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Srinivasan V, Brognaro H, Prabhu PR, de Souza EE, Günther S, Reinke PYA, Lane TJ, Ginn H, Han H, Ewert W, Sprenger J, Koua FHM, Falke S, Werner N, Andaleeb H, Ullah N, Franca BA, Wang M, Barra ALC, Perbandt M, Schwinzer M, Schmidt C, Brings L, Lorenzen K, Schubert R, Machado RRG, Candido ED, Oliveira DBL, Durigon EL, Niebling S, Garcia AS, Yefanov O, Lieske J, Gelisio L, Domaracky M, Middendorf P, Groessler M, Trost F, Galchenkova M, Mashhour AR, Saouane S, Hakanpää J, Wolf M, Alai MG, Turk D, Pearson AR, Chapman HN, Hinrichs W, Wrenger C, Meents A, Betzel C. Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease. Commun Biol 2022; 5:805. [PMID: 35953531 PMCID: PMC9366811 DOI: 10.1038/s42003-022-03737-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host's innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.
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Ivanov N, Lukas Dresselhaus J, Carnis J, Domaracky M, Fleckenstein H, Li C, Li T, Prasciolu M, Yefanov O, Zhang W, Bajt S, Chapman HN. Robust ptychographic X-ray speckle tracking with multilayer Laue lenses. OPTICS EXPRESS 2022; 30:25450-25473. [PMID: 36237075 DOI: 10.1364/oe.460903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/30/2022] [Indexed: 06/16/2023]
Abstract
In recent years, X-ray speckle tracking techniques have emerged as viable tools for wavefront metrology and sample imaging applications, and have been actively developed for use at synchrotron light sources. Speckle techniques can recover an image free of aberrations and can be used to measure wavefronts with a high angular sensitivity. Since they are compatible with low-coherence sources they can be also used with laboratory X-ray sources. A new implementation of the ptychographic X-ray speckle tracking method, suitable for the metrology of highly divergent wavefields, such as those created by multilayer Laue lenses, is presented here. This new program incorporates machine learning techniques such as Huber and non-parametric regression and enables robust and quick wavefield measurements and data evaluation even for low brilliance X-ray beams, and the imaging of low-contrast samples. To realize this, a software suite was written in Python 3, with a C back-end capable of concurrent calculations for high performance. It is accessible as a Python module and is available as source code under Version 3 or later of the GNU General Public License.
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Dresselhaus JL, Fleckenstein H, Domaracký M, Prasciolu M, Ivanov N, Carnis J, Murray KT, Morgan AJ, Chapman HN, Bajt S. Precise wavefront characterization of x-ray optical elements using a laboratory source. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:073704. [PMID: 35922318 DOI: 10.1063/5.0092269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
Improvements in x-ray optics critically depend on the measurement of their optical performance. The knowledge of wavefront aberrations, for example, can be used to improve the fabrication of optical elements or to design phase correctors to compensate for these errors. At present, the characterization of such optics is made using intense x-ray sources, such as synchrotrons. However, the limited access to these facilities can substantially slow down the development process. Improvements in the brightness of lab-based x-ray micro-sources in combination with the development of new metrology methods, particularly ptychographic x-ray speckle tracking, enable characterization of x-ray optics in the lab with a precision and sensitivity not possible before. Here, we present a laboratory setup that utilizes a commercially available x-ray source and can be used to characterize different types of x-ray optics. The setup is used in our laboratory on a routine basis to characterize multilayer Laue lenses of high numerical aperture and other optical elements. This typically includes measurements of the wavefront distortions, optimum operating photon energy, and focal length of the lens. To check the sensitivity and accuracy of this laboratory setup, we compared the results to those obtained at the synchrotron and saw no significant difference. To illustrate the feedback of measurements on performance, we demonstrated the correction of the phase errors of a particular multilayer Laue lens using a 3D printed compound refractive phase plate.
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Zhuang Y, Awel S, Barty A, Bean R, Bielecki J, Bergemann M, Daurer BJ, Ekeberg T, Estillore AD, Fangohr H, Giewekemeyer K, Hunter MS, Karnevskiy M, Kirian RA, Kirkwood H, Kim Y, Koliyadu J, Lange H, Letrun R, Lübke J, Mall A, Michelat T, Morgan AJ, Roth N, Samanta AK, Sato T, Shen Z, Sikorski M, Schulz F, Spence JCH, Vagovic P, Wollweber T, Worbs L, Xavier PL, Yefanov O, Maia FRNC, Horke DA, Küpper J, Loh ND, Mancuso AP, Chapman HN, Ayyer K. Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging. IUCRJ 2022; 9:204-214. [PMID: 35371510 PMCID: PMC8895023 DOI: 10.1107/s2052252521012707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/30/2021] [Indexed: 06/12/2023]
Abstract
One of the outstanding analytical problems in X-ray single-particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and the fact that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. Proposed here are two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA), provides a rough classification which is essentially parameter free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs), can generate 3D structures of the objects at any point in the structural landscape. Both these methods are implemented in combination with the noise-tolerant expand-maximize-compress (EMC) algorithm and its utility is demonstrated by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern. Both discrete structural classes and continuous deformations are recovered. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility of moving beyond the study of homogeneous sample sets to addressing open questions on topics such as nanocrystal growth and dynamics, as well as phase transitions which have not been externally triggered.
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Doppler D, Rabbani MT, Letrun R, Cruz Villarreal J, Kim DH, Gandhi S, Egatz-Gomez A, Sonker M, Chen J, Koua FHM, Yang J, Youssef M, Mazalova V, Bajt S, Shelby ML, Coleman MA, Wiedorn MO, Knoska J, Schön S, Sato T, Hunter MS, Hosseinizadeh A, Kuptiz C, Nazari R, Alvarez RC, Karpos K, Zaare S, Dobson Z, Discianno E, Zhang S, Zook JD, Bielecki J, de Wijn R, Round AR, Vagovic P, Kloos M, Vakili M, Ketawala GK, Stander NE, Olson TL, Morin K, Mondal J, Nguyen J, Meza-Aguilar JD, Kodis G, Vaiana S, Martin-Garcia JM, Mariani V, Schwander P, Schmidt M, Messerschmidt M, Ourmazd A, Zatsepin N, Weierstall U, Bruce BD, Mancuso AP, Grant T, Barty A, Chapman HN, Frank M, Fromme R, Spence JCH, Botha S, Fromme P, Kirian RA, Ros A. Co-flow injection for serial crystallography at X-ray free-electron lasers. J Appl Crystallogr 2022; 55:1-13. [PMID: 35153640 PMCID: PMC8805165 DOI: 10.1107/s1600576721011079] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/22/2021] [Indexed: 02/03/2023] Open
Abstract
Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macro-molecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.
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Pandey S, Calvey G, Katz AM, Malla TN, Koua FHM, Martin-Garcia JM, Poudyal I, Yang JH, Vakili M, Yefanov O, Zielinski KA, Bajt S, Awel S, Doerner K, Frank M, Gelisio L, Jernigan R, Kirkwood H, Kloos M, Koliyadu J, Mariani V, Miller MD, Mills G, Nelson G, Olmos JL, Sadri A, Sato T, Tolstikova A, Xu W, Ourmazd A, Spence JCH, Schwander P, Barty A, Chapman HN, Fromme P, Mancuso AP, Phillips GN, Bean R, Pollack L, Schmidt M. Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography. IUCRJ 2021; 8:878-895. [PMID: 34804542 PMCID: PMC8562667 DOI: 10.1107/s2052252521008125] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/06/2021] [Indexed: 05/22/2023]
Abstract
Here, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales. The initial phase of the enzymatic cycle is observed with near-atomic resolution using the most advanced X-ray source currently available: the European XFEL (EuXFEL). The high repetition rate of the EuXFEL combined with our mix-and-inject technology enables the initial phase of ceftriaxone binding to the Mycobacterium tuberculosis β-lactamase to be followed using time-resolved crystallography in real time. It is shown how a diffusion coefficient in enzyme crystals can be derived directly from the X-ray data, enabling the determination of ligand and enzyme-ligand concentrations at any position in the crystal volume as a function of time. In addition, the structure of the irreversible inhibitor sulbactam bound to the enzyme at a 66 ms time delay after mixing is described. This demonstrates that the EuXFEL can be used as an important tool for biomedically relevant research.
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Awel S, Bohne S, Ebrahimifard R, Trieu HK, Bajt S, Chapman HN. Optical bunching of particles in a liquid flow. OPTICS EXPRESS 2021; 29:34394-34410. [PMID: 34809231 DOI: 10.1364/oe.440173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
High-speed liquid micro-jets are used to rapidly and repeatedly deliver protein microcrystals to focused and pulsed X-ray beams in the method of serial femtosecond crystallography. However, the current continuous flow of crystals is mismatched to the arrival of X-ray pulses, wasting vast amounts of an often rare and precious sample. Here, we introduce a method to address this problem by periodically trapping and releasing crystals in the liquid flow, creating locally concentrated crystal bunches, using an optical trap integrated in the microfluidic supply line. We experimentally demonstrate a 30-fold increase of particle concentration into 10 Hz bunches of 6.4 μm diameter polystyrene particles. Furthermore, using particle trajectory simulations, a comprehensive description of the optical bunching process and parameter space is presented. Adding this compact optofluidics device to existing injection systems would thereby dramatically reduce sample consumption and extend the application of serial crystallography to a greater range of protein crystal systems that cannot be produced in high abundance. Our approach is suitable for other microfluidic systems that require synchronous measurements of flowing objects.
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Hadian-Jazi M, Sadri A, Barty A, Yefanov O, Galchenkova M, Oberthuer D, Komadina D, Brehm W, Kirkwood H, Mills G, de Wijn R, Letrun R, Kloos M, Vakili M, Gelisio L, Darmanin C, Mancuso AP, Chapman HN, Abbey B. Data reduction for serial crystallography using a robust peak finder. J Appl Crystallogr 2021; 54:1360-1378. [PMID: 34667447 PMCID: PMC8493619 DOI: 10.1107/s1600576721007317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
This article focuses on the challenges of hit finding and data reduction in serial crystallography (SX). An effective and reliable Bragg-peak-finding method, called robust peak finder (RPF), has been developed. RPF is based on the principle of robust statistics and can be used for SX data analysis. A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of ‘robust statistics’ has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or ‘vetoing’ of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.
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Chapman HN, Bajt S. High-resolution achromatic X-ray optical systems for broad-band imaging and for focusing attosecond pulses. Proc Math Phys Eng Sci 2021; 477:20210334. [PMID: 34276244 PMCID: PMC8277474 DOI: 10.1098/rspa.2021.0334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/15/2021] [Indexed: 11/12/2022] Open
Abstract
Achromatic focusing systems for hard X-rays are examined which consist of a refractive lens paired with a diffractive lens. Compared with previous analyses, we take into account the behaviour of thick refractive lenses, such as compound refractive lenses and waveguide gradient index refractive lenses, in which both the focal length and the position of the principal planes vary with wavelength. Achromatic systems formed by the combination of such a thick refractive lens with a multilayer Laue lens are found that can operate at a focusing resolution of about 3 nm, over a relative bandwidth of about 1%. With the appropriate distance between the refractive and diffractive lenses, apochromatic systems can also be found, which operate over relative bandwidth greater than 10%. These systems can be used to focus short pulses without distorting them in time by more than several attoseconds. Such systems are suitable for high-flux scanning microscopy and for creating high intensities from attosecond X-ray pulses.
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Günther S, Reinke PYA, Fernández-García Y, Lieske J, Lane TJ, Ginn HM, Koua FHM, Ehrt C, Ewert W, Oberthuer D, Yefanov O, Meier S, Lorenzen K, Krichel B, Kopicki JD, Gelisio L, Brehm W, Dunkel I, Seychell B, Gieseler H, Norton-Baker B, Escudero-Pérez B, Domaracky M, Saouane S, Tolstikova A, White TA, Hänle A, Groessler M, Fleckenstein H, Trost F, Galchenkova M, Gevorkov Y, Li C, Awel S, Peck A, Barthelmess M, Schlünzen F, Lourdu Xavier P, Werner N, Andaleeb H, Ullah N, Falke S, Srinivasan V, França BA, Schwinzer M, Brognaro H, Rogers C, Melo D, Zaitseva-Doyle JJ, Knoska J, Peña-Murillo GE, Mashhour AR, Hennicke V, Fischer P, Hakanpää J, Meyer J, Gribbon P, Ellinger B, Kuzikov M, Wolf M, Beccari AR, Bourenkov G, von Stetten D, Pompidor G, Bento I, Panneerselvam S, Karpics I, Schneider TR, Garcia-Alai MM, Niebling S, Günther C, Schmidt C, Schubert R, Han H, Boger J, Monteiro DCF, Zhang L, Sun X, Pletzer-Zelgert J, Wollenhaupt J, Feiler CG, Weiss MS, Schulz EC, Mehrabi P, Karničar K, Usenik A, Loboda J, Tidow H, Chari A, Hilgenfeld R, Uetrecht C, Cox R, Zaliani A, Beck T, Rarey M, Günther S, Turk D, Hinrichs W, Chapman HN, Pearson AR, Betzel C, Meents A. X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science 2021; 372:642-646. [PMID: 33811162 PMCID: PMC8224385 DOI: 10.1126/science.abf7945] [Citation(s) in RCA: 211] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 12/17/2022]
Abstract
The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied x-ray fragment screening experiments with molecules of low complexity, our screen tested already-approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.
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Villanueva-Perez P, Fleckenstein H, Prasciolu M, Murray KT, Domaracký M, Gregorič K, Mariani V, Gelisio L, Kuhn M, Hannappel J, Yefanov O, Ivanov N, Sarrou I, Pennicard D, Becker J, von Zimmermann M, Gutowski O, Dippel AC, Chapman HN, Bajt S. Scanning Compton X-ray microscopy. OPTICS LETTERS 2021; 46:1920-1923. [PMID: 33857104 DOI: 10.1364/ol.421232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
X-ray microscopy offers the opportunity to image biological and radiosensitive materials without special sample preparations, bridging optical and electron microscopy capabilities. However, the performance of such microscopes, when imaging radiosensitive samples, is not limited by their intrinsic resolution, but by the radiation damage induced on such samples. Here, we demonstrate a novel, to the best of our knowledge, radio-efficient microscope, scanning Compton X-ray microscopy (SCXM), which uses coherently and incoherently (Compton) scattered photons to minimize the deposited energy per unit of mass for a given imaging signal. We implemented SCXM, using lenses capable of efficiently focusing 60 keV X-ray photons into the sub-micrometer scale, and probe its radio-efficient capabilities. SCXM, when implemented in high-energy diffraction-limited storage rings, e.g., European Synchrotron Radiation Facility Extremely Brilliant Source and PETRA IV, will open the opportunity to explore the nanoscale of unstained, unsectioned, and undamaged radiosensitive materials.
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Sanchez-Cano C, Alvarez-Puebla RA, Abendroth JM, Beck T, Blick R, Cao Y, Caruso F, Chakraborty I, Chapman HN, Chen C, Cohen BE, Conceição ALC, Cormode DP, Cui D, Dawson KA, Falkenberg G, Fan C, Feliu N, Gao M, Gargioni E, Glüer CC, Grüner F, Hassan M, Hu Y, Huang Y, Huber S, Huse N, Kang Y, Khademhosseini A, Keller TF, Körnig C, Kotov NA, Koziej D, Liang XJ, Liu B, Liu S, Liu Y, Liu Z, Liz-Marzán LM, Ma X, Machicote A, Maison W, Mancuso AP, Megahed S, Nickel B, Otto F, Palencia C, Pascarelli S, Pearson A, Peñate-Medina O, Qi B, Rädler J, Richardson JJ, Rosenhahn A, Rothkamm K, Rübhausen M, Sanyal MK, Schaak RE, Schlemmer HP, Schmidt M, Schmutzler O, Schotten T, Schulz F, Sood AK, Spiers KM, Staufer T, Stemer DM, Stierle A, Sun X, Tsakanova G, Weiss PS, Weller H, Westermeier F, Xu M, Yan H, Zeng Y, Zhao Y, Zhao Y, Zhu D, Zhu Y, Parak WJ. X-ray-Based Techniques to Study the Nano-Bio Interface. ACS NANO 2021; 15:3754-3807. [PMID: 33650433 PMCID: PMC7992135 DOI: 10.1021/acsnano.0c09563] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/25/2021] [Indexed: 05/03/2023]
Abstract
X-ray-based analytics are routinely applied in many fields, including physics, chemistry, materials science, and engineering. The full potential of such techniques in the life sciences and medicine, however, has not yet been fully exploited. We highlight current and upcoming advances in this direction. We describe different X-ray-based methodologies (including those performed at synchrotron light sources and X-ray free-electron lasers) and their potentials for application to investigate the nano-bio interface. The discussion is predominantly guided by asking how such methods could better help to understand and to improve nanoparticle-based drug delivery, though the concepts also apply to nano-bio interactions in general. We discuss current limitations and how they might be overcome, particularly for future use in vivo.
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Ramakrishnan S, Stagno JR, Conrad CE, Ding J, Yu P, Bhandari YR, Lee YT, Pauly G, Yefanov O, Wiedorn MO, Knoska J, Oberthür D, White TA, Barty A, Mariani V, Li C, Brehm W, Heinz WF, Magidson V, Lockett S, Hunter MS, Boutet S, Zatsepin NA, Zuo X, Grant TD, Pandey S, Schmidt M, Spence JCH, Chapman HN, Wang YX. Synchronous RNA conformational changes trigger ordered phase transitions in crystals. Nat Commun 2021; 12:1762. [PMID: 33741910 PMCID: PMC7979858 DOI: 10.1038/s41467-021-21838-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/02/2020] [Indexed: 11/20/2022] Open
Abstract
Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals. Time-resolved crystallography (TRX) is used for monitoring only small conformational changes of biomacromolecules within the same lattice. Here, the authors report the interplay between synchronous molecular rearrangements and lattice phase transitions in RNA crystals, providing the basis for the investigation of large conformational changes using TRX.
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Chapman HN, Prasciolu M, Murray KT, Lukas Dresselhaus J, Bajt S. Analysis of X-ray multilayer Laue lenses made by masked deposition. OPTICS EXPRESS 2021; 29:3097-3113. [PMID: 33770916 DOI: 10.1364/oe.413916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Multilayer Laue lenses are diffractive optics for hard X-rays. To achieve high numerical aperture and resolution, diffracting structures of nanometer periods are required in such lenses, and a thickness (in the direction of propagation) of several micrometers is needed for high diffracting efficiency. Such structures must be oriented to satisfy Bragg's law, which can only be achieved consistently over the entire lens if the layers vary in their tilt relative to the incident beam. The correct tilt, for a particular wavelength, can be achieved with a very simple technique of using a straight-edge mask to give the necessary gradient of the layers. An analysis of the properties of lenses cut from such a shaded profile is presented and it is shown how to design, prepare, and characterize matched pairs of lenses that operate at a particular wavelength and focal length. It is also shown how to manufacture lenses with ideal curved layers for optimal efficiency.
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Xavier PL, Ayyer K, Yefanov O, Gelisio L, Bielecki J, Samanta AK, Bajt S, Sha R, Bushnell DA, Kornberg RD, Ovcharenko Y, Kuepper J, Meyer M, Seeman NC, Chapman HN. Femtosecond Single-Particle Diffractive Imaging of 3D DNA-Origami Molecular Scaffolds with XFEL Pulses. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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41
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Metz M, Arnal RD, Brehm W, Chapman HN, Morgan AJ, Millane RP. Macromolecular phasing using diffraction from multiple crystal forms. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:19-35. [PMID: 33399128 PMCID: PMC7842209 DOI: 10.1107/s2053273320013650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 10/12/2020] [Indexed: 11/23/2022]
Abstract
A phasing algorithm for protein crystallography using diffraction data from multiple crystal forms is proposed. The algorithm is evaluated by simulation, and practical aspects and potential for ab initio phasing are discussed. A phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms – crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). The approach is based on the method of iterated projections, starting with no initial phase information. The practicality of the method is demonstrated by simulation using known structures that exist in multiple crystal forms, assuming some information on the molecular envelope and positional relationships between the molecules in the different unit cells. With incorporation of new or existing methods for determination of these parameters, the approach has potential as a method for ab initio phasing.
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Morgan AJ, Murray KT, Quiney HM, Bajt S, Chapman HN. speckle-tracking: a software suite for ptychographic X-ray speckle tracking. J Appl Crystallogr 2020; 53:1603-1612. [PMID: 33304226 PMCID: PMC7710491 DOI: 10.1107/s1600576720011991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/31/2020] [Indexed: 11/13/2022] Open
Abstract
The program speckle-tracking is described, an open-source software suite for performing wavefront metrology and sample imaging from projection in-line holograms of a sample. In recent years, X-ray speckle-tracking techniques have emerged as viable tools for wavefront metrology and sample imaging applications. These methods are based on the measurement of near-field images. Thanks to their simple experimental setup, high angular sensitivity and compatibility with low-coherence sources, these methods have been actively developed for use with synchrotron and laboratory light sources. Not only do speckle-tracking techniques give the potential for high-resolution imaging, but they also provide rapid and robust characterization of aberrations of X-ray optical elements, focal spot profiles, and sample position and transmission properties. In order to realize these capabilities, software implementations are required that are equally rapid and robust. To address this need, a software suite has been developed for the ptychographic X-ray speckle-tracking technique, an X-ray speckle-based method suitable for highly divergent wavefields. The software suite is written in Python 3, with an OpenCL back end for GPU and multi-CPU core processing. It is accessible as a Python module, through the command line or through a graphical user interface, and is available as source code under Version 3 or later of the GNU General Public License.
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Li H, Nazari R, Abbey B, Alvarez R, Aquila A, Ayyer K, Barty A, Berntsen P, Bielecki J, Pietrini A, Bucher M, Carini G, Chapman HN, Contreras A, Daurer BJ, DeMirci H, Flűckiger L, Frank M, Hajdu J, Hantke MF, Hogue BG, Hosseinizadeh A, Hunter MS, Jönsson HO, Kirian RA, Kurta RP, Loh D, Maia FRNC, Mancuso AP, Morgan AJ, McFadden M, Muehlig K, Munke A, Reddy HKN, Nettelblad C, Ourmazd A, Rose M, Schwander P, Marvin Seibert M, Sellberg JA, Sierra RG, Sun Z, Svenda M, Vartanyants IA, Walter P, Westphal D, Williams G, Xavier PL, Yoon CH, Zaare S. Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source. Sci Data 2020; 7:404. [PMID: 33214568 PMCID: PMC7678860 DOI: 10.1038/s41597-020-00745-2] [Citation(s) in RCA: 2] [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: 08/11/2020] [Accepted: 10/29/2020] [Indexed: 11/18/2022] Open
Abstract
Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.
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Echelmeier A, Cruz Villarreal J, Messerschmidt M, Kim D, Coe JD, Thifault D, Botha S, Egatz-Gomez A, Gandhi S, Brehm G, Conrad CE, Hansen DT, Madsen C, Bajt S, Meza-Aguilar JD, Oberthür D, Wiedorn MO, Fleckenstein H, Mendez D, Knoška J, Martin-Garcia JM, Hu H, Lisova S, Allahgholi A, Gevorkov Y, Ayyer K, Aplin S, Ginn HM, Graafsma H, Morgan AJ, Greiffenberg D, Klujev A, Laurus T, Poehlsen J, Trunk U, Mezza D, Schmidt B, Kuhn M, Fromme R, Sztuk-Dambietz J, Raab N, Hauf S, Silenzi A, Michelat T, Xu C, Danilevski C, Parenti A, Mekinda L, Weinhausen B, Mills G, Vagovic P, Kim Y, Kirkwood H, Bean R, Bielecki J, Stern S, Giewekemeyer K, Round AR, Schulz J, Dörner K, Grant TD, Mariani V, Barty A, Mancuso AP, Weierstall U, Spence JCH, Chapman HN, Zatsepin N, Fromme P, Kirian RA, Ros A. Segmented flow generator for serial crystallography at the European X-ray free electron laser. Nat Commun 2020; 11:4511. [PMID: 32908128 PMCID: PMC7481229 DOI: 10.1038/s41467-020-18156-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.
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Morgan AJ, Murray KT, Prasciolu M, Fleckenstein H, Yefanov O, Villanueva-Perez P, Mariani V, Domaracky M, Kuhn M, Aplin S, Mohacsi I, Messerschmidt M, Stachnik K, Du Y, Burkhart A, Meents A, Nazaretski E, Yan H, Huang X, Chu YS, Chapman HN, Bajt S. Ptychographic X-ray speckle tracking with multi-layer Laue lens systems. J Appl Crystallogr 2020; 53:927-936. [PMID: 32788900 PMCID: PMC7401788 DOI: 10.1107/s1600576720006925] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/22/2020] [Indexed: 11/17/2022] Open
Abstract
The ever-increasing brightness of synchrotron radiation sources demands improved X-ray optics to utilize their capability for imaging and probing biological cells, nano-devices and functional matter on the nanometre scale with chemical sensitivity. Hard X-rays are ideal for high-resolution imaging and spectroscopic applications owing to their short wavelength, high penetrating power and chemical sensitivity. The penetrating power that makes X-rays useful for imaging also makes focusing them technologically challenging. Recent developments in layer deposition techniques have enabled the fabrication of a series of highly focusing X-ray lenses, known as wedged multi-layer Laue lenses. Improvements to the lens design and fabrication technique demand an accurate, robust, in situ and at-wavelength characterization method. To this end, a modified form of the speckle tracking wavefront metrology method has been developed. The ptychographic X-ray speckle tracking method is capable of operating with highly divergent wavefields. A useful by-product of this method is that it also provides high-resolution and aberration-free projection images of extended specimens. Three separate experiments using this method are reported, where the ray path angles have been resolved to within 4 nrad with an imaging resolution of 45 nm (full period). This method does not require a high degree of coherence, making it suitable for laboratory-based X-ray sources. Likewise, it is robust to errors in the registered sample positions, making it suitable for X-ray free-electron laser facilities, where beam-pointing fluctuations can be problematic for wavefront metrology.
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Morgan AJ, Quiney HM, Bajt S, Chapman HN. Ptychographic X-ray speckle tracking. J Appl Crystallogr 2020; 53:760-780. [PMID: 32684891 PMCID: PMC7312131 DOI: 10.1107/s1600576720005567] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/20/2020] [Indexed: 11/24/2022] Open
Abstract
A method is presented for the measurement of the phase gradient of a wavefront by tracking the relative motion of speckles in projection holograms as a sample is scanned across the wavefront. By removing the need to obtain an undistorted reference image of the sample, this method is suitable for the metrology of highly divergent wavefields. Such wavefields allow for large magnification factors that, according to current imaging capabilities, will allow for nanoradian angular sensitivity and nanoscale sample projection imaging. Both the reconstruction algorithm and the imaging geometry are nearly identical to that of ptychography, except that the sample is placed downstream of the beam focus and that no coherent propagation is explicitly accounted for. Like other X-ray speckle tracking methods, it is robust to low-coherence X-ray sources, making it suitable for laboratory-based X-ray sources. Likewise, it is robust to errors in the registered sample positions, making it suitable for X-ray free-electron laser facilities, where beam-pointing fluctuations can be problematic for wavefront metrology. A modified form of the speckle tracking approximation is also presented, based on a second-order local expansion of the Fresnel integral. This result extends the validity of the speckle tracking approximation and may be useful for similar approaches in the field.
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Gevorkov Y, Barty A, Brehm W, White TA, Tolstikova A, Wiedorn MO, Meents A, Grigat RR, Chapman HN, Yefanov O. pinkIndexer - a universal indexer for pink-beam X-ray and electron diffraction snapshots. Acta Crystallogr A Found Adv 2020; 76:121-131. [PMID: 32124850 PMCID: PMC7053222 DOI: 10.1107/s2053273319015559] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink-beam X-ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit-cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink-beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi-monochromatic X-rays and with electrons the algorithm indexed more patterns than other programs tested.
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Kierspel T, Morgan A, Wiese J, Mullins T, Aquila A, Barty A, Bean R, Boll R, Boutet S, Bucksbaum P, Chapman HN, Christensen L, Fry A, Hunter M, Koglin JE, Liang M, Mariani V, Natan A, Robinson J, Rolles D, Rudenko A, Schnorr K, Stapelfeldt H, Stern S, Thøgersen J, Yoon CH, Wang F, Küpper J. X-ray diffractive imaging of controlled gas-phase molecules: Toward imaging of dynamics in the molecular frame. J Chem Phys 2020; 152:084307. [DOI: 10.1063/1.5133963] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Xavier PL, Yefanov O, Ayyer K, Sha R, Knoška J, Seuring C, Boutet S, Liang M, Bushnell DA, Kornberg R, Barty A, Bajt S, Millane RP, Seeman NC, Chapman HN. DNA-Origami-Assisted Flow-Aligned Single-Particle Diffractive Imaging using XFEL Pulses. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Knoška J, Adriano L, Awel S, Beyerlein KR, Yefanov O, Oberthuer D, Peña Murillo GE, Roth N, Sarrou I, Villanueva-Perez P, Wiedorn MO, Wilde F, Bajt S, Chapman HN, Heymann M. Ultracompact 3D microfluidics for time-resolved structural biology. Nat Commun 2020; 11:657. [PMID: 32005876 PMCID: PMC6994545 DOI: 10.1038/s41467-020-14434-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/10/2019] [Indexed: 11/23/2022] Open
Abstract
To advance microfluidic integration, we present the use of two-photon additive manufacturing to fold 2D channel layouts into compact free-form 3D fluidic circuits with nanometer precision. We demonstrate this technique by tailoring microfluidic nozzles and mixers for time-resolved structural biology at X-ray free-electron lasers (XFELs). We achieve submicron jets with speeds exceeding 160 m s-1, which allows for the use of megahertz XFEL repetition rates. By integrating an additional orifice, we implement a low consumption flow-focusing nozzle, which is validated by solving a hemoglobin structure. Also, aberration-free in operando X-ray microtomography is introduced to study efficient equivolumetric millisecond mixing in channels with 3D features integrated into the nozzle. Such devices can be printed in minutes by locally adjusting print resolution during fabrication. This technology has the potential to permit ultracompact devices and performance improvements through 3D flow optimization in all fields of microfluidic engineering.
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