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Fletcher LB, Levitan AL, McBride EE, Kim JB, Alves EP, Aquila A, Frost M, Goede S, King G, Lane TJ, Liang M, MacDonald MJ, Ofori-Okai BK, Schönwälder C, Sun P, Hastings JB, Boutet S, Glenzer SH. X-ray diffraction of metastable structures from supercooled liquid hydrogen. Sci Rep 2024; 14:17283. [PMID: 39068229 PMCID: PMC11283507 DOI: 10.1038/s41598-024-67942-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 07/17/2024] [Indexed: 07/30/2024] Open
Abstract
We report time resolved observations of the crystallization from liquid hydrogen, supercooled to temperatures below the melting point, using 11.2 keV X-ray diffraction from the Linac Coherent Light Source (LCLS). Changes to the metastable solid and liquid structure factors have been dynamically measured. This allows for a direct determination of the lowest energy crystal polymorphs, the stacking probabilities, as well as the liquid and solid densities and temperatures. Such measurements provide experimental evidence of an Arrhenius-like growth kinetics along the stacking direction during supercooling.
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2
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Hutchison CDM, Baxter JM, Fitzpatrick A, Dorlhiac G, Fadini A, Perrett S, Maghlaoui K, Lefèvre SB, Cordon-Preciado V, Ferreira JL, Chukhutsina VU, Garratt D, Barnard J, Galinis G, Glencross F, Morgan RM, Stockton S, Taylor B, Yuan L, Romei MG, Lin CY, Marangos JP, Schmidt M, Chatrchyan V, Buckup T, Morozov D, Park J, Park S, Eom I, Kim M, Jang D, Choi H, Hyun H, Park G, Nango E, Tanaka R, Owada S, Tono K, DePonte DP, Carbajo S, Seaberg M, Aquila A, Boutet S, Barty A, Iwata S, Boxer SG, Groenhof G, van Thor JJ. Optical control of ultrafast structural dynamics in a fluorescent protein. Nat Chem 2023; 15:1607-1615. [PMID: 37563326 PMCID: PMC10624617 DOI: 10.1038/s41557-023-01275-1] [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: 11/11/2021] [Accepted: 06/12/2023] [Indexed: 08/12/2023]
Abstract
The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.
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3
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Welke N, Majernik N, Ash R, Moro A, Agustsson R, Manwani P, Li K, Sakdinawat A, Aquila A, Benediktovitch A, Halavanau A, Rosenzweig J, Bergmann U, Pellegrini C. Development of spinning-disk solid sample delivery system for high-repetition rate x-ray free electron laser experiments. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:103005. [PMID: 37801013 DOI: 10.1063/5.0168125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023]
Abstract
X-ray free-electron lasers (XFELs) deliver intense x-ray pulses that destroy the sample in a single shot by a Coulomb explosion. Experiments using XFEL pulse trains or the new generation of high-repetition rate XFELs require rapid sample replacement beyond those provided by the systems now used at low repletion-rate XFELs. We describe the development and characterization of a system based on a spinning disk to continuously deliver a solid sample into an XFEL interaction point at very high speeds. We tested our system at the Linac Coherent Light Source and European XFEL hard x-ray nano-focus instruments, employing it to deliver a 25 μm copper foil sample, which can be used as a gain medium for stimulated x-ray emission for the proposed x-ray laser oscillator.
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4
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Aleksich M, Paley DW, Schriber EA, Linthicum W, Oklejas V, Mittan-Moreau DW, Kelly RP, Kotei PA, Ghodsi A, Sierra RG, Aquila A, Poitevin F, Blaschke JP, Vakili M, Milne CJ, Dall'Antonia F, Khakhulin D, Ardana-Lamas F, Lima F, Valerio J, Han H, Gallo T, Yousef H, Turkot O, Bermudez Macias IJ, Kluyver T, Schmidt P, Gelisio L, Round AR, Jiang Y, Vinci D, Uemura Y, Kloos M, Hunter M, Mancuso AP, Huey BD, Parent LR, Sauter NK, Brewster AS, Hohman JN. XFEL Microcrystallography of Self-Assembling Silver n-Alkanethiolates. J Am Chem Soc 2023; 145:17042-17055. [PMID: 37524069 DOI: 10.1021/jacs.3c02183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd-even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd-even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd-even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. We conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.
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5
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Weakly RB, Liekhus-Schmaltz CE, Poulter BI, Biasin E, Alonso-Mori R, Aquila A, Boutet S, Fuller FD, Ho PJ, Kroll T, Loe CM, Lutman A, Zhu D, Bergmann U, Schoenlein RW, Govind N, Khalil M. Revealing core-valence interactions in solution with femtosecond X-ray pump X-ray probe spectroscopy. Nat Commun 2023; 14:3384. [PMID: 37291130 DOI: 10.1038/s41467-023-39165-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Femtosecond pump-probe spectroscopy using ultrafast optical and infrared pulses has become an essential tool to discover and understand complex electronic and structural dynamics in solvated molecular, biological, and material systems. Here we report the experimental realization of an ultrafast two-color X-ray pump X-ray probe transient absorption experiment performed in solution. A 10 fs X-ray pump pulse creates a localized excitation by removing a 1s electron from an Fe atom in solvated ferro- and ferricyanide complexes. Following the ensuing Auger-Meitner cascade, the second X-ray pulse probes the Fe 1s → 3p transitions in resultant novel core-excited electronic states. Careful comparison of the experimental spectra with theory, extracts +2 eV shifts in transition energies per valence hole, providing insight into correlated interactions of valence 3d with 3p and deeper-lying electrons. Such information is essential for accurate modeling and predictive synthesis of transition metal complexes relevant for applications ranging from catalysis to information storage technology. This study demonstrates the experimental realization of the scientific opportunities possible with the continued development of multicolor multi-pulse X-ray spectroscopy to study electronic correlations in complex condensed phase systems.
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6
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Adam V, Hadjidemetriou K, Jensen N, Shoeman RL, Woodhouse J, Aquila A, Banneville AS, Barends TRM, Bezchastnov V, Boutet S, Byrdin M, Cammarata M, Carbajo S, Eleni Christou N, Coquelle N, De la Mora E, El Khatib M, Moreno Chicano T, Bruce Doak R, Fieschi F, Foucar L, Glushonkov O, Gorel A, Grünbein ML, Hilpert M, Hunter M, Kloos M, Koglin JE, Lane TJ, Liang M, Mantovanelli A, Nass K, Nass Kovacs G, Owada S, Roome CM, Schirò G, Seaberg M, Stricker M, Thépaut M, Tono K, Ueda K, Uriarte LM, You D, Zala N, Domratcheva T, Jakobs S, Sliwa M, Schlichting I, Colletier JP, Bourgeois D, Weik M. Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement. Chemphyschem 2022; 23:e202200192. [PMID: 35959919 DOI: 10.1002/cphc.202200192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/25/2022] [Indexed: 01/07/2023]
Abstract
Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, one of the key parameters that dictate the achievable resolution in nanoscopy applications, and chromophore conformation in the non-fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off-state conformations, trans1 and trans2, located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off-state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high-level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue- and red-shifts of the absorption bands associated to trans1 and trans2, respectively. Thus, due to elimination of trans2, the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two-fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2-V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.
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7
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Adam V, Hadjidemetriou K, Jensen N, Shoeman RL, Woodhouse J, Aquila A, Banneville A, Barends TRM, Bezchastnov V, Boutet S, Byrdin M, Cammarata M, Carbajo S, Eleni Christou N, Coquelle N, De la Mora E, El Khatib M, Moreno Chicano T, Bruce Doak R, Fieschi F, Foucar L, Glushonkov O, Gorel A, Grünbein ML, Hilpert M, Hunter M, Kloos M, Koglin JE, Lane TJ, Liang M, Mantovanelli A, Nass K, Nass Kovacs G, Owada S, Roome CM, Schirò G, Seaberg M, Stricker M, Thépaut M, Tono K, Ueda K, Uriarte LM, You D, Zala N, Domratcheva T, Jakobs S, Sliwa M, Schlichting I, Colletier J, Bourgeois D, Weik M. Cover Feature: Rational Control of Off‐State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement (ChemPhysChem 19/2022). Chemphyschem 2022. [DOI: 10.1002/cphc.202200693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Wells DJ, Berntsen P, Balaur E, Kewish CM, Adams P, Aquila A, Binns J, Boutet S, Broomhall H, Caleman C, Christofferson A, Conn CE, Dahlqvist C, Flueckiger L, Gian Roque F, Greaves TL, Hejazian M, Hunter M, Hadian Jazi M, Jönsson HO, Pathirannahalage SK, Kirian RA, Kozlov A, Kurta RP, Marman H, Mendez D, Morgan A, Nugent K, Oberthuer D, Quiney H, Reinhardt J, Saha S, Sellberg JA, Sierra R, Wiedorn M, Abbey B, Martin AV, Darmanin C. Observations of phase changes in monoolein during high viscous injection. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:602-614. [PMID: 35510993 PMCID: PMC9070699 DOI: 10.1107/s1600577522001862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.
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Assalauova D, Kim YY, Bobkov S, Khubbutdinov R, Rose M, Alvarez R, Andreasson J, Balaur E, Contreras A, DeMirci H, Gelisio L, Hajdu J, Hunter MS, Kurta RP, Li H, McFadden M, Nazari R, Schwander P, Teslyuk A, Walter P, Xavier PL, Yoon CH, Zaare S, Ilyin VA, Kirian RA, Hogue BG, Aquila A, Vartanyants IA. Erratum: An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. Corrigendum. IUCRJ 2022; 9:328. [PMID: 35371497 PMCID: PMC8895016 DOI: 10.1107/s2052252522000501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
[This corrects the article DOI: 10.1107/S2052252520012798.].
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10
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Schriber EA, Paley DW, Bolotovsky R, Rosenberg DJ, Sierra RG, Aquila A, Mendez D, Poitevin F, Blaschke JP, Bhowmick A, Kelly RP, Hunter M, Hayes B, Popple DC, Yeung M, Pareja-Rivera C, Lisova S, Tono K, Sugahara M, Owada S, Kuykendall T, Yao K, Schuck PJ, Solis-Ibarra D, Sauter NK, Brewster AS, Hohman JN. Chemical crystallography by serial femtosecond X-ray diffraction. Nature 2022; 601:360-365. [PMID: 35046599 PMCID: PMC8770144 DOI: 10.1038/s41586-021-04218-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/07/2021] [Indexed: 01/13/2023]
Abstract
Inorganic-organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties1. This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction2,3 and electron microdiffraction4-11. Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals. We subjected microcrystalline suspensions to X-ray free-electron laser radiation12,13 and obtained thousands of randomly oriented diffraction patterns. We determined unit cells by aggregating spot-finding results into high-resolution powder diffractograms. After indexing the sparse serial patterns by a graph theory approach14, the resulting datasets can be solved and refined using standard tools for single-crystal diffraction data15-17. We describe the ab initio structure solutions of mithrene (AgSePh)18-20, thiorene (AgSPh) and tethrene (AgTePh), of which the latter two were previously unknown structures. In thiorene, we identify a geometric change in the silver-silver bonding network that is linked to its divergent optoelectronic properties20. We demonstrate that smSFX can be applied as a general technique for structure determination of beam-sensitive microcrystalline materials at near-ambient temperature and pressure.
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11
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Holmes S, Clabbers MTB, Muusse TW, Vajjhala PR, Thygesen SJ, Malde AK, Hunter DJB, Croll TI, Flueckiger L, Nanson JD, Rahaman MH, Aquila A, Hunter MS, Liang M, Yoon CH, Zhao J, Zatsepin NA, Abbey B, Sierecki E, Gambin Y, Stacey KJ, Darmanin C, Kobe B, Xu H, Ve T. MyD88 TIR domain higher-order assembly interactions revealed by serial femtosecond crystallography. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321088498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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12
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Clabbers MTB, Holmes S, Muusse TW, Vajjhala P, Thygesen SJ, Malde AK, Hunter DJB, Croll TI, Flueckiger L, Nanson JD, Rahaman MH, Aquila A, Hunter MS, Liang M, Yoon CH, Zhao J, Zatsepin NA, Abbey B, Sierecki E, Gambin Y, Stacey KJ, Darmanin C, Kobe B, Xu H, Ve T. MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321093879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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13
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Aquila A, Hunter M, Batyuk A, Fritz D, Liang M. High-energy upgrade of the Linac Coherent Light Source. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321097919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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14
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Liekhus-Schmaltz CE, Ho PJ, Weakly RB, Aquila A, Schoenlein RW, Khalil M, Govind N. Ultrafast x-ray pump x-ray probe transient absorption spectroscopy: A computational study and proposed experiment probing core-valence electronic correlations in solvated complexes. J Chem Phys 2021; 154:214107. [PMID: 34240961 DOI: 10.1063/5.0047381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Femtosecond x-ray pump-x-ray probe experiments are currently possible at free electron lasers such as the linac coherent light source, which opens new opportunities for studying solvated transition metal complexes. In order to make the most effective use of these kinds of experiments, it is necessary to determine which chemical properties an x-ray probe pulse will measure. We have combined electron cascade calculations and excited-state time-dependent density functional theory calculations to predict the initial state prepared by an x-ray pump and the subsequent x-ray probe spectra at the Fe K-edge in the solvated model transition metal complex, K4FeII(CN)6. We find several key spectral features that report on the ligand-field splitting and the 3p and 3d electron interactions. We then show how these features could be measured in an experiment.
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15
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Clabbers MTB, Holmes S, Muusse TW, Vajjhala PR, Thygesen SJ, Malde AK, Hunter DJB, Croll TI, Flueckiger L, Nanson JD, Rahaman MH, Aquila A, Hunter MS, Liang M, Yoon CH, Zhao J, Zatsepin NA, Abbey B, Sierecki E, Gambin Y, Stacey KJ, Darmanin C, Kobe B, Xu H, Ve T. MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography. Nat Commun 2021; 12:2578. [PMID: 33972532 PMCID: PMC8110528 DOI: 10.1038/s41467-021-22590-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/18/2021] [Indexed: 02/03/2023] Open
Abstract
MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.
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16
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Grünbein ML, Gorel A, Foucar L, Carbajo S, Colocho W, Gilevich S, Hartmann E, Hilpert M, Hunter M, Kloos M, Koglin JE, Lane TJ, Lewandowski J, Lutman A, Nass K, Nass Kovacs G, Roome CM, Sheppard J, Shoeman RL, Stricker M, van Driel T, Vetter S, Doak RB, Boutet S, Aquila A, Decker FJ, Barends TRM, Stan CA, Schlichting I. Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet. Nat Commun 2021; 12:1672. [PMID: 33723266 PMCID: PMC7960726 DOI: 10.1038/s41467-021-21819-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/15/2021] [Indexed: 01/31/2023] Open
Abstract
X-ray free-electron lasers (XFELs) enable obtaining novel insights in structural biology. The recently available MHz repetition rate XFELs allow full data sets to be collected in shorter time and can also decrease sample consumption. However, the microsecond spacing of MHz XFEL pulses raises new challenges, including possible sample damage induced by shock waves that are launched by preceding pulses in the sample-carrying jet. We explored this matter with an X-ray-pump/X-ray-probe experiment employing haemoglobin microcrystals transported via a liquid jet into the XFEL beam. Diffraction data were collected using a shock-wave-free single-pulse scheme as well as the dual-pulse pump-probe scheme. The latter, relative to the former, reveals significant degradation of crystal hit rate, diffraction resolution and data quality. Crystal structures extracted from the two data sets also differ. Since our pump-probe attributes were chosen to emulate EuXFEL operation at its 4.5 MHz maximum pulse rate, this prompts concern about such data collection.
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17
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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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18
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Assalauova D, Kim YY, Bobkov S, Khubbutdinov R, Rose M, Alvarez R, Andreasson J, Balaur E, Contreras A, DeMirci H, Gelisio L, Hajdu J, Hunter MS, Kurta RP, Li H, McFadden M, Nazari R, Schwander P, Teslyuk A, Walter P, Xavier PL, Yoon CH, Zaare S, Ilyin VA, Kirian RA, Hogue BG, Aquila A, Vartanyants IA. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. IUCRJ 2020; 7:1102-1113. [PMID: 33209321 PMCID: PMC7642788 DOI: 10.1107/s2052252520012798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/21/2020] [Indexed: 05/06/2023]
Abstract
An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.
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Lee MY, Geiger J, Ishchenko A, Han GW, Barty A, White TA, Gati C, Batyuk A, Hunter MS, Aquila A, Boutet S, Weierstall U, Cherezov V, Liu W. Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase. IUCRJ 2020; 7:976-984. [PMID: 33209312 PMCID: PMC7642783 DOI: 10.1107/s2052252520012701] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/17/2020] [Indexed: 05/31/2023]
Abstract
Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A2A receptor (A2AAR) at 2.0 Å resolution is determined and compared with previous A2AAR structures determined in vacuum and/or at cryogenic temperatures. Specifically, the capability of utilizing high XFEL beam transmissions is demonstrated, in conjunction with a high dynamic range detector, to collect high-resolution SFX data while reducing crystalline material consumption and shortening the collection time required for a complete dataset. The experimental setup presented herein can be applied to future SFX applications for protein nanocrystal samples to aid in structure-based discovery efforts of therapeutic targets that are difficult to crystallize.
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Nass K, Gorel A, Abdullah MM, V Martin A, Kloos M, Marinelli A, Aquila A, Barends TRM, Decker FJ, Bruce Doak R, Foucar L, Hartmann E, Hilpert M, Hunter MS, Jurek Z, Koglin JE, Kozlov A, Lutman AA, Kovacs GN, Roome CM, Shoeman RL, Santra R, Quiney HM, Ziaja B, Boutet S, Schlichting I. Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses. Nat Commun 2020; 11:1814. [PMID: 32286284 PMCID: PMC7156470 DOI: 10.1038/s41467-020-15610-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 03/20/2020] [Indexed: 11/10/2022] Open
Abstract
X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter’s correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics. The local X-ray-induced dynamics that occur in protein crystals during serial femtosecond crystallography (SFX) measurements at XFELs are not well understood. Here the authors performed a time-resolved X-ray pump X-ray probe SFX experiment, and they observe distinct structural changes in the disulfide bridges and peptide backbone of proteins; complementing theoretical approaches allow them to further characterize the details of the X-ray induced ionization and local structural dynamics.
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Pardini T, Alameda J, Aquila A, Boutet S, Decker T, Gleason AE, Guillet S, Hamilton P, Hayes M, Hill R, Koglin J, Kozioziemski B, Robinson J, Sokolowski-Tinten K, Soufli R, Hau-Riege SP. Erratum: Delayed Onset of Nonthermal Melting in Single-Crystal Silicon Pumped with Hard X Rays [Phys. Rev. Lett. 120, 265701 (2018)]. PHYSICAL REVIEW LETTERS 2020; 124:129903. [PMID: 32281872 DOI: 10.1103/physrevlett.124.129903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
This corrects the article DOI: 10.1103/PhysRevLett.120.265701.
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Wolff AM, Young ID, Sierra RG, Brewster AS, Martynowycz MW, Nango E, Sugahara M, Nakane T, Ito K, Aquila A, Bhowmick A, Biel JT, Carbajo S, Cohen AE, Cortez S, Gonzalez A, Hino T, Im D, Koralek JD, Kubo M, Lazarou TS, Nomura T, Owada S, Samelson AJ, Tanaka T, Tanaka R, Thompson EM, van den Bedem H, Woldeyes RA, Yumoto F, Zhao W, Tono K, Boutet S, Iwata S, Gonen T, Sauter NK, Fraser JS, Thompson MC. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals. IUCRJ 2020; 7:306-323. [PMID: 32148858 PMCID: PMC7055375 DOI: 10.1107/s205225252000072x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.
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Nass K, Redecke L, Perbandt M, Yefanov O, Klinge M, Koopmann R, Stellato F, Gabdulkhakov A, Schönherr R, Rehders D, Lahey-Rudolph JM, Aquila A, Barty A, Basu S, Doak RB, Duden R, Frank M, Fromme R, Kassemeyer S, Katona G, Kirian R, Liu H, Majoul I, Martin-Garcia JM, Messerschmidt M, Shoeman RL, Weierstall U, Westenhoff S, White TA, Williams GJ, Yoon CH, Zatsepin N, Fromme P, Duszenko M, Chapman HN, Betzel C. In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors. Nat Commun 2020; 11:620. [PMID: 32001697 PMCID: PMC6992785 DOI: 10.1038/s41467-020-14484-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/06/2020] [Indexed: 02/07/2023] Open
Abstract
Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds. Trypanosoma brucei inosine-5′-monophosphate dehydrogenase (IMPDH) is an enzyme in the guanine nucleotide biosynthesis pathway and of interest as a drug target. Here the authors present the 2.8 Å room temperature structure of TbIMPDH determined by utilizing X-ray free-electron laser radiation and crystals that were grown in insect cells and find that ATP and GMP are bound at the canonical sites of the Bateman domains.
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Ayyer K, Morgan AJ, Aquila A, DeMirci H, Hogue BG, Kirian RA, Xavier PL, Yoon CH, Chapman HN, Barty A. Low-signal limit of X-ray single particle diffractive imaging. OPTICS EXPRESS 2019; 27:37816-37833. [PMID: 31878556 DOI: 10.1364/oe.27.037816] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
An outstanding question in X-ray single particle imaging experiments has been the feasibility of imaging sub 10-nm-sized biomolecules under realistic experimental conditions where very few photons are expected to be measured in a single snapshot and instrument background may be significant relative to particle scattering. While analyses of simulated data have shown that the determination of an average image should be feasible using Bayesian methods such as the EMC algorithm, this has yet to be demonstrated using experimental data containing realistic non-isotropic instrument background, sample variability and other experimental factors. In this work, we show that the orientation and phase retrieval steps work at photon counts diluted to the signal levels one expects from smaller molecules or with weaker pulses, using data from experimental measurements of 60-nm PR772 viruses. Even when the signal is reduced to a fraction as little as 1/256, the virus electron density determined using ab initio phasing is of almost the same quality as the high-signal data. However, we are still limited by the total number of patterns collected, which may soon be mitigated by the advent of high repetition-rate sources like the European XFEL and LCLS-II.
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Wolff AM, Young ID, Sierra RG, Brewster AS, Martynowycz MW, Aquila A, Nango E, Nakane T, Koralek JD, Sugahara M, Tanaka R, Zhao W, Ito K, Woldeyes RA, Biel JT, Thompson EM, Samelson A, Cortez S, van den Bedem H, Yumoto F, Tono K, Gonen T, Iwata S, Boutet S, Sauter NS, Fraser JS, Thompson MC. Optimizing and evaluating protein microcrystallography experiments: strengths and weaknesses of X-rays and electrons. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319096156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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