Journal of Applied Crystallography最新文献_第2页

IF 5.2 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-05-29

引用次数: 0

Efficient analysis of small-angle scattering curves for large biomolecular assemblies using Monte Carlo methods 利用蒙特卡罗方法对大型生物分子组装体的小角散射曲线进行有效分析

IF 5.2 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-05-23 DOI: 10.1107/S1600576725003267

Huat Thart Chiang, Zhiyin Zhang, Kiran Vaddi, F. Akif Tezcan, Lilo D. Pozzo

{"title":"Efficient analysis of small-angle scattering curves for large biomolecular assemblies using Monte Carlo methods","authors":"Huat Thart Chiang, Zhiyin Zhang, Kiran Vaddi, F. Akif Tezcan, Lilo D. Pozzo","doi":"10.1107/S1600576725003267","DOIUrl":"https://doi.org/10.1107/S1600576725003267","url":null,"abstract":"Structure elucidation from small-angle scattering curves of large biomolecular assemblies is notoriously challenging. This is because the simulation of high-resolution features in the structure of large macromolecular assemblies, such as de novo protein assemblies, is computationally demanding when it needs to cover a broad range of length scales. Conventional methods, such as the numerical approximation to the Debye equation or the use of spherical harmonics, do not scale well as the size of the assembly increases, which limits their application to small structures (e.g. individual proteins). This work explores the effectiveness of a Monte Carlo method to simulate and fit scattering curves for large biomolecular assemblies spanning over ranges covering atomic and molecular detail (e.g. spacing and orientation of proteins in an assembly) as well as large-scale (hundreds of nanometres) features. Owing to its speed and scalability, it can be combined with a fitting algorithm to extract structural features from experimental small-angle scattering curves in biomolecular assemblies that are otherwise intractable for interpretation. This work first demonstrates the effectiveness of the tool using experimental small-angle X-ray scattering (SAXS) data from tile-like proteins that assemble into 1D tube-like macromolecular structures. The diameter distribution of tubes is extracted from SAXS fits, and this is quantitatively compared with distributions from electron microscopy. SAXS data are also obtained from 2D sheet-like protein assemblies, and the proposed method is used to quantify structural features such as the separation distance between protein building blocks and the flexing of the sheet. An open-source implementation of the methodology is provided for use in a broad range of biological systems involving multi-scale scattering analysis.","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 3","pages":"963-975"},"PeriodicalIF":5.2,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144206541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Elongated particles in flow: commentary on small-angle scattering investigations 流动中的细长粒子：对小角散射研究的评论

IF 5.2 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-05-23 DOI: 10.1107/S1600576725002900

Guan-Rong Huang, Lionel Porcar, Ryan P. Murphy, Yuya Shinohara, Yangyang Wang, Jan-Michael Carrillo, Bobby G. Sumpter, Chi-Huan Tung, Lijie Ding, Changwoo Do, Wei-Ren Chen

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IF 5.2 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-05-23

引用次数: 0

IGUAPE, a graphical user interface for in situ/operando X-ray diffraction experiments at the PAINEIRA beamline: development and application IGUAPE，用于PAINEIRA光束线上的原位/操作x射线衍射实验的图形用户界面：开发和应用

IF 5.2 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-05-23 DOI: 10.1107/S1600576725003309

João L. Biondo Neto, Junior Cintra Mauricio, Cristiane B. Rodella

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IF 5.2 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-05-12

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Modeling small-angle X-ray scattering in quiescently crystallized polymers in the absence of long-period dispersity 在不存在长周期分散性的情况下，静态结晶聚合物的小角度x射线散射建模

IF 5.2 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-05-12 DOI: 10.1107/S1600576725002705

Xiangyang Li, Jianjun Ding, Lin Chen, Xingyou Tian

{"title":"Modeling small-angle X-ray scattering in quiescently crystallized polymers in the absence of long-period dispersity","authors":"Xiangyang Li, Jianjun Ding, Lin Chen, Xingyou Tian","doi":"10.1107/S1600576725002705","DOIUrl":"https://doi.org/10.1107/S1600576725002705","url":null,"abstract":"To explain the single and wide first-order long-period peak observed in semicrystalline polymers, classical small-angle X-ray scattering (SAXS) theory regards the dispersity in lamellar thickness/long period as the key structural feature of semicrystalline polymers. Other factors affecting the SAXS pattern such as the lateral size of a lamellar stack, the number of lamellar crystals in a stack and linear crystallinity have been overlooked as secondary factors, preventing structure extraction from SAXS. In this study, we attempted to establish a scattering equation for semicrystalline polymers formed during quiescent crystallization without considering dispersity in the long period/lamellar thickness. The results indicate that the lateral size is the key factor leading to the unique SAXS pattern in semicrystalline polymers and the absence of the linear region in the correlation function. SAXS in semicrystalline polymers results from minor lamellar stacks with small intersection angles with the incident X-rays. On the basis of the results, we suggest employing a revised interface distribution function to obtain structural information after recovering higher-order weak long-period peaks by a difference method. Half of the q4 correction is to eliminate the influence of the form factor, while the other half is to remove the factor of 1/q2 in the structure factor. This study helps to further our understanding of SAXS in semicrystalline polymers.","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 3","pages":"948-962"},"PeriodicalIF":5.2,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144206708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

IF 5.2 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-05-12

引用次数: 0

IF 5.2 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-05-12

引用次数: 0

IF 5.2 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-05-12

引用次数: 0