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Acta Crystallographica. Section D, Structural Biology最新文献

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Photosystem II: light-dependent oscillation of ligand composition at its active site. 光系统II:活性位点配体组成的光依赖性振荡。
IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-12-01 Epub Date: 2024-11-28 DOI: 10.1107/S2059798324011392
Jimin Wang

Recently, the conclusions drawn from crystallographic data about the number of oxygen ligands associated with the CaMn4 cofactor in the oxygen-evolving center (OEC) of Thermosynechococcus vulcanus photosystem II (PSII) have been called into question. Here, using OEC-omit, metal ion-omit and ligand-omit electron-density maps, it is shown that the number of oxygen ligands ranges from three in the functional OEC of monomer B following dark adaption (0F), i.e. in its ground state (PDB entry 6jlj/0F and PDB entry 6jlm/0F), to five for both monomers of PSII in photo-advanced states following exposure to one and two flashes of light. For a significant fraction of the 0F OECs in monomer A, the number is four (PDB entry 6jlj/0F). Following one flash it increases to five (PDB entry 6jlk/1F), where it remains after a second flash (PDB entry 6jlj/2F). Following a third flash (3F), it decreases to three (PDB entry 6jlp/3F), suggesting that an O2 molecule has been produced. These observations suggest a mechanism for the reaction that transforms the O atoms of the water molecules bound at the O3 and O1 sites of the OEC into O2.

最近,从热共生球菌光系统II (PSII)的氧进化中心(OEC)中与CaMn4辅因子相关的氧配体数量的晶体学数据得出的结论受到了质疑。在这里,使用OEC-省略,金属离子-省略和配体-省略电子密度图,表明氧配体的数量范围从暗适应(0F)后单体B的功能OEC中的3个,即在基态(PDB输入6jlj/0F和PDB输入6jlm/0F),到曝光一次和两次闪光后PSII的两个单体在光超前状态下的5个。对于单体a中很大一部分的0F oec,编号为4 (PDB条目6jlj/0F)。在一次闪光之后,它增加到五次(PDB条目6jlj/ 1F),在第二次闪光之后(PDB条目6jlj/2F),它保持不变。在第三次闪光(3F)之后,它减少到3次(PDB输入6jlp/3F),表明O2分子已经产生。这些观察结果提示了一种反应机制,该反应将OEC的O3和O1位点结合的水分子的O原子转化为O2。
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引用次数: 0
Improving macromolecular structure refinement with metal-coordination restraints. 利用金属配位约束改善大分子结构的细化。
IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-12-01 Epub Date: 2024-12-03 DOI: 10.1107/S2059798324011458
Kaveh H Babai, Fei Long, Martin Malý, Keitaro Yamashita, Garib N Murshudov

Metals are essential components for the structure and function of many proteins. However, accurate modelling of their coordination environments remains a challenge due to the complexity and diversity of metal-coordination geometries. To address this, a method is presented for extracting and analysing coordination information, including bond lengths and angles, from the Crystallography Open Database. By using these data, comprehensive descriptions of metal-containing components are generated. A stereochemical information generator for a particular component within a specific macromolecule leverages an example PDB/mmCIF file containing the component to account for the actual surrounding environment. A matching process has been developed and implemented to align the derived metal structures with idealized coordinates from a coordination geometry library. Additionally, various strategies, depending on the quality of the matches, were employed to compile distance and angle statistics for the refinement of macromolecular structures. The developed methods were implemented in a new program, MetalCoord, that classifies and utilizes the metal-coordination geometry. The effectiveness of the developed algorithms was tested using metal-containing components from the PDB. As a result, metal-containing components from the CCP4 monomer library have been updated. The updated monomer dictionaries, in concert with the derived restraints, can be used in most structural biology computations, including macromolecular crystallography, single-particle cryo-EM and even molecular mechanics.

金属是许多蛋白质的结构和功能的重要组成部分。然而,由于金属配位几何的复杂性和多样性,对其配位环境的精确建模仍然是一个挑战。为了解决这个问题,提出了一种从晶体学开放数据库中提取和分析配位信息的方法,包括键长和键角。利用这些数据,生成含金属构件的综合描述。特定大分子中特定组分的立体化学信息生成器利用包含该组分的示例PDB/mmCIF文件来解释实际的周围环境。开发并实现了一种匹配过程,将导出的金属结构与坐标几何库中的理想坐标对齐。此外,根据匹配的质量,采用各种策略来编制距离和角度统计数据,以改进大分子结构。开发的方法在一个新的程序MetalCoord中实现,该程序对金属配位几何进行分类和利用。使用PDB中的含金属组件测试了所开发算法的有效性。因此,CCP4单体库中的含金属组分已经更新。更新的单体字典,与衍生的约束相一致,可以用于大多数结构生物学计算,包括大分子晶体学,单粒子低温电镜,甚至分子力学。
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引用次数: 0
Peter Main (1939-2024). 彼得·梅因(1939-2024)。
IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-12-01 Epub Date: 2024-11-29 DOI: 10.1107/S2059798324010854
Eleanor Dodson, Kathryn Cowtan

Peter Main is remembered.

彼得·梅因被铭记。
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引用次数: 0
Everyone is using biological structures, but how does one find the structure(s) one wants? 每个人都在使用生物结构,但是如何找到自己想要的结构呢?
IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-12-01 Epub Date: 2024-12-05 DOI: 10.1107/S2059798324007848
Charles S Bond, Joel L Sussman

A comment on how easy (or difficult) it is to find a stucture of interest and some suggestions on what could be done to start to address the problem.

关于找到一个感兴趣的结构是多么容易(或困难)的评论,以及如何开始解决这个问题的一些建议。
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引用次数: 0
The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era. 分子置换中经过处理的预测模型的成功率:对 AlphaFold 时代实验分期的影响。
IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-01 Epub Date: 2024-10-03 DOI: 10.1107/S2059798324009380
Ronan M Keegan, Adam J Simpkin, Daniel J Rigden

The availability of highly accurate protein structure predictions from AlphaFold2 (AF2) and similar tools has hugely expanded the applicability of molecular replacement (MR) for crystal structure solution. Many structures can be solved routinely using raw models, structures processed to remove unreliable parts or models split into distinct structural units. There is therefore an open question around how many and which cases still require experimental phasing methods such as single-wavelength anomalous diffraction (SAD). Here, this question is addressed using a large set of PDB depositions that were solved by SAD. A large majority (87%) could be solved using unedited or minimally edited AF2 predictions. A further 18 (4%) yield straightforwardly to MR after splitting of the AF2 prediction using Slice'N'Dice, although different splitting methods succeeded on slightly different sets of cases. It is also found that further unique targets can be solved by alternative modelling approaches such as ESMFold (four cases), alternative MR approaches such as ARCIMBOLDO and AMPLE (two cases each), and multimeric model building with AlphaFold-Multimer or UniFold (three cases). Ultimately, only 12 cases, or 3% of the SAD-phased set, did not yield to any form of MR tested here, offering valuable hints as to the number and the characteristics of cases where experimental phasing remains essential for macromolecular structure solution.

AlphaFold2(AF2)和类似工具提供的高精度蛋白质结构预测极大地扩展了分子置换(MR)在晶体结构求解中的应用。许多结构可以使用原始模型、经过处理以去除不可靠部分的结构或拆分成不同结构单元的模型进行常规求解。因此,有多少结构和哪些结构仍然需要使用单波长反常衍射(SAD)等实验相位分析方法是一个未决问题。在此,我们使用大量通过 SAD 解决的 PDB 沉积物来解决这一问题。其中绝大多数(87%)可以使用未经编辑或编辑极少的 AF2 预测来求解。另外 18 个(4%)在使用 Slice'N'Dice 对 AF2 预测进行拆分后,直接产生了 MR,尽管不同的拆分方法成功的案例集略有不同。研究还发现,更多的独特目标可以通过其他建模方法(如 ESMFold,4 个案例)、其他 MR 方法(如 ARCIMBOLDO 和 AMPLE,各 2 个案例)以及使用 AlphaFold-Multimer 或 UniFold 建立多聚物模型(3 个案例)来解决。最终,只有 12 个案例(占 SAD 相位集的 3%)没有通过本文测试的任何形式的 MR,这对实验相位对于大分子结构求解仍然至关重要的案例数量和特征提供了宝贵的提示。
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引用次数: 0
Welcoming two new Co-editors. 欢迎两位新任联合编辑。
IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-01 Epub Date: 2024-11-06 DOI: 10.1107/S2059798324010350
Charles S Bond, Elspeth F Garman, Randy J Read

Two new Co-editors are welcomed to Acta Cryst. D - Structural Biology.

晶体学报》(Acta Cryst.D - 结构生物学。
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引用次数: 0
EMhub: a web platform for data management and on-the-fly processing in scientific facilities. EMhub:用于科学设施数据管理和即时处理的网络平台。
IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-01 Epub Date: 2024-10-07 DOI: 10.1107/S2059798324009471
Jose M de la Rosa-Trevin, Grigory Sharov, Stefan Fleischmann, Dustin Morado, John C Bollinger, Darcie J Miller, Daniel S Terry, Scott C Blanchard, Israel S Fernandez, Marta Carroni

Most scientific facilities produce large amounts of heterogeneous data at a rapid pace. Managing users, instruments, reports and invoices presents additional challenges. To address these challenges, EMhub, a web platform designed to support the daily operations and record-keeping of a scientific facility, has been introduced. EMhub enables the easy management of user information, instruments, bookings and projects. The application was initially developed to meet the needs of a cryoEM facility, but its functionality and adaptability have proven to be broad enough to be extended to other data-generating centers. The expansion of EMHub is enabled by the modular nature of its core functionalities. The application allows external processes to be connected via a REST API, automating tasks such as folder creation, user and password generation, and the execution of real-time data-processing pipelines. EMhub has been used for several years at the Swedish National CryoEM Facility and has been installed in the CryoEM center at the Structural Biology Department at St. Jude Children's Research Hospital. A fully automated single-particle pipeline has been implemented for on-the-fly data processing and analysis. At St. Jude, the X-Ray Crystallography Center and the Single-Molecule Imaging Center have already expanded the platform to support their operational and data-management workflows.

大多数科研机构都能快速生成大量异构数据。管理用户、仪器、报告和发票带来了额外的挑战。为应对这些挑战,EMhub 推出了一个网络平台,旨在支持科学设施的日常运作和记录保存。EMhub 可以轻松管理用户信息、仪器、预订和项目。该应用程序最初是为满足低温电子显微镜设施的需要而开发的,但其功能和适应性已被证明足以扩展到其他数据生成中心。EMHub 核心功能的模块化特性使其得以扩展。该应用程序允许通过 REST API 连接外部进程,自动执行文件夹创建、用户和密码生成以及实时数据处理管道执行等任务。EMhub 已在瑞典国家低温电子显微镜设施使用多年,并已安装在圣裘德儿童研究医院结构生物学部的低温电子显微镜中心。该系统采用了全自动单颗粒管道,可进行即时数据处理和分析。在圣裘德,X 射线晶体学中心和单分子成像中心已经扩展了该平台,以支持其操作和数据管理工作流程。
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引用次数: 0
Structural studies of β-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus. 嗜热细菌钙纤维糖苷酶β-葡萄糖苷酶的结构研究。
IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-01 DOI: 10.1107/S2059798324009252
Anastasia I Sotiropoulou, Dimitris G Hatzinikolaou, Evangelia D Chrysina

β-Glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus (Bgl1) has been denoted as having an attractive catalytic profile for various industrial applications. Bgl1 catalyses the final step of in the decomposition of cellulose, an unbranched glucose polymer that has attracted the attention of researchers in recent years as it is the most abundant renewable source of reduced carbon in the biosphere. With the aim of enhancing the thermostability of Bgl1 for a broad spectrum of biotechnological processes, it has been subjected to structural studies. Crystal structures of Bgl1 and its complex with glucose were determined at 1.47 and 1.95 Å resolution, respectively. Bgl1 is a member of glycosyl hydrolase family 1 (GH1 superfamily, EC 3.2.1.21) and the results showed that the 3D structure of Bgl1 follows the overall architecture of the GH1 family, with a classical (β/α)8 TIM-barrel fold. Comparisons of Bgl1 with sequence or structural homologues of β-glucosidase reveal quite similar structures but also unique structural features in Bgl1 with plausible functional roles.

嗜热细菌钙纤维糖苷酶(Caldicellulosiruptor saccharolyticus,Bgl1)的β-葡萄糖苷酶被认为在各种工业应用中具有诱人的催化特性。Bgl1 催化纤维素分解的最后一步,纤维素是一种未支链的葡萄糖聚合物,是生物圈中最丰富的可再生还原碳源,因此近年来引起了研究人员的关注。为了提高 Bgl1 在广泛的生物技术过程中的耐热性,我们对其进行了结构研究。分别以 1.47 和 1.95 Å 的分辨率测定了 Bgl1 及其与葡萄糖的复合物的晶体结构。Bgl1 是糖基水解酶家族 1(GH1 超家族,EC 3.2.1.21)的成员,研究结果表明 Bgl1 的三维结构遵循 GH1 家族的整体结构,具有经典的 (β/α)8 TIM 桶折叠。将 Bgl1 与 β-葡萄糖苷酶的序列或结构同源物进行比较发现,Bgl1 的结构十分相似,但也有独特的结构特征,并具有可信的功能作用。
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引用次数: 0
CHiMP: deep-learning tools trained on protein crystallization micrographs to enable automation of experiments. CHiMP:在蛋白质结晶显微照片上训练的深度学习工具,实现实验自动化。
IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-01 DOI: 10.1107/S2059798324009276
Oliver N F King, Karl E Levik, James Sandy, Mark Basham

A group of three deep-learning tools, referred to collectively as CHiMP (Crystal Hits in My Plate), were created for analysis of micrographs of protein crystallization experiments at the Diamond Light Source (DLS) synchrotron, UK. The first tool, a classification network, assigns images into categories relating to experimental outcomes. The other two tools are networks that perform both object detection and instance segmentation, resulting in masks of individual crystals in the first case and masks of crystallization droplets in addition to crystals in the second case, allowing the positions and sizes of these entities to be recorded. The creation of these tools used transfer learning, where weights from a pre-trained deep-learning network were used as a starting point and repurposed by further training on a relatively small set of data. Two of the tools are now integrated at the VMXi macromolecular crystallography beamline at DLS, where they have the potential to absolve the need for any user input, both for monitoring crystallization experiments and for triggering in situ data collections. The third is being integrated into the XChem fragment-based drug-discovery screening platform, also at DLS, to allow the automatic targeting of acoustic compound dispensing into crystallization droplets.

为了分析英国钻石光源(DLS)同步加速器蛋白质结晶实验的显微照片,我们创建了一组三个深度学习工具,统称为 CHiMP(Crystal Hits in My Plate)。第一个工具是一个分类网络,将图像分配到与实验结果相关的类别中。另外两个工具是同时执行对象检测和实例分割的网络,在第一种情况下可生成单个晶体的掩膜,在第二种情况下除晶体外还可生成结晶液滴的掩膜,从而记录这些实体的位置和大小。这些工具的创建使用了迁移学习,即以预先训练好的深度学习网络的权重为起点,通过在相对较小的数据集上进行进一步训练来重新使用。其中两个工具现已集成到 DLS 的 VMXi 大分子晶体学光束线,在那里,无论是监测结晶实验还是触发原位数据收集,它们都有可能免除用户输入的需要。第三个系统正在被集成到同样位于 DLS 的 XChem 片段药物发现筛选平台中,以便将声学化合物自动分配到结晶液滴中。
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引用次数: 0
Robust and automatic beamstop shadow outlier rejection: combining crystallographic statistics with modern clustering under a semi-supervised learning strategy. 稳健而自动的光束止影异常点剔除:在半监督学习策略下将晶体学统计与现代聚类相结合。
IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-01 DOI: 10.1107/S2059798324008519
Yunyun Gao, Helen M Ginn, Andrea Thorn

During the automatic processing of crystallographic diffraction experiments, beamstop shadows are often unaccounted for or only partially masked. As a result of this, outlier reflection intensities are integrated, which is a known issue. Traditional statistical diagnostics have only limited effectiveness in identifying these outliers, here termed Not-Excluded-unMasked-Outliers (NEMOs). The diagnostic tool AUSPEX allows visual inspection of NEMOs, where they form a typical pattern: clusters at the low-resolution end of the AUSPEX plots of intensities or amplitudes versus resolution. To automate NEMO detection, a new algorithm was developed by combining data statistics with a density-based clustering method. This approach demonstrates a promising performance in detecting NEMOs in merged data sets without disrupting existing data-reduction pipelines. Re-refinement results indicate that excluding the identified NEMOs can effectively enhance the quality of subsequent structure-determination steps. This method offers a prospective automated means to assess the efficacy of a beamstop mask, as well as highlighting the potential of modern pattern-recognition techniques for automating outlier exclusion during data processing, facilitating future adaptation to evolving experimental strategies.

在晶体学衍射实验的自动处理过程中,光束止点的阴影经常被忽略或仅被部分遮挡。因此,异常反射强度会被整合进来,这是一个已知的问题。传统的统计诊断方法在识别这些异常值(这里称为未排除-未掩蔽-异常值(NEMOs))方面效果有限。诊断工具 AUSPEX 可以对 NEMOs 进行目视检查,NEMOs 在这里形成一种典型模式:在 AUSPEX 强度或振幅与分辨率关系图的低分辨率端形成群集。为了自动检测 NEMO,我们开发了一种新算法,将数据统计与基于密度的聚类方法相结合。这种方法在检测合并数据集中的 NEMO 方面表现出良好的性能,而且不会破坏现有的数据还原管道。再提纯结果表明,排除已识别的 NEMO 可有效提高后续结构确定步骤的质量。该方法提供了一种评估光束阻挡掩膜有效性的前瞻性自动化手段,同时也突出了现代模式识别技术在数据处理过程中自动排除离群点的潜力,便于未来适应不断发展的实验策略。
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引用次数: 0
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Acta Crystallographica. Section D, Structural Biology
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