IUCrJ最新文献

{"title":"A step towards 6D WAXD tensor tomography","authors":"Xiaoyi Zhao ,&nbsp;Zheng Dong ,&nbsp;Chenglong Zhang ,&nbsp;Himadri Gupta ,&nbsp;Zhonghua Wu ,&nbsp;Wenqiang Hua ,&nbsp;Junrong Zhang ,&nbsp;Pengyu Huang ,&nbsp;Yuhui Dong ,&nbsp;Yi Zhang ,&nbsp;V. T. Forsyth (Editor)","doi":"10.1107/S2052252524003750","DOIUrl":"10.1107/S2052252524003750","url":null,"abstract":"<div><p>A novel approach is reported for 6D wide-angle X-ray diffraction tensor tomography characterization based on the concept of virtual reciprocal-space scanning.</p></div><div><p>X-ray scattering/diffraction tensor tomography techniques are promising methods to acquire the 3D texture information of heterogeneous biological tissues at micrometre resolution. However, the methods suffer from a long overall acquisition time due to multi-dimensional scanning across real and reciprocal space. Here, a new approach is introduced to obtain 3D reciprocal information of each illuminated scanning volume using mathematic modeling, which is equivalent to a physical scanning procedure for collecting the full reciprocal information required for voxel reconstruction. The virtual reciprocal scanning scheme was validated by a simulated 6D wide-angle X-ray diffraction tomography experiment. The theoretical validation of the method represents an important technological advancement for 6D diffraction tensor tomography and a crucial step towards pervasive applications in the characterization of heterogeneous materials.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 502-509"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897409","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}

{"title":"A modified phase-retrieval algorithm to facilitate automatic de novo macromolecular structure determination in single-wavelength anomalous diffraction","authors":"Xingke Fu ,&nbsp;Zhi Geng ,&nbsp;Zhichao Jiao ,&nbsp;Wei Ding ,&nbsp;T. Ishikawa (Editor)","doi":"10.1107/S2052252524004846","DOIUrl":"10.1107/S2052252524004846","url":null,"abstract":"<div><p>A modified phase-retrieval algorithm has been built on the framework of the relaxed alternating averaged reflection (RAAR) algorithm, incorporating the π-half phase perturbation for weak reflections and the direct-methods based tangent formula for strong reflections in reciprocal space. The modified phase-retrieval algorithm exhibits significantly improved effectiveness and accuracy of various forms of SAD substructure determination to facilitate automatic <em>de novo</em> macromolecular structure determination.</p></div><div><p>The success of experimental phasing in macromolecular crystallography relies primarily on the accurate locations of heavy atoms bound to the target crystal. To improve the process of substructure determination, a modified phase-retrieval algorithm built on the framework of the relaxed alternating averaged reflection (RAAR) algorithm has been developed. Importantly, the proposed algorithm features a combination of the π-half phase perturbation for weak reflections and enforces the direct-method-based tangent formula for strong reflections in reciprocal space. The proposed algorithm is extensively demonstrated on a total of 100 single-wavelength anomalous diffraction (SAD) experimental datasets, comprising both protein and nucleic acid structures of different qualities. Compared with the standard RAAR algorithm, the modified phase-retrieval algorithm exhibits significantly improved effectiveness and accuracy in SAD substructure determination, highlighting the importance of additional constraints for algorithmic performance. Furthermore, the proposed algorithm can be performed without human intervention under most conditions owing to the self-adaptive property of the input parameters, thus making it convenient to be integrated into the structural determination pipeline. In conjunction with the <em>IPCAS</em> software suite, we demonstrated experimentally that automatic <em>de novo</em> structure determination is possible on the basis of our proposed algorithm.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 587-601"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432032","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}

{"title":"Chemistry and crystal engineering.","authors":"Susan A Bourne","doi":"10.1107/S2052252524006249","DOIUrl":"10.1107/S2052252524006249","url":null,"abstract":"<p><p>Recent studies published in the Chemistry and crystal engineering section of IUCrJ emphasize developments both in methodology and techniques as well as the diverse range of classes of compounds being studied and of problems being tackled.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 Pt 4","pages":"434-435"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492011","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}

{"title":"Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure","authors":"Stephanie A. Wankowicz ,&nbsp;James S. Fraser ,&nbsp;Z.-J. Liu (Editor)","doi":"10.1107/S2052252524005098","DOIUrl":"10.1107/S2052252524005098","url":null,"abstract":"<div><p>Traditional structural models of biomolecules typically represent only a single conformational state, even though biomolecules naturally exist in multiple states crucial for their function. Here, we propose enhancements to the macromolecular crystallographic information file (mmCIF) to better capture the complex conformational and compositional heterogeneity of biomolecules that is human- and machine-interpretable.</p></div><div><p>In the folded state, biomolecules exchange between multiple conformational states crucial for their function. However, most structural models derived from experiments and computational predictions only encode a single state. To represent biomolecules accurately, we must move towards modeling and predicting structural ensembles. Information about structural ensembles exists within experimental data from X-ray crystallography and cryo-electron microscopy. Although new tools are available to detect conformational and compositional heterogeneity within these ensembles, the legacy PDB data structure does not robustly encapsulate this complexity. We propose modifications to the macromolecular crystallographic information file (mmCIF) to improve the representation and interrelation of conformational and compositional heterogeneity. These modifications will enable the capture of macromolecular ensembles in a human and machine-interpretable way, potentially catalyzing breakthroughs for ensemble–function predictions, analogous to the achievements of <em>AlphaFold</em> with single-structure prediction.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 494-501"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492013","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}

{"title":"Exploring crystal structure–physical property relationships with pressure","authors":"David R. Allan","doi":"10.1107/S205225252400602X","DOIUrl":"10.1107/S205225252400602X","url":null,"abstract":"<div><p>From its conception, X-ray crystallography has provided a unique understanding of the structure, bonding and electronic state of materials, which, in turn, unlocks a means of examining the properties and function of crystalline systems. Using state-of-the-art single-crystal X-ray diffraction, along with UV–Vis spectroscopy and DFT calculations, Zwolenik <em>et al.</em> [(2024). <em>IUCrJ</em>, <strong>11</strong>, 519–527] have provided a comprehensive study of the structure–optical property relationship of 1,3-di­acetyl­pyrene with methodologies that are increasingly accessible to non-specialist laboratories.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 438-439"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492015","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}

{"title":"Structural insight into piezo-solvatochromism of Reichardt’s dye","authors":"Szymon Sobczak ,&nbsp;Andrzej Katrusiak ,&nbsp;P. Lightfoot (Editor)","doi":"10.1107/S2052252524004603","DOIUrl":"10.1107/S2052252524004603","url":null,"abstract":"<div><p>This work employs the preference of compounds to crystallize at high-pressure in the form of solvates to explore the solvation process and piezo-solvatochromic effects of Reichardt’s dye, ET(1). The solute–solvent interactions of this dye affect the optical properties of the dye in various solvents as shown by X-ray diffraction and UV–Vis spectroscopy, revealing applications in nonlinear optoelectronics and molecular pressure sensor development.</p></div><div><p>To date, accurate modelling of the solvation process is challenging, often over-simplifying the solvent–solute interactions. The interplay between the molecular arrangement associated with the solvation process and crystal nucleation has been investigated by analysis of the piezo-solvatochromic behaviour of Reichardt’s dye, ET(1), in methanol, ethanol and acetone under high pressure. High-pressure single-crystal X-ray diffraction and UV–Vis spectroscopy reveal the impact of solute–solvent interactions on the optical properties of ET(1). The study underscores the intricate relationship between solvent properties, molecular conformation and crystal packing. The connection between liquid and solid phases emphasizes the capabilities of high-pressure methods for expanding the field of crystal engineering. The high-pressure environment allowed the determination of the crystal structures reported here that are built from organic molecules fourfold solvated with ethanol or methanol: ET(1)·4CH₃OH and ET(1)·4C₂H₅OH·H₂O. The observed piezo-solvatochromic effects highlight the potential of ET(1) in nonlinear optoelectronics and expand the application of solvatochromic chemical indicators to pressure sensors.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 528-537"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141248016","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}

{"title":"Crystal structure via fluctuation scattering","authors":"Patrick Adams ,&nbsp;Tamar L. Greaves ,&nbsp;Andrew V. Martin ,&nbsp;T. Ishikawa (Editor)","doi":"10.1107/S2052252524003932","DOIUrl":"10.1107/S2052252524003932","url":null,"abstract":"<div><p>Fluctuation X-ray scattering measures the correlation of scattered X-rays in diffraction experiments. Here, the Bragg peak intensity from fluctuation X-ray scattering correlations is recovered using an iterative algorithm.</p></div><div><p>Crystallography is a quintessential method for determining the atomic structure of crystals. The most common implementation of crystallography uses single crystals that must be of sufficient size, typically tens of micrometres or larger, depending on the complexity of the crystal structure. The emergence of serial data-collection methods in crystallography, particularly for time-resolved experiments, opens up opportunities to develop new routes to structure determination for nanocrystals and ensembles of crystals. Fluctuation X-ray scattering is a correlation-based approach for single-particle imaging from ensembles of identical particles, but has yet to be applied to crystal structure determination. Here, an iterative algorithm is presented that recovers crystal structure-factor intensities from fluctuation X-ray scattering correlations. The capabilities of this algorithm are demonstrated by recovering the structure of three small-molecule crystals and a protein crystal from simulated fluctuation X-ray scattering correlations. This method could facilitate the recovery of structure-factor intensities from crystals in serial crystallography experiments and relax sample requirements for crystallography experiments.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 538-555"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141260556","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}

{"title":"In some cases more complicated approaches to refinement of macromolecular structures are not necessary","authors":"Zbigniew Dauter ,&nbsp;Alexander Wlodawer ,&nbsp;E. N. Baker (Editor)","doi":"10.1107/S2052252524005803","DOIUrl":"10.1107/S2052252524005803","url":null,"abstract":"<div><p>The manuscript ‘Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform <em>Amber</em>’ presents a novel protein structure refinement method claimed to offer improvements over traditional techniques like <em>Refmac5</em> and <em>Phenix</em>. Our re-evaluation suggests that while the new method provides improvements, traditional methods achieve comparable results with less computational effort.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 643-644"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220886/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492016","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}

{"title":"From X-ray crystallographic structure to intrinsic thermodynamics of protein–ligand binding using carbonic anhydrase isozymes as a model system","authors":"Vaida Paketurytė-Latvė ,&nbsp;Alexey Smirnov ,&nbsp;Elena Manakova ,&nbsp;Lina Baranauskiene ,&nbsp;Vytautas Petrauskas ,&nbsp;Asta Zubrienė ,&nbsp;Jurgita Matulienė ,&nbsp;Virginija Dudutienė ,&nbsp;Edita Čapkauskaitė ,&nbsp;Audrius Zakšauskas ,&nbsp;Janis Leitans ,&nbsp;Saulius Gražulis ,&nbsp;Kaspars Tars ,&nbsp;Daumantas Matulis ,&nbsp;Z.-J. Liu (Editor)","doi":"10.1107/S2052252524004627","DOIUrl":"10.1107/S2052252524004627","url":null,"abstract":"<div><p>Rational drug discovery and design require a deep understanding of the structure and thermodynamics of protein–ligand interactions. Here, the human carbonic anhydrase family of enzymes and their specific sulfonamide ligands are used to describe binding assays and crystal structures for understanding of protein–compound recognition principles.</p></div><div><p>Carbonic anhydrase (CA) was among the first proteins whose X-ray crystal structure was solved to atomic resolution. CA proteins have essentially the same fold and similar active centers that differ in only several amino acids. Primary sulfonamides are well defined, strong and specific binders of CA. However, minor variations in chemical structure can significantly alter their binding properties. Over 1000 sulfonamides have been designed, synthesized and evaluated to understand the correlations between the structure and thermodynamics of their binding to the human CA isozyme family. Compound binding was determined by several binding assays: fluorescence-based thermal shift assay, stopped-flow enzyme activity inhibition assay, isothermal titration calorimetry and competition assay for enzyme expressed on cancer cell surfaces. All assays have advantages and limitations but are necessary for deeper characterization of these protein–ligand interactions. Here, the concept and importance of intrinsic binding thermodynamics is emphasized and the role of structure–thermodynamics correlations for the novel inhibitors of CA IX is discussed – an isozyme that is overexpressed in solid hypoxic tumors, and thus these inhibitors may serve as anticancer drugs. The abundant structural and thermodynamic data are assembled into the Protein–Ligand Binding Database to understand general protein–ligand recognition principles that could be used in drug discovery.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 556-569"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220870/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141296053","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}

{"title":"A predicted model-aided reconstruction algorithm for X-ray free-electron laser single-particle imaging","authors":"Zhichao Jiao ,&nbsp;Yao He ,&nbsp;Xingke Fu ,&nbsp;Xin Zhang ,&nbsp;Zhi Geng ,&nbsp;Wei Ding ,&nbsp;T. Ishikawa (Editor)","doi":"10.1107/S2052252524004858","DOIUrl":"10.1107/S2052252524004858","url":null,"abstract":"<div><p>A predicted model-aided reconstruction algorithm is proposed for orientation determination and phase retrieval in X-ray free-electron laser single-particle imaging. The predicted model-aided algorithm exhibits significant improvements in the success rate, accuracy and efficiency of the reconstruction process.</p></div><div><p>Ultra-intense, ultra-fast X-ray free-electron lasers (XFELs) enable the imaging of single protein molecules under ambient temperature and pressure. A crucial aspect of structure reconstruction involves determining the relative orientations of each diffraction pattern and recovering the missing phase information. In this paper, we introduce a predicted model-aided algorithm for orientation determination and phase retrieval, which has been tested on various simulated datasets and has shown significant improvements in the success rate, accuracy and efficiency of XFEL data reconstruction.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 602-619"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432033","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}