Acta Crystallographica. Section D, Structural Biology最新文献_第3页

Managing macromolecular crystallographic data with a laboratory information management system. 利用实验室信息管理系统管理大分子晶体学数据。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-08-01 Epub Date: 2024-07-10 DOI: 10.1107/S2059798324005680

Edward Daniel, Rik K Wierenga, Lari Lehtiö

{"title":"Managing macromolecular crystallographic data with a laboratory information management system.","authors":"Edward Daniel, Rik K Wierenga, Lari Lehtiö","doi":"10.1107/S2059798324005680","DOIUrl":"10.1107/S2059798324005680","url":null,"abstract":"Protein crystallography is an established method to study the atomic structures of macromolecules and their complexes. A prerequisite for successful structure determination is diffraction-quality crystals, which may require extensive optimization of both the protein and the conditions, and hence projects can stretch over an extended period, with multiple users being involved. The workflow from crystallization and crystal treatment to deposition and publication is well defined, and therefore an electronic laboratory information management system (LIMS) is well suited to management of the data. Completion of the project requires key information on all the steps being available and this information should also be made available according to the FAIR principles. As crystallized samples are typically shipped between facilities, a key feature to be captured in the LIMS is the exchange of metadata between the crystallization facility of the home laboratory and, for example, synchrotron facilities. On completion, structures are deposited in the Protein Data Bank (PDB) and the LIMS can include the PDB code in its database, completing the chain of custody from crystallization to structure deposition and publication. A LIMS designed for macromolecular crystallography, IceBear, is available as a standalone installation and as a hosted service, and the implementation of key features for the capture of metadata in IceBear is discussed as an example.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"580-587"},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11301755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141562411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystal structure of glycerol kinase from Trypanosoma cruzi, a potential molecular target in Chagas disease. 南美锥虫甘油激酶的晶体结构，它是南美锥虫病的潜在分子靶标。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-08-01 Epub Date: 2024-07-25 DOI: 10.1107/S2059798324006594

Oskar Lipiński, Ravi R Sonani, Grzegorz Dubin

引用次数: 0

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX. ChimeraX 中基于似然法的低温电子显微镜图交互式局部对接。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-08-01 Epub Date: 2024-07-26 DOI: 10.1107/S2059798324006776

Randy J Read, Eric F Pettersen, Airlie J McCoy, Tristan I Croll, Thomas C Terwilliger, Billy K Poon, Elaine C Meng, Dorothee Liebschner, Paul D Adams

{"title":"Likelihood-based interactive local docking into cryo-EM maps in ChimeraX.","authors":"Randy J Read, Eric F Pettersen, Airlie J McCoy, Tristan I Croll, Thomas C Terwilliger, Billy K Poon, Elaine C Meng, Dorothee Liebschner, Paul D Adams","doi":"10.1107/S2059798324006776","DOIUrl":"10.1107/S2059798324006776","url":null,"abstract":"The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"588-598"},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11301754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystal-packing analysis of translation initiation factor 2 reveals new details of its function. 翻译启动因子 2 的晶体堆积分析揭示了其功能的新细节。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-07-01 Epub Date: 2024-06-07 DOI: 10.1107/S2059798324004029

O S Nikonov, E Y Nikonova, N V Lekontseva, N A Nevskaya, S V Nikonov

引用次数: 0

Validation of electron-microscopy maps using solution small-angle X-ray scattering. 利用溶液小角 X 射线散射验证电子显微镜图。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-07-01 Epub Date: 2024-06-27 DOI: 10.1107/S2059798324005497

Kristian Lytje, Jan Skov Pedersen

{"title":"Validation of electron-microscopy maps using solution small-angle X-ray scattering.","authors":"Kristian Lytje, Jan Skov Pedersen","doi":"10.1107/S2059798324005497","DOIUrl":"10.1107/S2059798324005497","url":null,"abstract":"The determination of the atomic resolution structure of biomacromolecules is essential for understanding details of their function. Traditionally, such a structure determination has been performed with crystallographic or nuclear resonance methods, but during the last decade, cryogenic transmission electron microscopy (cryo-TEM) has become an equally important tool. As the blotting and flash-freezing of the samples can induce conformational changes, external validation tools are required to ensure that the vitrified samples are representative of the solution. Although many validation tools have already been developed, most of them rely on fully resolved atomic models, which prevents early screening of the cryo-TEM maps. Here, a novel and automated method for performing such a validation utilizing small-angle X-ray scattering measurements, publicly available through the new software package AUSAXS, is introduced and implemented. The method has been tested on both simulated and experimental data, where it was shown to work remarkably well as a validation tool. The method provides a dummy atomic model derived from the EM map which best represents the solution structure.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"493-505"},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A structural role for tryptophan in proteins, and the ubiquitous Trp C^δ1-H...O=C (backbone) hydrogen bond. 色氨酸在蛋白质中的结构作用，以及无处不在的 Trp Cδ1-H...O=C （骨架）氢键。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-07-01 Epub Date: 2024-06-28 DOI: 10.1107/S2059798324005515

Michal Szczygiel, Urszula Derewenda, Steve Scheiner, Wladek Minor, Zygmunt S Derewenda

{"title":"A structural role for tryptophan in proteins, and the ubiquitous Trp Cδ1-H...O=C (backbone) hydrogen bond.","authors":"Michal Szczygiel, Urszula Derewenda, Steve Scheiner, Wladek Minor, Zygmunt S Derewenda","doi":"10.1107/S2059798324005515","DOIUrl":"10.1107/S2059798324005515","url":null,"abstract":"Tryptophan is the most prominent amino acid found in proteins, with multiple functional roles. Its side chain is made up of the hydrophobic indole moiety, with two groups that act as donors in hydrogen bonds: the Nϵ-H group, which is a potent donor in canonical hydrogen bonds, and a polarized Cδ1-H group, which is capable of forming weaker, noncanonical hydrogen bonds. Due to adjacent electron-withdrawing moieties, C-H...O hydrogen bonds are ubiquitous in macromolecules, albeit contingent on the polarization of the donor C-H group. Consequently, Cα-H groups (adjacent to the carbonyl and amino groups of flanking peptide bonds), as well as the Cϵ1-H and Cδ2-H groups of histidines (adjacent to imidazole N atoms), are known to serve as donors in hydrogen bonds, for example stabilizing parallel and antiparallel β-sheets. However, the nature and the functional role of interactions involving the Cδ1-H group of the indole ring of tryptophan are not well characterized. Here, data mining of high-resolution (r ≤ 1.5 Å) crystal structures from the Protein Data Bank was performed and ubiquitous close contacts between the Cδ1-H groups of tryptophan and a range of electronegative acceptors were identified, specifically main-chain carbonyl O atoms immediately upstream and downstream in the polypeptide chain. The stereochemical analysis shows that most of the interactions bear all of the hallmarks of proper hydrogen bonds. At the same time, their cohesive nature is confirmed by quantum-chemical calculations, which reveal interaction energies of 1.5-3.0 kcal mol-1, depending on the specific stereochemistry.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"551-562"},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220837/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Factors affecting macromolecule orientations in thin films formed in cryo-EM. 影响冷冻电镜形成的薄膜中大分子取向的因素。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-07-01 Epub Date: 2024-06-27 DOI: 10.1107/S2059798324005229

Swati Yadav, Kutti R Vinothkumar

{"title":"Factors affecting macromolecule orientations in thin films formed in cryo-EM.","authors":"Swati Yadav, Kutti R Vinothkumar","doi":"10.1107/S2059798324005229","DOIUrl":"10.1107/S2059798324005229","url":null,"abstract":"The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air-water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of selected well studied macromolecules, and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of the interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and to provide a framework to design small-molecule additives to enhance sample stability and behaviour.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"535-550"},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deep-learning map segmentation for protein X-ray crystallographic structure determination. 用于蛋白质 X 射线晶体学结构测定的深度学习地图分割。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-07-01 Epub Date: 2024-06-27 DOI: 10.1107/S2059798324005217

Pavol Skubák

引用次数: 0

The crystal structure of the N-terminal domain of the backbone pilin LrpA reveals a new closure-and-twist motion for assembling dynamic pili in Ligilactobacillus ruminis. 骨干纤毛虫 LrpA N 端结构域的晶体结构揭示了反刍利格氏乳杆菌组装动态纤毛虫的一种新的闭合-扭转运动。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-07-01 Epub Date: 2024-06-27 DOI: 10.1107/S2059798324005114

Amar Prajapati, Airi Palva, Ingemar von Ossowski, Vengadesan Krishnan

{"title":"The crystal structure of the N-terminal domain of the backbone pilin LrpA reveals a new closure-and-twist motion for assembling dynamic pili in Ligilactobacillus ruminis.","authors":"Amar Prajapati, Airi Palva, Ingemar von Ossowski, Vengadesan Krishnan","doi":"10.1107/S2059798324005114","DOIUrl":"10.1107/S2059798324005114","url":null,"abstract":"Sortase-dependent pili are long surface appendages that mediate attachment, colonization and biofilm formation in certain genera and species of Gram-positive bacteria. Ligilactobacillus ruminis is an autochthonous gut commensal that relies on sortase-dependent LrpCBA pili for host adherence and persistence. X-ray crystal structure snapshots of the backbone pilin LrpA were captured in two atypical bent conformations leading to a zigzag morphology in the LrpCBA pilus structure. Small-angle X-ray scattering and structural analysis revealed that LrpA also adopts the typical linear conformation, resulting in an elongated pilus morphology. Various conformational analyses and biophysical experiments helped to demonstrate that a hinge region located at the end of the flexible N-terminal domain of LrpA facilitates a new closure-and-twist motion for assembling dynamic pili during the assembly process and host attachment. Further, the incongruent combination of flexible domain-driven conformational dynamics and rigid isopeptide bond-driven stability observed in the LrpCBA pilus might also extend to the sortase-dependent pili of other bacteria colonizing a host.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"474-492"},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Towards a dependable data set of structures for L-asparaginase research. 为 L-天冬酰胺酶研究建立可靠的结构数据集。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-07-01 Epub Date: 2024-06-27 DOI: 10.1107/S2059798324005461

Alexander Wlodawer, Zbigniew Dauter, Jacek Lubkowski, Joanna I Loch, Dariusz Brzezinski, Miroslaw Gilski, Mariusz Jaskolski

{"title":"Towards a dependable data set of structures for L-asparaginase research.","authors":"Alexander Wlodawer, Zbigniew Dauter, Jacek Lubkowski, Joanna I Loch, Dariusz Brzezinski, Miroslaw Gilski, Mariusz Jaskolski","doi":"10.1107/S2059798324005461","DOIUrl":"10.1107/S2059798324005461","url":null,"abstract":"The Protein Data Bank (PDB) includes a carefully curated treasury of experimentally derived structural data on biological macromolecules and their various complexes. Such information is fundamental for a multitude of projects that involve large-scale data mining and/or detailed evaluation of individual structures of importance to chemistry, biology and, most of all, to medicine, where it provides the foundation for structure-based drug discovery. However, despite extensive validation mechanisms, it is almost inevitable that among the ∼215 000 entries there will occasionally be suboptimal or incorrect structure models. It is thus vital to apply careful verification procedures to those segments of the PDB that are of direct medicinal interest. Here, such an analysis was carried out for crystallographic models of L-asparaginases, enzymes that include approved drugs for the treatment of certain types of leukemia. The focus was on the adherence of the atomic coordinates to the rules of stereochemistry and their agreement with the experimental electron-density maps. Whereas the current clinical application of L-asparaginases is limited to two bacterial proteins and their chemical modifications, the field of investigations of such enzymes has expanded tremendously in recent years with the discovery of three entirely different structural classes and with numerous reports, not always quite reliable, of the anticancer properties of L-asparaginases of different origins.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"506-527"},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0