IUCrJ最新文献

{"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":"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":"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}

{"title":"High-accuracy measurement, advanced theory and analysis of the evolution of satellite transitions in manganese Kα using XR-HERFD","authors":"Daniel Sier ,&nbsp;Jonathan W. Dean ,&nbsp;Nicholas T. T. Tran ,&nbsp;Tony Kirk ,&nbsp;Chanh Q. Tran ,&nbsp;J. Frederick W. Mosselmans ,&nbsp;Sofia Diaz-Moreno ,&nbsp;Christopher T. Chantler ,&nbsp;V. K. Peterson (Editor)","doi":"10.1107/S2052252524005165","DOIUrl":"10.1107/S2052252524005165","url":null,"abstract":"<div><p>Here, the <em>n</em> = 2 satellite present for manganese-containing materials and across materials science has been successfully observed by applying the new technique of extended-range high-energy-resolution fluorescence detection (XR-HERFD), developed from high-resolution resonant inelastic X-ray scattering and HERFD, and the spectra have been predicted with new advanced theory.</p></div><div><p>Here, the novel technique of extended-range high-energy-resolution fluorescence detection (XR-HERFD) has successfully observed the <em>n</em> = 2 satellite in manganese to a high accuracy. The significance of the satellite signature presented is many hundreds of standard errors and well beyond typical discovery levels of three to six standard errors. This satellite is a sensitive indicator for all manganese-containing materials in condensed matter. The uncertainty in the measurements has been defined, which clearly observes multiple peaks and structure indicative of complex physical quantum-mechanical processes. Theoretical calculations of energy eigenvalues, shake-off probability and Auger rates are also presented, which explain the origin of the satellite from physical <em>n</em> = 2 shake-off processes. The evolution in the intensity of this satellite is measured relative to the full <em>K</em>α spectrum of manganese to investigate satellite structure, and therefore many-body processes, as a function of incident energy. Results demonstrate that the many-body reduction factor <em>S</em>₀² should not be modelled with a constant value as is currently done. This work makes a significant contribution to the challenge of understanding many-body processes and interpreting HERFD or resonant inelastic X-ray scattering spectra in a quantitative manner.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 620-633"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432034","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":"Chromic and dynamic: soft crystals of platinum(II) complexes pave the way for multi-responsive materials","authors":"Gonzalo Campillo-Alvarado","doi":"10.1107/S2052252524006055","DOIUrl":"10.1107/S2052252524006055","url":null,"abstract":"<div><p>The development of smart, stimuli-responsive materials has received increased attention in the past decade for their applications as sensing technologies. This commentary discusses a timely topical review by Kato [(2024). <em>IUCrJ</em>, <strong>11</strong>, 442–452] on the fabrication of multi-stimuli responsive crystals comprised of luminescent platinum(II) complexes, which exhibit intriguing chromic phenomena in response to stimuli.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 436-437"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492012","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":"Relating solvatochromism and solvatomorphism in organic dyes using high pressure","authors":"Elena Boldyreva","doi":"10.1107/S2052252524005773","DOIUrl":"10.1107/S2052252524005773","url":null,"abstract":"<div><p>By using complementary experimental methods including <em>in situ</em> high-pressure single-crystal X-ray diffraction and UV–Vis spectroscopy, the intricate connection between solvatochromism and solvatomorphism has been elucidated in a recent publication [Sobczak &amp; Katrusiak (2024). <em>IUCrJ</em>, <strong>11</strong>, 528–537]. The connection was demonstrated for an important pigment – Reichardt’s dye – with potential applications in nonlinear optoelectronics and molecular pressure sensor development.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 440-441"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492017","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":"Photoinduced bidirectional mesophase transition in vesicles containing azo­benzene amphiphiles","authors":"Svenja C. Hövelmann ,&nbsp;Ella Dieball ,&nbsp;Jule Kuhn ,&nbsp;Michelle Dargasz ,&nbsp;Rajendra P. Giri ,&nbsp;Franziska Reise ,&nbsp;Michael Paulus ,&nbsp;Thisbe K. Lindhorst ,&nbsp;Bridget M. Murphy ,&nbsp;F. Maia (Editor)","doi":"10.1107/S2052252524004032","DOIUrl":"10.1107/S2052252524004032","url":null,"abstract":"<div><p>In this work, a reversible non-invasive light-induced mesophase transition from lamellar to cubic <em>Pn</em>3<em>m</em> is observed in mixed azo­benzene-lipid and phospho­lipid vesicles using small-angle X-ray scattering.</p></div><div><p>The functionality and efficiency of proteins within a biological membrane are highly dependent on both the membrane lipid composition and the physiochemical properties of the solution. Lipid mesophases are directly influenced by changes in temperature, pH, water content or due to individual properties of single lipids such as photoswitchability. In this work, we were able to induce light- and temperature-driven mesophase transitions in a model membrane system containing a mixture of 1,2-dipalmitoyl-phosphatidylcholine phospho­lipids and azo­benzene amphiphiles. We observed reversible and reproducible transitions between the lamellar and <em>Pn</em>3<em>m</em> cubic phase after illuminating the sample for 5 min with light of 365 and 455 nm wavelengths, respectively, to switch between the <em>cis</em> and <em>trans</em> states of the azo­benzene N=N double bond. These light-controlled mesophase transitions were found for mixed complexes with up to 20% content of the photosensitive molecule and at temperatures below the gel-to-liquid crystalline phase transition temperature of 33°C. Our results demonstrate the potential to design bespoke model systems to study the response of membrane lipids and proteins upon changes in mesophase without altering the environment and thus provide a possible basis for drug delivery systems.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 486-493"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141160492","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":"Statistical optimization of guest uptake in crystalline sponges: grading structural outcomes","authors":"Robert C. Carroll ,&nbsp;Simon J. Coles ,&nbsp;P. Lightfoot (Editor)","doi":"10.1107/S2052252524004871","DOIUrl":"10.1107/S2052252524004871","url":null,"abstract":"<div><p>A statistical design of experiments approach applied to crystalline sponge analysis enables greater understanding of experimental influences and the development of a novel molecular structure quality grading system.</p></div><div><p>Investigation of the analyte soaking conditions on the crystalline sponge {[(ZnI₂)₃(tpt)₂·<em>x</em>(solvent)]_n} method using a statistical design of experiments model has provided fundamental insights into the influence of experimental variables. This approach focuses on a single analyte tested via 60 experiments (20 unique conditions) to identify the main effects for success and overall guest structure quality. This is employed as a basis for the development of a novel molecular structure grading system that enables the quantification of guest exchange quality.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 578-586"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141306025","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}