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Unity gives strength: combining Bertaut’s and Belov’s concepts and the formalism of aperiodic crystals to solve magnetic structures of unprecedented complexity 团结就是力量:将贝尔托和别洛夫的概念与非周期晶体的形式主义相结合,解决前所未有的复杂磁结构问题。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-11-01 DOI: 10.1107/S2052252524010182
Václav Petříček , Margarida Sousa Henriques
{"title":"Unity gives strength: combining Bertaut’s and Belov’s concepts and the formalism of aperiodic crystals to solve magnetic structures of unprecedented complexity","authors":"Václav Petříček ,&nbsp;Margarida Sousa Henriques","doi":"10.1107/S2052252524010182","DOIUrl":"10.1107/S2052252524010182","url":null,"abstract":"<div><div>We draw attention to the exceptional work of Geers <em>et al.</em>[(2024). <em>IUCrJ</em>, <strong>11</strong>, 910–920] on the analysis of magnetic phases, in which challenging magnetic structures are determined by a combination of modern computational methods and a connection between nuclear modulation and the ordering of magnetic moments is shown.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 6","pages":"Pages 901-902"},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533992/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structure of MltG from Mycobacterium abscessus reveals structural plasticity between composed domains 脓肿分枝杆菌 MltG 的结构揭示了组成结构域之间的结构可塑性。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-11-01 DOI: 10.1107/S2052252524008443
Gwan Hee Lee , Subin Kim , Do Yeon Kim , Ju Hee Han , So Yeon Lee , Jun Hyuck Lee , Chang Sup Lee , Hyun Ho Park
{"title":"Structure of MltG from Mycobacterium abscessus reveals structural plasticity between composed domains","authors":"Gwan Hee Lee ,&nbsp;Subin Kim ,&nbsp;Do Yeon Kim ,&nbsp;Ju Hee Han ,&nbsp;So Yeon Lee ,&nbsp;Jun Hyuck Lee ,&nbsp;Chang Sup Lee ,&nbsp;Hyun Ho Park","doi":"10.1107/S2052252524008443","DOIUrl":"10.1107/S2052252524008443","url":null,"abstract":"<div><div>We provide the structure of MltG of the lytic transglycosyl­ase family in this study. We show that MltG has a flexible peptidoglycan-binding domain and exists as a monomer in solution. Further, the putative active site of <em>Mycobacterium abscessus</em> MltG has been revealed using structural analysis and sequence comparison. This research significantly advances our comprehension of the transglycosyl­ation process mediated by the MltG family, providing valuable insights that can inform the development of next-generation antibiotics to specifically target <em>M. abscessus</em>.</div></div><div><div>MltG, a membrane-bound lytic transglycosyl­ase, has roles in terminating glycan polymerization in peptidoglycan and incorporating glycan chains into the cell wall, making it significant in bacterial cell-wall biosynthesis and remodeling. This study provides the first reported MltG structure from <em>Mycobacterium abscessus</em> (maMltG), a superbug that has high antibiotic resistance. Our structural and biochemical analyses revealed that MltG has a flexible peptidoglycan-binding domain and exists as a monomer in solution. Further, the putative active site of maMltG was disclosed using structural analysis and sequence comparison. Overall, this study contributes to our understanding of the transglycosyl­ation reaction of the MltG family, aiding the design of next-generation antibiotics targeting <em>M. abscessus.</em></div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 6","pages":"Pages 903-909"},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142287691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Waterless structures in the Protein Data Bank 蛋白质数据库中的无水结构。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-11-01 DOI: 10.1107/S2052252524009928
Alexander Wlodawer , Zbigniew Dauter , Pawel Rubach , Wladek Minor , Joanna I. Loch , Dariusz Brzezinski , Miroslaw Gilski , Mariusz Jaskolski
{"title":"Waterless structures in the Protein Data Bank","authors":"Alexander Wlodawer ,&nbsp;Zbigniew Dauter ,&nbsp;Pawel Rubach ,&nbsp;Wladek Minor ,&nbsp;Joanna I. Loch ,&nbsp;Dariusz Brzezinski ,&nbsp;Miroslaw Gilski ,&nbsp;Mariusz Jaskolski","doi":"10.1107/S2052252524009928","DOIUrl":"10.1107/S2052252524009928","url":null,"abstract":"<div><div>A global analysis of protein crystal structures in the Protein Data Bank reveals many medium-to-high-resolution entries that lack any solvent molecules. Also, there are many cases with impossible occupancies of water molecules and/or uninterpreted very high difference electron-density peaks that indicate the presence of unmodeled water molecules.</div></div><div><div>The absence of solvent molecules in high-resolution protein crystal structure models deposited in the Protein Data Bank (PDB) contradicts the fact that, for proteins crystallized from aqueous media, water molecules are always expected to bind to the protein surface, as well as to some sites in the protein interior. An analysis of the contents of the PDB indicated that the expected ratio of the number of water molecules to the number of amino-acid residues exceeds 1.5 in atomic resolution structures, decreasing to 0.25 at around 2.5 Å resolution. Nevertheless, almost 800 protein crystal structures determined at a resolution of 2.5 Å or higher are found in the current release of the PDB without any water molecules, whereas some other depositions have unusually low or high occupancies of modeled solvent. Detailed analysis of these depositions revealed that the lack of solvent molecules might be an indication of problems with either the diffraction data, the refinement protocol, the deposition process or a combination of these factors. It is postulated that problems with solvent structure should be flagged by the PDB and addressed by the depositors.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 6","pages":"Pages 966-976"},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533996/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142500703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Roodmus: a toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions Roodmus:异构电子冷冻显微镜重建基准工具包。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-11-01 DOI: 10.1107/S2052252524009321
Maarten Joosten , Joel Greer , James Parkhurst , Tom Burnley , Arjen J. Jakobi
{"title":"Roodmus: a toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions","authors":"Maarten Joosten ,&nbsp;Joel Greer ,&nbsp;James Parkhurst ,&nbsp;Tom Burnley ,&nbsp;Arjen J. Jakobi","doi":"10.1107/S2052252524009321","DOIUrl":"10.1107/S2052252524009321","url":null,"abstract":"<div><div><em>Roodmus</em> is a toolkit sourcing conformational heterogeneity of biomacromolecules from molecular dynamics simulations to generate high-quality synthetic data for the development and benchmarking of heterogeneous reconstruction algorithms.</div></div><div><div>Conformational heterogeneity of biological macromolecules is a challenge in single-particle averaging (SPA). Current standard practice is to employ classification and filtering methods that may allow a discrete number of conformational states to be reconstructed. However, the conformation space accessible to these molecules is continuous and, therefore, explored incompletely by a small number of discrete classes. Recently developed heterogeneous reconstruction algorithms (HRAs) to analyse continuous heterogeneity rely on machine-learning methods that employ low-dimensional latent space representations. The non-linear nature of many of these methods poses a challenge to their validation and interpretation and to identifying functionally relevant conformational trajectories. These methods would benefit from in-depth benchmarking using high-quality synthetic data and concomitant ground truth information. We present a framework for the simulation and subsequent analysis with respect to the ground truth of cryo-EM micrographs containing particles whose conformational heterogeneity is sourced from molecular dynamics simulations. These synthetic data can be processed as if they were experimental data, allowing aspects of standard SPA workflows as well as heterogeneous reconstruction methods to be compared with known ground truth using available utilities. The simulation and analysis of several such datasets are demonstrated and an initial investigation into HRAs is presented.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 6","pages":"Pages 951-965"},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142465948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry 原位串行晶体学有助于在低对称性条件下进行 96 孔板结构分析。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524005785
Nicolas Foos , Jean-Baptise Florial , Mathias Eymery , Jeremy Sinoir , Franck Felisaz , Marcus Oscarsson , Antonia Beteva , Matthew W. Bowler , Didier Nurizzo , Gergely Papp , Montserrat Soler-Lopez , Max Nanao , Shibom Basu , Andrew A. McCarthy
{"title":"In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry","authors":"Nicolas Foos ,&nbsp;Jean-Baptise Florial ,&nbsp;Mathias Eymery ,&nbsp;Jeremy Sinoir ,&nbsp;Franck Felisaz ,&nbsp;Marcus Oscarsson ,&nbsp;Antonia Beteva ,&nbsp;Matthew W. Bowler ,&nbsp;Didier Nurizzo ,&nbsp;Gergely Papp ,&nbsp;Montserrat Soler-Lopez ,&nbsp;Max Nanao ,&nbsp;Shibom Basu ,&nbsp;Andrew A. McCarthy","doi":"10.1107/S2052252524005785","DOIUrl":"10.1107/S2052252524005785","url":null,"abstract":"<div><p>The determination of a challenging structure in the <em>P</em>1 space group, the lowest symmetry possible, shows how our <em>in situ</em> serial crystallography approach expands the application of crystallization plates as a robust sample delivery method.</p></div><div><p>The advent of serial crystallography has rejuvenated and popularized room-temperature X-ray crystal structure determination. Structures determined at physiological temperature reveal protein flexibility and dynamics. In addition, challenging samples (<em>e.g.</em> large complexes, membrane proteins and viruses) form fragile crystals that are often difficult to harvest for cryo-crystallography. Moreover, a typical serial crystallography experiment requires a large number of microcrystals, mainly achievable through batch crystallization. Many medically relevant samples are expressed in mammalian cell lines, producing a meager quantity of protein that is incompatible with batch crystallization. This can limit the scope of serial crystallography approaches. Direct <em>in situ</em> data collection from a 96-well crystallization plate enables not only the identification of the best diffracting crystallization condition but also the possibility for structure determination under ambient conditions. Here, we describe an <em>in situ</em> serial crystallography (iSX) approach, facilitating direct measurement from crystallization plates mounted on a rapidly exchangeable universal plate holder deployed at a microfocus beamline, ID23-2, at the European Synchrotron Radiation Facility. We applied our iSX approach on a challenging project, autotaxin, a therapeutic target expressed in a stable human cell line, to determine the structure in the lowest-symmetry <em>P</em>1 space group at 3.0 Å resolution. Our <em>in situ</em> data collection strategy provided a complete dataset for structure determination while screening various crystallization conditions. Our data analysis reveals that the iSX approach is highly efficient at a microfocus beamline, improving throughput and demonstrating how crystallization plates can be routinely used as an alternative method of presenting samples for serial crystallography experiments at synchrotrons.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 780-791"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141616469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The structure of Chlamydomonas LOV1 as revealed by time-resolved serial synchrotron crystallography 时间分辨串行同步辐射晶体学揭示的衣藻 LOV1 结构。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524008327
Marius Schmidt
{"title":"The structure of Chlamydomonas LOV1 as revealed by time-resolved serial synchrotron crystallography","authors":"Marius Schmidt","doi":"10.1107/S2052252524008327","DOIUrl":"10.1107/S2052252524008327","url":null,"abstract":"<div><p>The photo-reaction of the LOV1 domain of the <em>Chlamydomonas reinhardtii</em> phototropin is investigated by room-temperature time-resolved serial crystallography. A covalent adduct forms between the C4a atom of the central flavin-mononucleotide chromophore and a protein cysteine. The structure of the adduct is very similar to that of LOV2 determined 23 years ago from the maidenhair fern Phy3.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 645-646"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364020/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142107581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Refinement of cryo-EM 3D maps with a self-supervised denoising model: crefDenoiser 利用自监督去噪模型完善冷冻电子显微镜三维图:crefDenoiser。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524005918
Ishaant Agarwal , Joanna Kaczmar-Michalska , Simon F. Nørrelykke , Andrzej J. Rzepiela
{"title":"Refinement of cryo-EM 3D maps with a self-supervised denoising model: crefDenoiser","authors":"Ishaant Agarwal ,&nbsp;Joanna Kaczmar-Michalska ,&nbsp;Simon F. Nørrelykke ,&nbsp;Andrzej J. Rzepiela","doi":"10.1107/S2052252524005918","DOIUrl":"10.1107/S2052252524005918","url":null,"abstract":"<div><p>State-of-the-art 3D cryo-EM map denoising with a self-supervised neural network model optimized for theoretical noise-free maps is introduced.</p></div><div><p>Cryogenic electron microscopy (cryo-EM) is a pivotal technique for imaging macromolecular structures. However, despite extensive processing of large image sets collected in cryo-EM experiments to amplify the signal-to-noise ratio, the reconstructed 3D protein-density maps are often limited in quality due to residual noise, which in turn affects the accuracy of the macromolecular representation. Here, <em>crefDenoiser</em> is introduced, a denoising neural network model designed to enhance the signal in 3D cryo-EM maps produced with standard processing pipelines. The <em>crefDenoiser</em> model is trained without the need for ‘clean’ ground-truth target maps. Instead, a custom dataset is employed, composed of real noisy protein half-maps sourced from the Electron Microscopy Data Bank repository. Competing with the current state-of-the-art, <em>crefDenoiser</em> is designed to optimize for the theoretical noise-free map during self-supervised training. We demonstrate that our model successfully amplifies the signal across a wide variety of protein maps, outperforming a classic map denoiser and following a network-based sharpening model. Without biasing the map, the proposed denoising method leads to improved visibility of protein structural features, including protein domains, secondary structure elements and modest high-resolution feature restoration.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 821-830"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364040/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141788077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The crystal structure of olanzapine form III 奥氮平 III 型的晶体结构。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524007383
Goulielmina Anyfanti , Elena Husanu , Iryna Andrusenko , Danilo Marchetti , Mauro Gemmi
{"title":"The crystal structure of olanzapine form III","authors":"Goulielmina Anyfanti ,&nbsp;Elena Husanu ,&nbsp;Iryna Andrusenko ,&nbsp;Danilo Marchetti ,&nbsp;Mauro Gemmi","doi":"10.1107/S2052252524007383","DOIUrl":"10.1107/S2052252524007383","url":null,"abstract":"<div><p>This paper reports the crystal structure determination of olanzapine form III by 3D electron diffraction, the last unknown anhydrous polymorph in the olanzapine complex polytypism scenario.</p></div><div><p>The antipsychotic drug olanzapine is well known for its complex polymorphism. Although widely investigated, the crystal structure of one of its anhydrous polymorphs, form III, is still unknown. Its appearance, always in concomitance with forms II and I, and the impossibility of isolating it from that mixture, have prevented its structure determination so far. The scenario has changed with the emerging field of 3D electron diffraction (3D ED) and its great advantages in the characterization of polyphasic mixtures of nanosized crystals. In this study, we show how the application of 3D ED allows the <em>ab initio</em> structure determination and dynamical refinement of this elusive crystal structure that remained unknown for more than 20 years. Olanzapine form III is monoclinic and shows a similar but shifted packing with respect to form II. It is remarkably different from the lowest-energy structures predicted by the energy-minimization algorithms of crystal structure prediction.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 843-848"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141788078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography 利用时间分辨串行同步辐射晶体学捕捉衣藻 Phot-LOV1 结构域的蓝光激活状态。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524005608
Guillaume Gotthard , Sandra Mous , Tobias Weinert , Raiza Nara Antonelli Maia , Daniel James , Florian Dworkowski , Dardan Gashi , Antonia Furrer , Dmitry Ozerov , Ezequiel Panepucci , Meitian Wang , Gebhard F. X. Schertler , Joachim Heberle , Joerg Standfuss , Przemyslaw Nogly
{"title":"Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography","authors":"Guillaume Gotthard ,&nbsp;Sandra Mous ,&nbsp;Tobias Weinert ,&nbsp;Raiza Nara Antonelli Maia ,&nbsp;Daniel James ,&nbsp;Florian Dworkowski ,&nbsp;Dardan Gashi ,&nbsp;Antonia Furrer ,&nbsp;Dmitry Ozerov ,&nbsp;Ezequiel Panepucci ,&nbsp;Meitian Wang ,&nbsp;Gebhard F. X. Schertler ,&nbsp;Joachim Heberle ,&nbsp;Joerg Standfuss ,&nbsp;Przemyslaw Nogly","doi":"10.1107/S2052252524005608","DOIUrl":"10.1107/S2052252524005608","url":null,"abstract":"<div><p>A crystalline sample of CrLOV1 was optimized for serial crystallography. Time-resolved serial synchrotron crystallography provides high-resolution insights into structural changes of CrLOV1 from Δ<em>t</em> = 2.5 ms up to Δ<em>t</em> = 95 ms post-photoactivation, resolving the geometry of the thio­ether adduct and alteration of the C-terminal region implicated in the signal transduction.</p></div><div><p>Light–oxygen–voltage (LOV) domains are small photosensory flavoprotein modules that allow the conversion of external stimuli (sunlight) into intra­cellular signals responsible for various cell behaviors (<em>e.g.</em> phototropism and chloro­plast relocation). This ability relies on the light-induced formation of a covalent thio­ether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that result in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the activation cascade of the LOV domain to be observed in real time, which has been elusive. In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 from <em>Chlamydomonas reinhardtii</em> (<em>Cr</em>PhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to data collection, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the crystals obtained preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations of <em>Cr</em>PhotLOV1 from Δ<em>t</em> = 2.5 ms up to Δ<em>t</em> = 95 ms post-photoactivation, including resolving the geometry of the thio­ether adduct and the C-terminal region implicated in the signal transduction process.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 792-808"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141734146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Texture tomography, a versatile framework to study crystalline texture in 3D 纹理层析技术--研究三维晶体纹理的多功能框架。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524006547
M. P. K. Frewein , J. Mason , B. Maier , H. Cölfen , A. Medjahed , M. Burghammer , M. Allain , T. A. Grünewald
{"title":"Texture tomography, a versatile framework to study crystalline texture in 3D","authors":"M. P. K. Frewein ,&nbsp;J. Mason ,&nbsp;B. Maier ,&nbsp;H. Cölfen ,&nbsp;A. Medjahed ,&nbsp;M. Burghammer ,&nbsp;M. Allain ,&nbsp;T. A. Grünewald","doi":"10.1107/S2052252524006547","DOIUrl":"10.1107/S2052252524006547","url":null,"abstract":"<div><p>The crystallographic texture is a key feature of crystalline organization in materials, yet no technique exists to locally characterize complex textured materials in 3D. In this manuscript, we present <em>Texture Tomography</em> (<em>TexTOM</em>) as a computational tool to provide full 3D texture information from X-ray diffraction measurements.</p></div><div><p>Crystallographic texture is a key organization feature of many technical and biological materials. In these materials, especially hierarchically structured ones, the preferential alignment of the nano constituents heavily influences the macroscopic behavior of the material. To study local crystallographic texture with both high spatial and angular resolution, we developed <em>Texture Tomography</em> (<em>TexTOM</em>). This approach allows the user to model the diffraction data of polycrystalline materials using the full reciprocal space of the crystal ensemble and describe the texture in each voxel via an orientation distribution function, hence it provides 3D reconstructions of the local texture by measuring the probabilities of all crystal orientations. The <em>TexTOM</em> approach addresses limitations associated with existing models: it correlates the intensities from several Bragg reflections, thus reducing ambiguities resulting from symmetry. Further, it yields quantitative probability distributions of local real space crystal orientations without further assumptions about the sample structure. Finally, its efficient mathematical formulation enables reconstructions faster than the time scale of the experiment. This manuscript presents the mathematical model, the inversion strategy and its current experimental implementation. We show characterizations of simulated data as well as experimental data obtained from a synthetic, inorganic model sample: the silica–witherite biomorph. <em>TexTOM</em> provides a versatile framework to reconstruct 3D quantitative texture information for polycrystalline samples; it opens the door for unprecedented insights into the nanostructural makeup of natural and technical materials.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 809-820"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364025/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141751773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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