Acta Crystallographica Section D最新文献

Structural characterization of the ACDC domain from ApiAP2 proteins, a potential molecular target against apicomplexan parasites.

Acta Crystallographica Section D Pub Date : 2025-01-01 DOI: 10.1107/s2059798324012518

Marine Le Berre,Thibault Tubiana,Philippa Reuterswärd Waldner,Noureddine Lazar,Ines Li de la Sierra-Gallay,Joana M Santos,Manuel Llinás,Sylvie Nessler

引用次数: 0

Structure and stability of an apo thermophilic esterase that hydrolyzes polyhydroxybutyrate. 水解多羟丁酸的嗜热酯酶的结构和稳定性。

Acta Crystallographica Section D Pub Date : 2024-11-01 DOI: 10.1107/s2059798324009707

Gwendell M Thomas,Stephen Quirk,Raquel L Lieberman

{"title":"Structure and stability of an apo thermophilic esterase that hydrolyzes polyhydroxybutyrate.","authors":"Gwendell M Thomas,Stephen Quirk,Raquel L Lieberman","doi":"10.1107/s2059798324009707","DOIUrl":"https://doi.org/10.1107/s2059798324009707","url":null,"abstract":"Pollution from plastics is a global problem that threatens the biosphere for a host of reasons, including the time scale that it takes for most plastics to degrade. Biodegradation is an ideal solution for remediating bioplastic waste as it does not require the high temperatures necessary for thermal degradation and does not introduce additional pollutants into the environment. Numerous organisms can scavenge for bioplastics, such as polylactic acid (PLA) or poly-(R)-hydroxybutyrate (PHB), which they can use as an energy source. Recently, a promiscuous PHBase from the thermophilic soil bacterium Lihuaxuella thermophila (LtPHBase) was identified. LtPHBase can accommodate many substrates, including PHB granules and films and PHB block copolymers, as well as the unrelated polymers polylactic acid (PLA) and polycaprolactone (PCL). LtPHBase uses the expected Ser-His-Asp catalytic triad for hydrolysis at an optimal enzyme activity near 70°C. Here, the 1.75 Å resolution crystal structure of apo LtPHBase is presented and its chemical stability is profiled. Knowledge of its substrate preferences was extended to different-sized PHB granules. It is shown that LtPHBase is highly resistant to unfolding, with barriers typical for thermophilic enzymes, and shows a preference for low-molecular-mass PHB granules. These insights have implications for the long-term potential of LtPHBase as an industrial PHB hydrolase and shed light on the evolutionary role that this enzyme plays in bacterial metabolism.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"235 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142488228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Analysis of crystallographic phase retrieval using iterative projection algorithms. 使用迭代投影算法的晶体学相位检索分析。

Acta Crystallographica Section D Pub Date : 2024-11-01 DOI: 10.1107/s2059798324009902

Michael J Barnett,Rick P Millane,Richard L Kingston

{"title":"Analysis of crystallographic phase retrieval using iterative projection algorithms.","authors":"Michael J Barnett,Rick P Millane,Richard L Kingston","doi":"10.1107/s2059798324009902","DOIUrl":"https://doi.org/10.1107/s2059798324009902","url":null,"abstract":"For protein crystals in which more than two thirds of the volume is occupied by solvent, the featureless nature of the solvent region often generates a constraint that is powerful enough to allow direct phasing of X-ray diffraction data. Practical implementation relies on the use of iterative projection algorithms with good global convergence properties to solve the difficult nonconvex phase-retrieval problem. In this paper, some aspects of phase retrieval using iterative projection algorithms are systematically explored, where the diffraction data and density-value distributions in the protein and solvent regions provide the sole constraints. The analysis is based on the addition of random error to the phases of previously determined protein crystal structures, followed by evaluation of the ability to recover the correct phase set as the distance from the solution increases. The properties of the difference-map (DM), relaxed-reflect-reflect (RRR) and relaxed averaged alternating reflectors (RAAR) algorithms are compared. All of these algorithms prove to be effective for crystallographic phase retrieval, and the useful ranges of the adjustable parameter which controls their behavior are established. When these algorithms converge to the solution, the algorithm trajectory becomes stationary; however, the density function continues to fluctuate significantly around its mean position. It is shown that averaging over the algorithm trajectory in the stationary region, following convergence, improves the density estimate, with this procedure outperforming previous approaches for phase or density refinement.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142488227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Utilizing anomalous signals for element identification in macromolecular crystallography. 利用异常信号识别大分子晶体学中的元素。

Acta Crystallographica Section D Pub Date : 2024-10-01 DOI: 10.1107/s2059798324008659

Kamel El Omari,Ismay Forsyth,Ramona Duman,Christian M Orr,Vitaliy Mykhaylyk,Erika J Mancini,Armin Wagner

{"title":"Utilizing anomalous signals for element identification in macromolecular crystallography.","authors":"Kamel El Omari,Ismay Forsyth,Ramona Duman,Christian M Orr,Vitaliy Mykhaylyk,Erika J Mancini,Armin Wagner","doi":"10.1107/s2059798324008659","DOIUrl":"https://doi.org/10.1107/s2059798324008659","url":null,"abstract":"AlphaFold2 has revolutionized structural biology by offering unparalleled accuracy in predicting protein structures. Traditional methods for determining protein structures, such as X-ray crystallography and cryo-electron microscopy, are often time-consuming and resource-intensive. AlphaFold2 provides models that are valuable for molecular replacement, aiding in model building and docking into electron density or potential maps. However, despite its capabilities, models from AlphaFold2 do not consistently match the accuracy of experimentally determined structures, need to be validated experimentally and currently miss some crucial information, such as post-translational modifications, ligands and bound ions. In this paper, the advantages are explored of collecting X-ray anomalous data to identify chemical elements, such as metal ions, which are key to understanding certain structures and functions of proteins. This is achieved through methods such as calculating anomalous difference Fourier maps or refining the imaginary component of the anomalous scattering factor f''. Anomalous data can serve as a valuable complement to the information provided by AlphaFold2 models and this is particularly significant in elucidating the roles of metal ions.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142245298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microcrystal electron diffraction structure of Toll-like receptor 2 TIR-domain-nucleated MyD88 TIR-domain higher-order assembly. Toll-like receptor 2 TIR-domain-nucleated MyD88 TIR-domain higher-order assembly 的微晶电子衍射结构。

Acta Crystallographica Section D Pub Date : 2024-09-04 DOI: 10.1107/s2059798324008210

Y Li,L C Pacoste,W Gu,S J Thygesen,K J Stacey,T Ve,B Kobe,H Xu,J D Nanson

{"title":"Microcrystal electron diffraction structure of Toll-like receptor 2 TIR-domain-nucleated MyD88 TIR-domain higher-order assembly.","authors":"Y Li,L C Pacoste,W Gu,S J Thygesen,K J Stacey,T Ve,B Kobe,H Xu,J D Nanson","doi":"10.1107/s2059798324008210","DOIUrl":"https://doi.org/10.1107/s2059798324008210","url":null,"abstract":"Eukaryotic TIR (Toll/interleukin-1 receptor protein) domains signal via TIR-TIR interactions, either by self-association or by interaction with other TIR domains. In mammals, TIR domains are found in Toll-like receptors (TLRs) and cytoplasmic adaptor proteins involved in pro-inflammatory signaling. Previous work revealed that the MAL TIR domain (MALTIR) nucleates the assembly of MyD88TIR into crystalline arrays in vitro. A microcrystal electron diffraction (MicroED) structure of the MyD88TIR assembly has previously been solved, revealing a two-stranded higher-order assembly of TIR domains. In this work, it is demonstrated that the TIR domain of TLR2, which is reported to signal as a heterodimer with either TLR1 or TLR6, induces the formation of crystalline higher-order assemblies of MyD88TIR in vitro, whereas TLR1TIR and TLR6TIR do not. Using an improved data-collection protocol, the MicroED structure of TLR2TIR-induced MyD88TIR microcrystals was determined at a higher resolution (2.85 Å) and with higher completeness (89%) compared with the previous structure of the MALTIR-induced MyD88TIR assembly. Both assemblies exhibit conformational differences in several areas that are important for signaling (for example the BB loop and CD loop) compared with their monomeric structures. These data suggest that TLR2TIR and MALTIR interact with MyD88 in an analogous manner during signaling, nucleating MyD88TIR assemblies unidirectionally.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"4 1","pages":"699-712"},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

STOPGAP: an open-source package for template matching, subtomogram alignment and classification STOPGAP：用于模板匹配、子图配准和分类的开源软件包

Acta Crystallographica Section D Pub Date : 2024-04-12 DOI: 10.1107/s205979832400295x

Wan, W., Khavnekar, S., Wagner, J.

引用次数: 0

HEIDI: an experiment-management platform enabling high-throughput fragment and compound screening HEIDI：实现高通量片段和化合物筛选的实验管理平台

Acta Crystallographica Section D Pub Date : 2024-04-12 DOI: 10.1107/s2059798324002833

Metz, A., Stegmann, D.P., Panepucci, E.H., Buehlmann, S., Huang, C.-Y., McAuley, K.E., Wang, M., Wojdyla, J.A., Sharpe, M.E., Smith, K.M.L.

引用次数: 0

Scaling and merging macromolecular diffuse scattering with mdx2 用 mdx2 对大分子漫散射进行缩放与合并

Acta Crystallographica Section D Pub Date : 2024-04-12 DOI: 10.1107/s2059798324002705

Meisburger, S.P., Ando, N.

引用次数: 0

EMinsight: a tool to capture cryoEM microscope configuration and experimental outcomes for analysis and deposition EMinsight：捕捉冷冻电镜显微镜配置和实验结果以进行分析和沉积的工具

Acta Crystallographica Section D Pub Date : 2024-03-26 DOI: 10.1107/s2059798324001578

Hatton, D., Cha, J., Riggs, S., Harrison, P.J., Thiyagalingam, J., Clare, D.K., Morris, K.L.

引用次数: 0

From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons 从飞秒到分钟：在 XFEL 和同步加速器上进行时间分辨大分子晶体学研究

Acta Crystallographica Section D Pub Date : 2024-01-24 DOI: 10.1107/s2059798323011002

Caramello, N., Royant, A.

引用次数: 0