IUCrJ最新文献

{"title":"A large, general and modular DARPin–apoferritin scaffold enables the visualization of small proteins by cryo-EM","authors":"Xin Lu ,&nbsp;Ming Yan ,&nbsp;Yang Cai ,&nbsp;Xi Song ,&nbsp;Huan Chen ,&nbsp;Mengtan Du ,&nbsp;Zhenyi Wang ,&nbsp;Jia’an Li ,&nbsp;Liwen Niu ,&nbsp;Fuxing Zeng ,&nbsp;Quan Hao ,&nbsp;Hongmin Zhang","doi":"10.1107/S2052252525003021","DOIUrl":"10.1107/S2052252525003021","url":null,"abstract":"<div><div>This study introduces a modular scaffold strategy utilizing designed ankyrin-repeat proteins (DARPins) and a symmetric apoferritin base to overcome size limitations in single-particle cryo-EM, enabling near-atomic-resolution structural determination of medium-sized proteins like GFP and MBP. The high-symmetry, near-spherical scaffold not only resolves the common preferred-orientation challenges in single-particle cryo-EM but also reduces data-processing demands, offering a versatile platform for structural analysis of diverse proteins.</div></div><div><div>Single-particle cryo-electron microscopy (cryo-EM) has emerged as an indispensable technique in structural biology that is pivotal for deciphering protein architectures. However, the medium-sized proteins (30–40 kDa) that are prevalent in both eukaryotic and prokaryotic organisms often elude the resolving capabilities of contemporary cryo-EM methods. To address this challenge, we engineered a scaffold strategy that securely anchors proteins of interest to a robust, symmetric base via a selective adapter. Our most efficacious constructs, namely models 4 and 6c, feature a designed ankyrin-repeat protein (DARPin) rigidly linked to an octahedral human apoferritin via a helical linker. By utilizing these large, highly symmetric scaffolds (∼1 MDa), we achieved near-atomic-resolution cryo-EM structures of green fluorescent protein (GFP) and maltose-binding protein (MBP), revealing nearly all side-chain densities of GFP and the distinct structural features of MBP. The modular design of our scaffold allows the adaptation of new DARPins through minor amino-acid-sequence modifications, enabling the binding and visualization of a diverse array of proteins. The high symmetry and near-spherical shape of the scaffold not only mitigates the prevalent challenge of preferred particle orientation in cryo-EM but also significantly reduces the demands of image collection and data processing. This approach presents a versatile solution, breaking through the size constraints that have traditionally limited single-particle cryo-EM.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 393-402"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure of ice VII with Hirshfeld atom refinement","authors":"Roman Gajda ,&nbsp;Michał Chodkiewicz ,&nbsp;Dongzhou Zhang ,&nbsp;Phuong Nguyen ,&nbsp;Vitali Prakapenka ,&nbsp;Krzysztof Wozniak","doi":"10.1107/S2052252525002581","DOIUrl":"10.1107/S2052252525002581","url":null,"abstract":"<div><div>The crystal structure of cubo-ice (ice VII) has been established by single-crystal X-ray diffraction using both synchrotron and laboratory data collected at high pressure. X-ray diffraction data in both cases were refined with Hirshfeld atom refinement. Various structural models including those with ‘split’ positions of atoms were refined.</div></div><div><div>In the refinement of the crystal structures of ice, the best results obtained so far have been with neutron diffraction because the most troublemaking aspects are the hydrogen atoms. In nine out of twenty ice structures, the hydrogen atoms are disordered, which makes proper refinement more difficult. In our previous paper describing the structure of ice VI we proved that, using Hirshfeld atom refinement (HAR) based on synchrotron X-ray data, it is possible to obtain results comparable with those from neutron experiments. In this work, we investigate another structure of high-pressure disordered ice, cubo-ice (ice VII). Single crystals of cubo-ice were grown under pressure in diamond anvil cells. X-ray diffraction measurements were conducted at a synchrotron source facility (APS, University of Chicago, USA) as well as on our regular in-house laboratory diffractometer with Ag radiation. The data collected were further refined with HAR. Comparison of the structural parameters obtained with those derived from neutron diffraction showed very good agreement in terms of bond lengths and fairly good agreement in terms of hydrogen atom ADPs. We were also able to perform unconstrained refinements with various split-atom models.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 288-294"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prospects for coherent X-ray diffraction imaging at fourth-generation synchrotron sources","authors":"Yuriy Chushkin ,&nbsp;Federico Zontone","doi":"10.1107/S2052252525001526","DOIUrl":"10.1107/S2052252525001526","url":null,"abstract":"<div><div>A review of plane-wave coherent X-ray diffraction imaging in small-angle X-ray scattering geometry is presented, together with a discussion of the new opportunities offered by fourth-generation synchrotron sources.</div></div><div><div>Coherent X-ray diffraction imaging is a lens-less microscopy technique that emerged with the advent of third-generation synchrotrons, modern detectors and computers. It can image isolated micrometre-sized objects with a spatial resolution of a few nanometres. The method is based on the inversion of the speckle pattern in the far field produced by the scattering from the object under coherent illumination. The retrieval of the missing phase is performed using an iterative algorithm that numerically phases the amplitudes from the intensities of speckles measured with sufficient oversampling. Two- and three-dimensional imaging is obtained by simple inverse Fourier transform. This lens-less imaging technique has been applied to various specimens for their structural characterization on the nanoscale. Here, we review the theoretical and experimental elements of the technique, its achievements, and its limitations at third-generation synchrotrons. We also discuss the new opportunities offered by modern fourth-generation synchrotrons and outline the developments necessary to maximize the potential of the technique.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 280-287"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electrostatic landscapes in crystal engineering: a new perspective on synthons","authors":"Alexander S. Novikov","doi":"10.1107/S2052252525003148","DOIUrl":"10.1107/S2052252525003148","url":null,"abstract":"<div><div>The design of crystalline solids relies on understanding and controlling intermolecular and intramolecular interactions. Through theoretical charge density analysis and database mining, Shukla <em>et al.</em> [(2025). <em>IUCrJ</em>, <strong>12</strong>, 334–357] have found a new way of viewing supramolecular assembly through the lens of electrostatic complementarity.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 255-256"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Peptide bonds revisited","authors":"Santosh Panjikar ,&nbsp;Manfred S. Weiss","doi":"10.1107/S2052252525002106","DOIUrl":"10.1107/S2052252525002106","url":null,"abstract":"&lt;div&gt;&lt;div&gt;High-resolution crystal structures reveal that peptide bonds in α-helices exhibit a slightly more pronounced enol-like character than those in β-strands. This can go as far as peptide oxygen atoms in protein structures being protonated.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;div&gt;Understanding the structural and chemical properties of peptide bonds within protein secondary structures is vital for elucidating their roles in protein folding, stability and function. This study examines the distinct characteristics of peptide bonds in α-helices and β-strands using a nonredundant data set comprising 1024 high-resolution protein crystal structures from the Protein Data Bank (PDB). The analysis reveals surprising and intriguing insights into bond lengths, angles, dihedral angles, electron-density distributions and hydrogen bonding within α-helices and β-strands. While the respective bond lengths (CN and CO) do not differ much between helices and strands, the bond angles (∠CNC&lt;sub&gt;α&lt;/sub&gt; and ∠OCN) are significantly larger in strands compared with helices. Furthermore, the peptide dihedral angle (ω) in helices clusters around 180° and follows a sharp Gaussian distribution with a standard deviation of 4.1°. In contrast, the distribution of dihedral angles in strands spans a much wider range, with a more flattened Gaussian peak around 180°. This distinct difference in the distribution of dihedral angles reflects the unique structural characteristics of helices and strands, highlighting their respective conformational preferences. Additionally, if the ratio of the electron-density values (2&lt;em&gt;mF&lt;/em&gt;&lt;sub&gt;o&lt;/sub&gt; − &lt;em&gt;DF&lt;/em&gt;&lt;sub&gt;c&lt;/sub&gt;) at the midpoint of the CO bond and of the CN bond is calculated, a skewed distribution is observed, with the ratio being lower for helices than for strands. Moreover, higher normalized mean atomic displacement parameters (ADPs) for peptide atoms in helices relative to strands suggest increased flexibility or a more dynamic structure within helical regions. Analysis of hydrogen-bond distances between O and N atoms of the main chain reveals larger distances in helices compared with strands, indicative of distinct hydrogen-bonding patterns associated with different secondary structures. All of these observations taken together led us to conclude that peptide bonds in α-helices are different from peptide bonds in β-strands. Overall, α-helical peptide bonds seem to display a more enol-like character. This suggests that peptide oxygen atoms in helices are more likely to be protonated. These findings have several important implications for refining protein structures, particularly in regions susceptible to enol-like transitions or protonation. By recognizing the distinct bond-angle and bond-length variations associated with protonated carbonyl oxygen atoms, current refinement protocols can be adapted to apply more flexible restraints in these regions. This could improve the accuracy of modelling local geometries, where protonation or enol fo","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 307-321"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel starting points for fragment-based drug design against human heat-shock protein 90 identified using crystallographic fragment screening","authors":"Liqing Huang ,&nbsp;Weiwei Wang ,&nbsp;Zhimin Zhu ,&nbsp;Qianhui Li ,&nbsp;Minjun Li ,&nbsp;Huan Zhou ,&nbsp;Qin Xu ,&nbsp;Wen Wen ,&nbsp;Qisheng Wang ,&nbsp;Feng Yu","doi":"10.1107/S2052252524012247","DOIUrl":"10.1107/S2052252524012247","url":null,"abstract":"<div><div>In this first instance of crystallographic fragment screening completed by the crystallographic fragment-screening platform of the Shanghai Synchrotron Radiation Facility (SSRF) in China, 800 fragments were screened and 91 compounds were identified to bind at eight different sites.</div></div><div><div>Heat-shock protein 90 (HSP90) is a highly active molecular chaperone that plays a crucial role in cellular function. It facilitates the folding, assembly and stability of various oncogenic proteins, particularly kinases and transcription factors involved in regulating tumor growth and maintenance signaling pathways. Consequently, HSP90 inhibitors are being explored as drugs for cancer therapy. Crystallographic fragment screening is a novel screening method that has been developed in recent years for fragment-based drug discovery and is known for its high hit rate and its ability to provide direct insights into the complex structures of proteins and compounds. In this paper, high-diffraction-resolution crystals of the N-terminal domain of human HSP90α were employed in crystallographic fragment screening to discover binding fragments and binding sites. A diverse library of 800 structurally distinct fragments was screened, yielding 91 starting points for the fragment-based drug design of new HSP90α N-terminal inhibitors. Nearly a thousand crystals were measured, with 738 being processed and phased using a highly automated data-processing pipeline including data reduction and phasing, refinement and hit identification via <em>PanDDA</em> multi-data-set analysis. The 91 identified compounds bind to eight distinct regions of the HSP90α N-terminus, with 63 fragments located in the ATP-binding pocket and its surroundings, thus demonstrating the potential for the development of HSP90α- and ATP-binding inhibitors. This study emphasizes crystallographic fragment screening as a powerful method that can effectively identify fragment molecules and inhibitors that bind to HSP90α, contributing to ongoing efforts in cancer drug discovery.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 2","pages":"Pages 177-187"},"PeriodicalIF":2.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143005581","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":"FLEXR-MSA: electron-density map comparisons of sequence-diverse structures","authors":"Timothy R. Stachowski ,&nbsp;Marcus Fischer","doi":"10.1107/S2052252525001332","DOIUrl":"10.1107/S2052252525001332","url":null,"abstract":"<div><div><em>FLEXR-MSA</em> extends the <em>FLEXR</em> suite of tools by enabling electron-density map comparisons of sequence-diverse proteins.</div></div><div><div>Proteins with near-identical sequences often share similar static structures. Yet, comparing crystal structures is limited or even biased by what has been included or omitted in the deposited model. Information about unique dynamics is often hidden in electron-density maps. Currently, automatic map comparisons are limited to sequence-identical structures. To overcome this limitation, we developed <em>FLEXR-MSA</em>, which enables unbiased electron-density map comparisons of sequence-diverse structures by coupling multiple sequence alignment (MSA) with electron-density sampling. <em>FLEXR-MSA</em> generates visualizations that pinpoint low-occupancy features on the residue level and chart them across the protein surface to reveal global changes. To exemplify the utility of this tool, we probed electron densities for protein-wide alternative conformations of HSP90 across four human isoforms and other homologs. Our analysis demonstrates that <em>FLEXR-MSA</em> can reveal hidden differences among HSP90 variants bound to clinically important ligands. Integrating this new functionality into the <em>FLEXR</em> suite of tools links the comparison of conformational landscapes hidden in electron-density maps to the building of multi-conformer models that reveal structural/functional differences that might be of interest when designing selective ligands.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 2","pages":"Pages 245-254"},"PeriodicalIF":2.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143515747","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":"On interrogating electron microscopy images to discover proteins in the cell","authors":"Jose-Maria Carazo","doi":"10.1107/S2052252525001861","DOIUrl":"10.1107/S2052252525001861","url":null,"abstract":"<div><div>Interrogating individual two-dimensional (2D) cryo-EM images for the presence of defined three-dimensional (3D) structures that correspond to previously known (or predicted) macromolecular complexes is very challenging, but offers attractive opportunities for the analysis of large numbers of specimens. The work of Zhang <em>et al.</em>[(2025), <em>IUCrJ</em>, <strong>12</strong>, 155–176] represents a significant step forward towards this goal.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 2","pages":"Pages 139-140"},"PeriodicalIF":2.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536953","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":"Combining experiment and prediction to explore surface chemistry and dissolution","authors":"Andrew G. P. Maloney","doi":"10.1107/S2052252525001782","DOIUrl":"10.1107/S2052252525001782","url":null,"abstract":"<div><div>A crystal structure is often an integral component in the development of a new pharmaceutical product, and these structures are frequently used to understand, assess and often predict both the manufacturing and <em>in vivo</em> behaviour of these compounds. Combining a range of analytical methods with computational analysis of the crystal surfaces, Zmeškalová <em>et al.</em> [(2025). <em>IUCrJ</em>, <strong>12</strong>, 141–154] link the properties of three solid forms of a biologically active molecule to its dissolution behaviour.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 2","pages":"Pages 137-138"},"PeriodicalIF":2.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143515745","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":"Single-shot X-ray imaging of two-dimensional strain fields in colloidal crystals","authors":"Jiecheng Diao ,&nbsp;Zichen Gao ,&nbsp;Jiadong Fan ,&nbsp;Yajun Tong ,&nbsp;Hang Ren ,&nbsp;Yonggan Nie ,&nbsp;Ian Robinson ,&nbsp;Huaidong Jiang","doi":"10.1107/S2052252524012521","DOIUrl":"10.1107/S2052252524012521","url":null,"abstract":"<div><div>We used the Bragg coherent diffraction imaging method at the Coherent Scattering and Imaging endstation of the Shanghai Soft X-ray Free Electron Laser Facility to characterize colloidal crystals. This method successfully reproduced the static shape of crystals and we observed the defect structure of colloidal samples.</div></div><div><div>We used a soft X-ray free-electron laser and the Bragg coherent diffraction imaging method to characterize the defect structure of colloidal crystals. The single-shot X-ray pulse allowed us to reach four powder rings and measured all six reflections of the hexagonal lattice. We reproduced the static shape of the 2D crystal and mapped out the 2D strain tensors inside the crystal. The observed defect structures agreed with electron microscope images of similar colloidal samples.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 2","pages":"Pages 239-244"},"PeriodicalIF":2.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143391038","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}