas Mühle
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
- MAX IV Laboratory, Lund University, Fotongatan 2, 224 84 Lund, Sweden
| | - Juliane John
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - May Marsh
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Celestino Padeste
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
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18
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Lahey-Rudolph JM, Schönherr R, Barthelmess M, Fischer P, Seuring C, Wagner A, Meents A, Redecke L. Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals. IUCRJ 2021; 8:665-677. [PMID: 34258014 PMCID: PMC8256716 DOI: 10.1107/s2052252521005297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/18/2021] [Indexed: 05/05/2023]
Abstract
The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approach is presented for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micometre-sized crystals of the protein HEX-1 from the fungus Neurospora crassa on a fixed target. Employing the fast and highly accurate Roadrunner II translation-stage system allowed efficient raster scanning of the pores of micro-patterned, single-crystalline silicon chips loaded with living, crystal-containing insect cells. Compared with liquid-jet and LCP injection systems, the increased hit rates of up to 30% and reduced background scattering enabled elucidation of the HEX-1 structure. Using diffraction data from only a single chip collected within 12 min at the Linac Coherent Light Source, a 1.8 Å resolution structure was obtained with significantly reduced sample consumption compared with previous SFX experiments using liquid-jet injection. This HEX-1 structure is almost superimposable with that previously determined using synchrotron radiation from single HEX-1 crystals grown by sitting-drop vapour diffusion, validating the approach. This study demonstrates that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection using living, crystal-containing cells, and offers huge potential for the straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.
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Affiliation(s)
- J. Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Carolin Seuring
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, 22671 Hamburg, Germany
| | - Armin Wagner
- Diamond Light Source, Diamond House DH2-52, Chilton, Didcot OX11 0DE, United Kingdom
| | - Alke Meents
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
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19
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Ross B, Krapp S, Geiss-Friedlander R, Littmann W, Huber R, Kiefersauer R. Aerosol-based ligand soaking of reservoir-free protein crystals. J Appl Crystallogr 2021; 54:895-902. [PMID: 34188616 PMCID: PMC8202026 DOI: 10.1107/s1600576721003551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/01/2021] [Indexed: 11/10/2022] Open
Abstract
Soaking of macromolecular crystals allows the formation of complexes via diffusion of molecules into a preformed crystal for structural analysis. Soaking offers various advantages over co-crystallization, e.g. small samples and high-throughput experimentation. However, this method has disadvantages, such as inducing mechanical stress on crystals and reduced success rate caused by low affinity/solubility of the ligand. To bypass these issues, the Picodropper was previously developed in the authors' laboratory. This technique aimed to deliver small volumes of compound solution in response to crystal dehydration supported by the Free Mounting System humidity control or by IR-laser-induced protein crystal transformation. Herein, a new related soaking development, the Aerosol-Generator, is introduced. This device delivers compounds onto the solution-free surface of protein crystals using an ultrasonic technique. The produced aerosol stream enables an easier and more accurate control of solution volumes, reduced crystal handling, and crystal-size-independent soaking. The Aerosol-Generator has been used to produce complexes of DPP8 crystals, where otherwise regular soaking did not achieve complex formation. These results demonstrate the potential of this device in challenging ligand-binding scenarios and contribute to further understanding of DPP8 inhibitor binding.
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Affiliation(s)
- Breyan Ross
- Max Planck Institut für Biochemie, D-82152 Martinsried, Germany
- Proteros Biostructures GmbH, D-82152 Martinsried, Germany
| | - Stephan Krapp
- Proteros Biostructures GmbH, D-82152 Martinsried, Germany
| | - Ruth Geiss-Friedlander
- Center of Biochemistry and Molecular Cell Research, Albert-Ludwigs-Universität, D-79104 Freiburg, Germany
| | - Walter Littmann
- ATHENA Technologie Beratung GmbH, Technologiepark 13, D-33100 Paderborn, Germany
| | - Robert Huber
- Max Planck Institut für Biochemie, D-82152 Martinsried, Germany
- Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, D-45147 Essen, Germany
- Fakultät für Chemie, Technische Universität München, D-85747 Garching, Germany
| | - Reiner Kiefersauer
- Max Planck Institut für Biochemie, D-82152 Martinsried, Germany
- Proteros Biostructures GmbH, D-82152 Martinsried, Germany
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20
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Norton-Baker B, Mehrabi P, Boger J, Schönherr R, von Stetten D, Schikora H, Kwok AO, Martin RW, Miller RJD, Redecke L, Schulz EC. A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip. Acta Crystallogr D Struct Biol 2021; 77:820-834. [PMID: 34076595 PMCID: PMC8171066 DOI: 10.1107/s2059798321003855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/10/2021] [Indexed: 11/12/2022] Open
Abstract
Fixed-target serial crystallography has become an important method for the study of protein structure and dynamics at synchrotrons and X-ray free-electron lasers. However, sample homogeneity, consumption and the physical stress on samples remain major challenges for these high-throughput experiments, which depend on high-quality protein microcrystals. The batch crystallization procedures that are typically applied require time- and sample-intensive screening and optimization. Here, a simple protein crystallization method inside the features of the HARE serial crystallography chips is reported that circumvents batch crystallization and allows the direct transfer of canonical vapor-diffusion conditions to in-chip crystallization. Based on conventional hanging-drop vapor-diffusion experiments, the crystallization solution is distributed into the wells of the HARE chip and equilibrated against a reservoir with mother liquor. Using this simple method, high-quality microcrystals were generated with sufficient density for the structure determination of four different proteins. A new protein variant was crystallized using the protein concentrations encountered during canonical crystallization experiments, enabling structure determination from ∼55 µg of protein. Additionally, structure determination from intracellular crystals grown in insect cells cultured directly in the features of the HARE chips is demonstrated. In cellulo crystallization represents a comparatively unexplored space in crystallization, especially for proteins that are resistant to crystallization using conventional techniques, and eliminates any need for laborious protein purification. This in-chip technique avoids harvesting the sensitive crystals or any further physical handling of the crystal-containing cells. These proof-of-principle experiments indicate the potential of this method to become a simple alternative to batch crystallization approaches and also as a convenient extension to canonical crystallization screens.
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Affiliation(s)
- Brenna Norton-Baker
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Pedram Mehrabi
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Juliane Boger
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Robert Schönherr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - David von Stetten
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Hendrik Schikora
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Ashley O. Kwok
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - R. J. Dwayne Miller
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St George Street, Toronto, ON M5S 3H6, Canada
| | - Lars Redecke
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Eike C. Schulz
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
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21
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Bill RM, Hedfalk K. Aquaporins - Expression, purification and characterization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183650. [PMID: 34019902 DOI: 10.1016/j.bbamem.2021.183650] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022]
Abstract
Aquaporin water channels facilitate the bi-directional flow of water and small, neutral solutes down an osmotic gradient in all kingdoms of life. Over the last two decades, the availability of high-quality protein has underpinned progress in the structural and functional characterization of these water channels. In particular, recombinant protein technology has guaranteed the supply of aquaporin samples that were of sufficient quality and quantity for further study. Here we review the features of successful expression, purification and characterization strategies that have underpinned these successes and that will drive further breakthroughs in the field. Overall, Escherichia coli is a suitable host for prokaryotic isoforms, while Pichia pastoris is the most commonly-used recombinant host for eukaryotic variants. Generally, a two-step purification procedure is suitable after solubilization in glucopyranosides and most structures are determined by X-ray following crystallization.
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Affiliation(s)
- Roslyn M Bill
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Kristina Hedfalk
- Department of Chemistry and Molecular Biology, Gothenburg University, Box 462, 405 30 Göteborg, Sweden.
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22
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Illava G, Jayne R, Finke AD, Closs D, Zeng W, Milano SK, Huang Q, Kriksunov I, Sidorenko P, Wise FW, Zipfel WR, Apker BA, Thorne RE. Integrated sample-handling and mounting system for fixed-target serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2021; 77:628-644. [PMID: 33950019 PMCID: PMC8098472 DOI: 10.1107/s2059798321001868] [Citation(s) in RCA: 3] [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: 08/28/2020] [Accepted: 02/15/2021] [Indexed: 11/15/2022] Open
Abstract
Serial synchrotron crystallography (SSX) is enabling the efficient use of small crystals for structure-function studies of biomolecules and for drug discovery. An integrated SSX system has been developed comprising ultralow background-scatter sample holders suitable for room and cryogenic temperature crystallographic data collection, a sample-loading station and a humid `gloveless' glovebox. The sample holders incorporate thin-film supports with a variety of designs optimized for different crystal-loading challenges. These holders facilitate the dispersion of crystals and the removal of excess liquid, can be cooled at extremely high rates, generate little background scatter, allow data collection over >90° of oscillation without obstruction or the risk of generating saturating Bragg peaks, are compatible with existing infrastructure for high-throughput cryocrystallography and are reusable. The sample-loading station allows sample preparation and loading onto the support film, the application of time-varying suction for optimal removal of excess liquid, crystal repositioning and cryoprotection, and the application of sealing films for room-temperature data collection, all in a controlled-humidity environment. The humid glovebox allows microscope observation of the sample-loading station and crystallization trays while maintaining near-saturating humidities that further minimize the risks of sample dehydration and damage, and maximize working times. This integrated system addresses common problems in obtaining properly dispersed, properly hydrated and isomorphous microcrystals for fixed-orientation and oscillation data collection. Its ease of use, flexibility and optimized performance make it attractive not just for SSX but also for single-crystal and few-crystal data collection. Fundamental concepts that are important in achieving desired crystal distributions on a sample holder via time-varying suction-induced liquid flows are also discussed.
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Affiliation(s)
- Gabrielle Illava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | | | - David Closs
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
| | - Wenjie Zeng
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Shawn K. Milano
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Pavel Sidorenko
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Frank W. Wise
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Warren R. Zipfel
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
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23
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Sarrou I, Feiler CG, Falke S, Peard N, Yefanov O, Chapman H. C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening. Acta Crystallogr D Struct Biol 2021; 77:224-236. [PMID: 33559611 PMCID: PMC7869899 DOI: 10.1107/s2059798320016071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 01/08/2023] Open
Abstract
The unique crystallization properties of the antenna protein C-phycocyanin (C-PC) from the thermophilic cyanobacterium Thermosynechococcus elongatus are reported and discussed. C-PC crystallizes in hundreds of significantly different conditions within a broad pH range and in the presence of a wide variety of precipitants and additives. Remarkably, the crystal dimensions vary from a few micrometres, as used in serial crystallography, to several hundred micrometres, with a very diverse crystal morphology. More than 100 unique single-crystal X-ray diffraction data sets were collected from randomly selected crystals and analysed. The addition of small-molecule additives revealed three new crystal packings of C-PC, which are discussed in detail. The high propensity of this protein to crystallize, combined with its natural blue colour and its fluorescence characteristics, make it an excellent candidate as a superior and highly adaptable model system in crystallography. C-PC can be used in technical and methods development approaches for X-ray and neutron diffraction techniques, and as a system for comprehending the fundamental principles of protein crystallography.
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Affiliation(s)
- Iosifina Sarrou
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian G. Feiler
- Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Nolan Peard
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Oleksandr Yefanov
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry Chapman
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
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24
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Han H, Round E, Schubert R, Gül Y, Makroczyová J, Meza D, Heuser P, Aepfelbacher M, Barák I, Betzel C, Fromme P, Kursula I, Nissen P, Tereschenko E, Schulz J, Uetrecht C, Ulicný J, Wilmanns M, Hajdu J, Lamzin VS, Lorenzen K. The XBI BioLab for life science experiments at the European XFEL. J Appl Crystallogr 2021; 54:7-21. [PMID: 33833637 PMCID: PMC7941304 DOI: 10.1107/s1600576720013989] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/19/2020] [Indexed: 11/26/2022] Open
Abstract
The science of X-ray free-electron lasers (XFELs) critically depends on the performance of the X-ray laser and on the quality of the samples placed into the X-ray beam. The stability of biological samples is limited and key biomolecular transformations occur on short timescales. Experiments in biology require a support laboratory in the immediate vicinity of the beamlines. The XBI BioLab of the European XFEL (XBI denotes XFEL Biology Infrastructure) is an integrated user facility connected to the beamlines for supporting a wide range of biological experiments. The laboratory was financed and built by a collaboration between the European XFEL and the XBI User Consortium, whose members come from Finland, Germany, the Slovak Republic, Sweden and the USA, with observers from Denmark and the Russian Federation. Arranged around a central wet laboratory, the XBI BioLab provides facilities for sample preparation and scoring, laboratories for growing prokaryotic and eukaryotic cells, a Bio Safety Level 2 laboratory, sample purification and characterization facilities, a crystallization laboratory, an anaerobic laboratory, an aerosol laboratory, a vacuum laboratory for injector tests, and laboratories for optical microscopy, atomic force microscopy and electron microscopy. Here, an overview of the XBI facility is given and some of the results of the first user experiments are highlighted.
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Affiliation(s)
- Huijong Han
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Ekaterina Round
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Yasmin Gül
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jana Makroczyová
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovak Republic
| | - Domingo Meza
- Biodesign Center for Applied Structural Discovery and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Philipp Heuser
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Imrich Barák
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovak Republic
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Inari Kursula
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Poul Nissen
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK – 8000 Aarhus C, Denmark
| | - Elena Tereschenko
- Institute of Crystallography, Russian Academy of Sciences, 59 Leninsky prospekt, Moscow, 117333, Russian Federation
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Charlotte Uetrecht
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Jozef Ulicný
- Department of Biophysics, Institute of Physics, Faculty of Science, P. J. Šafárik University, Jesenná 5, 04154 Košice, Slovak Republic
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Janos Hajdu
- The European Extreme Light Infrastructure, Institute of Physics, Academy of Sciences of the Czech Republic, Za Radnici 835, 25241 Dolní Břežany, Czech Republic
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
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Abstract
X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at RT to demystify preconceived impracticalities that freeze progress of routine RT data collection at synchrotron sources. Examples are presented as conceptual and experimental templates to enable the design of RT-inspired studies; they illustrate the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics enables opportunities to advance basic and biomedical research.
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26
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Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. Methods Mol Biol 2021; 2305:203-228. [PMID: 33950392 DOI: 10.1007/978-1-0716-1406-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.
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27
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Picado A, Chaikuad A, Wells CI, Shrestha S, Zuercher WJ, Pickett JE, Kwarcinski FE, Sinha P, de Silva CS, Zutshi R, Liu S, Kannan N, Knapp S, Drewry DH, Willson TM. A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation. J Med Chem 2020; 63:14626-14646. [PMID: 33215924 DOI: 10.1021/acs.jmedchem.0c01174] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
STK17B is a member of the death-associated protein kinase family and has been genetically linked to the development of diverse diseases. However, the role of STK17B in normal and disease pathology is poorly defined. Here, we present the discovery of thieno[3,2-d] pyrimidine SGC-STK17B-1 (11s), a high-quality chemical probe for this understudied "dark" kinase. 11s is an ATP-competitive inhibitor that showed remarkable selectivity over other kinases including the closely related STK17A. X-ray crystallography of 11s and related thieno[3,2-d]pyrimidines bound to STK17B revealed a unique P-loop conformation characterized by a salt bridge between R41 and the carboxylic acid of the inhibitor. Molecular dynamic simulations of STK17B revealed the flexibility of the P-loop and a wide range of R41 conformations available to the apo-protein. The isomeric thieno[2,3-d]pyrimidine SGC-STK17B-1N (19g) was identified as a negative control compound. The >100-fold lower activity of 19g on STK17B was attributed to the reduced basicity of its pyrimidine N1.
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Affiliation(s)
- Alfredo Picado
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Julie E Pickett
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Frank E Kwarcinski
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Parvathi Sinha
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Chandi S de Silva
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Reena Zutshi
- Luceome Biotechnologies, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany.,German Translational Cancer Network (DKTK) site Frankfurt/Mainz, Frankfurt am Main 60596, Germany.,Frankfurt Cancer Institute (FCI), Paul-Ehrlich-Straße 42-44, Frankfurt am Main 60596, Germany
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Timothy M Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
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28
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Shelby M, Gilbile D, Grant T, Bauer W, Segelke B, He W, Evans A, Crespo N, Fischer P, Pakendorf T, Hennicke V, Hunter M, Batyuk A, Barthelmess M, Meents A, Kuhl T, Frank M, Coleman M. Crystallization of ApoA1 and ApoE4 nanolipoprotein particles and initial XFEL-based structural studies. CRYSTALS 2020; 10. [PMID: 35686136 PMCID: PMC9175823 DOI: 10.3390/cryst10100886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via HDL and LDL maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics and develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar in characteristics to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.
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Affiliation(s)
- M.L. Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - D. Gilbile
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - T.D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - W.J. Bauer
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - B. Segelke
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - W. He
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - A.C. Evans
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - N. Crespo
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - P. Fischer
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - T. Pakendorf
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - V. Hennicke
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - M.S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - A. Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - M. Barthelmess
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - A. Meents
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - T.L. Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - M. Frank
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
- Correspondence: ; Tel: +1-925-423-7687 or ; Tel: 1-925-423-5068
| | - M.A. Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
- Correspondence: ; Tel: +1-925-423-7687 or ; Tel: 1-925-423-5068
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29
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Pearson AR, Mehrabi P. Serial synchrotron crystallography for time-resolved structural biology. Curr Opin Struct Biol 2020; 65:168-174. [PMID: 32846363 DOI: 10.1016/j.sbi.2020.06.019] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022]
Abstract
The current state-of-the-art experiments in time-resolved structural biology are undoubtedly the recent extremely impressive results that are emerging from XFEL-based experiments. However, there is a large range of macromolecular systems where the biological interest is predominantly in the slower dynamics (μs-s), that produce well diffracting microcrystals, and for which synchrotron-based experiments are extremely well suited. The combination of microfocus X-ray beams and the development of a range of sample delivery platforms has now made routine millisecond time-resolved experiments at microfocus macromolecular crystallography beamlines a real possibility and is driving development of dedicated endstations for time-resolved serial synchrotron crystallography.
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Affiliation(s)
- Arwen R Pearson
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, CFEL, Luruper Chaussee 149, Hamburg 22761, Germany.
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, Hamburg 22761, Germany
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30
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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.
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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
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31
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Fenton RA, Murali SK, Moeller HB. Advances in aquaporin-2 trafficking mechanisms and their implications for treatment of water balance disorders. Am J Physiol Cell Physiol 2020; 319:C1-C10. [PMID: 32432927 DOI: 10.1152/ajpcell.00150.2020] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In mammals, conservation of body water is critical for survival and is dependent on the kidneys' ability to minimize water loss in the urine during periods of water deprivation. The collecting duct water channel aquaporin-2 (AQP2) plays an essential role in this homeostatic response by facilitating water reabsorption along osmotic gradients. The ability to increase the levels of AQP2 in the apical plasma membrane following an increase in plasma osmolality is a rate-limiting step in water reabsorption, a process that is tightly regulated by the antidiuretic hormone arginine vasopressin (AVP). In this review, the focus is on the role of the carboxyl-terminus of AQP2 as a key regulatory point for AQP2 trafficking. We provide an overview of AQP2 structure, disease-causing mutations in the AQP2 carboxyl-terminus, the role of posttranslational modifications such as phosphorylation and ubiquitylation in the tail domain, and their implications for balanced trafficking of AQP2. Finally, we discuss how various modifications of the AQP2 tail facilitate selective protein-protein interactions that modulate the AQP2 trafficking mechanism.
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Affiliation(s)
- Robert A Fenton
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Hanne B Moeller
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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32
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Abstract
The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction.
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33
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Mehrabi P, Müller-Werkmeister HM, Leimkohl JP, Schikora H, Ninkovic J, Krivokuca S, Andriček L, Epp SW, Sherrell D, Owen RL, Pearson AR, Tellkamp F, Schulz EC, Miller RJD. The HARE chip for efficient time-resolved serial synchrotron crystallography. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:360-370. [PMID: 32153274 PMCID: PMC7064102 DOI: 10.1107/s1600577520000685] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/20/2020] [Indexed: 05/02/2023]
Abstract
Serial synchrotron crystallography (SSX) is an emerging technique for static and time-resolved protein structure determination. Using specifically patterned silicon chips for sample delivery, the `hit-and-return' (HARE) protocol allows for efficient time-resolved data collection. The specific pattern of the crystal wells in the HARE chip provides direct access to many discrete time points. HARE chips allow for optical excitation as well as on-chip mixing for reaction initiation, making a large number of protein systems amenable to time-resolved studies. Loading of protein microcrystals onto the HARE chip is streamlined by a novel vacuum loading platform that allows fine-tuning of suction strength while maintaining a humid environment to prevent crystal dehydration. To enable the widespread use of time-resolved serial synchrotron crystallography (TR-SSX), detailed technical descriptions of a set of accessories that facilitate TR-SSX workflows are provided.
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Affiliation(s)
- Pedram Mehrabi
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Henrike M. Müller-Werkmeister
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Institute of Chemistry – Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Jan-Philipp Leimkohl
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Hendrik Schikora
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Jelena Ninkovic
- Halbleiterlabor der Max-Planck-Gesellschaft, Otto-Hahn-Ring 6, D-81739 Munich, Germany
| | - Silvia Krivokuca
- Halbleiterlabor der Max-Planck-Gesellschaft, Otto-Hahn-Ring 6, D-81739 Munich, Germany
| | - Ladislav Andriček
- Halbleiterlabor der Max-Planck-Gesellschaft, Otto-Hahn-Ring 6, D-81739 Munich, Germany
| | - Sascha W. Epp
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Darren Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Arwen R. Pearson
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Friedjof Tellkamp
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Eike C. Schulz
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R. J. Dwayne Miller
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St George Street, Toronto, Ontario M5S 3H6, Canada
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34
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Abstract
The history of serial crystallography (SC) has its origins in the earliest attempts to merge data from several crystals. This preface provides an overview of some recent work, with a survey of the rapid advances made over the past decade in both sample delivery and data analysis.
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35
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Shelby ML, Gilbile D, Grant TD, Seuring C, Segelke BW, He W, Evans AC, Pakendorf T, Fischer P, Hunter MS, Batyuk A, Barthelmess M, Meents A, Coleman MA, Kuhl TL, Frank M. A fixed-target platform for serial femtosecond crystallography in a hydrated environment. IUCRJ 2020; 7:30-41. [PMID: 31949902 PMCID: PMC6949605 DOI: 10.1107/s2052252519014003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/15/2019] [Indexed: 05/19/2023]
Abstract
For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while maintaining low background remains a technical challenge for some experiments, especially where this methodology is applied to relatively low-ordered samples or those difficult to purify and crystallize in large quantities. This work demonstrates a scheme to encapsulate biological samples using polymer thin films and graphene to maintain sample hydration in vacuum conditions. The encapsulated sample is delivered into the X-ray beam on fixed targets for rapid scanning using the Roadrunner fixed-target system towards a long-term goal of low-background measurements on weakly diffracting samples. As a proof of principle, we used microcrystals of the 24 kDa rapid encystment protein (REP24) to provide a benchmark for polymer/graphene sandwich performance. The REP24 microcrystal unit cell obtained from our sandwiched in-vacuum sample was consistent with previously established unit-cell parameters and with those measured by us without encapsulation in humidified helium, indicating that the platform is robust against evaporative losses. While significant scattering from water was observed because of the sample-deposition method, the polymer/graphene sandwich itself was shown to contribute minimally to background scattering.
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Affiliation(s)
- M. L. Shelby
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - D. Gilbile
- University of California at Davis, California, USA
| | - T. D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, Hauptman-Woodward Institute, SUNY University at Buffalo, Buffalo, New York, USA
| | - C. Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - B. W. Segelke
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - W. He
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - A. C. Evans
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
| | - T. Pakendorf
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - P. Fischer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - M. S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - A. Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - M. Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - A. Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - M. A. Coleman
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
| | - T. L. Kuhl
- University of California at Davis, California, USA
| | - M. Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
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36
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Tolstikova A, Levantino M, Yefanov O, Hennicke V, Fischer P, Meyer J, Mozzanica A, Redford S, Crosas E, Opara NL, Barthelmess M, Lieske J, Oberthuer D, Wator E, Mohacsi I, Wulff M, Schmitt B, Chapman HN, Meents A. 1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector. IUCRJ 2019; 6:927-937. [PMID: 31576225 PMCID: PMC6760437 DOI: 10.1107/s205225251900914x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/25/2019] [Indexed: 05/18/2023]
Abstract
Reliable sample delivery and efficient use of limited beam time have remained bottlenecks for serial crystallography (SX). Using a high-intensity polychromatic X-ray beam in combination with a newly developed charge-integrating JUNGFRAU detector, we have applied the method of fixed-target SX to collect data at a rate of 1 kHz at a synchrotron-radiation facility. According to our data analysis for the given experimental conditions, only about 3 000 diffraction patterns are required for a high-quality diffraction dataset. With indexing rates of up to 25%, recording of such a dataset takes less than 30 s.
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Affiliation(s)
- A. Tolstikova
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - M. Levantino
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - O. Yefanov
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - V. Hennicke
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - P. Fischer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - J. Meyer
- Deutsches Elektronen Synchrotron, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - A. Mozzanica
- Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland
| | - S. Redford
- Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland
| | - E. Crosas
- Deutsches Elektronen Synchrotron, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - N. L. Opara
- Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland
- C-CINA, Biozentrum, University of Basel, Mattenstrasse 26, 4002 Basel, Switzerland
| | - M. Barthelmess
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - J. Lieske
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - D. Oberthuer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - E. Wator
- Malopolska Centre of Biotechnology, Jagiellonian University, Cracow 30-387, Poland
| | - I. Mohacsi
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - M. Wulff
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - B. Schmitt
- Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland
| | - H. N. Chapman
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - A. Meents
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Deutsches Elektronen Synchrotron, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
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