Acta Crystallographica Section A Foundations and Advances最新文献_第4页

Group II intron splicing mechanisms – ribozymes and retrotransposons 第二类内含子剪接机制--核酶和反转座子

Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323097395

Ling Xu, Kevin Chung, Tianshuo Liu, Pengxin Chai, Junhui Peng, Swapnil Devarkar, A. Pyle

引用次数: 0

Realizing autonomous, real-time, AI-driven multimodal studies at X-ray light sources 在 X 射线光源上实现自主、实时、人工智能驱动的多模态研究

Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323097887

Daniel Olds, Phil Maffettone, Bruce Ravel, Thomas Caswell, Stuart Campbell, H. Joress

引用次数: 0

Structural and functional divergence of a 'new' class of phosphoenolpyruvate carboxykinase – insights into allosteric regulation via oligomeric changes 一类 "新 "磷酸烯醇丙酮酸羧激酶的结构和功能差异--通过低聚物变化了解异构调节

Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323099801

M. Mcleod, Siddhi Balamurali, Robert Thorne, T. Holyoak

{"title":"Structural and functional divergence of a 'new' class of phosphoenolpyruvate carboxykinase – insights into allosteric regulation via oligomeric changes","authors":"M. Mcleod, Siddhi Balamurali, Robert Thorne, T. Holyoak","doi":"10.1107/s2053273323099801","DOIUrl":"https://doi.org/10.1107/s2053273323099801","url":null,"abstract":"Phosphoenolpyruvate carboxykinases (PEPCK) are metabolic enzymes controlling the TCA - cycle. They have been implicated as potential targets in treating diabetes, cancer, and Mycobacterium tuberculosis infections, and have a role in aging and longevity. These enzymes interconvert oxaloacetic acid (OAA) to form phosphoenolpyruvate (PEP). PEPCKs are widely distributed across life and occur in three classes depending on the nature of phosphoryl donor used for their catalyzed reactions. Of the three classes, the most understudied are PPi-dependent PEPCKs, which are structurally and functionally distinct from the nucleotide -using classes (GTP and ATP). PPi-dependent PEPCKs have a conserved core (~60 kDa) that comprises the general fold of both nucleotide-dependent classes. However, their structure has signiﬁcant additions (~70 kDa) that form allosteric sites and oligomeric interfaces, and that have likely l ed to divergent functional properties. Here we have used size-exclusion chromatography, enzyme kinetics, crystallography and small-angle x-ray scattering to understand the structural and functional aspects of three PPi - dependent PEPCK isozymes. Actinomyces israelii PPi-dependent PEPCK is found as a constitutive dimer with signiﬁcantly reduced activity. Propionibacterium freudenreichii (Pf - PPi-PEPCK) diﬀers from its nucleotide counterparts in its enzyme - catalyzed reaction, metal - dependencies, and alloste rically induced activity - regulation via monomer - dimer transition. The third isozyme is from the human parasite Entamoeba histolytica (Eh-PPi-PEPCK). Eh-PPi-PEPCK occurs in three paralogs with diﬀerent sequences,","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"26 11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361447","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

Recent development of operando neutron diffraction and its application in studying energy storage materials 操作中子衍射的最新发展及其在储能材料研究中的应用

Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323097760

Jue Liu, Zhijia Du, Michelle Everrett

引用次数: 0

Disruption of a key hydrogen-bond network dissociates glucocorticoid receptor-mediated drug efficacy from side effects for anti-inflammation treatment 关键氢键网络的破坏使糖皮质激素受体介导的药物疗效与抗炎治疗的副作用相分离

Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323099989

Xu Liu

引用次数: 0

Novel macrocyclic antibiotic structure targeting BamA against gram-negative pathogens 针对革兰氏阴性病原体的 BamA 的新型大环抗生素结构

Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323097413

Byung-Kuk Yoo, Ryan Miller, Sarah Bowman, Douglas Rees, Kim Lewis

{"title":"Novel macrocyclic antibiotic structure targeting BamA against gram-negative pathogens","authors":"Byung-Kuk Yoo, Ryan Miller, Sarah Bowman, Douglas Rees, Kim Lewis","doi":"10.1107/s2053273323097413","DOIUrl":"https://doi.org/10.1107/s2053273323097413","url":null,"abstract":"Discovery of antibiotics against Gram - negative species is uniquely challenging due to their restrictive penetration barrier. BamA, which assists in folding and insertion of proteins into the outer membrane, is an attractive target because of its surface location, exposed to the extracellular environment. In this study, we identify dynobactin A, a novel peptide antibiotic from Photorhabdus australis which targets BamA, and unveil two unique unlinked rings by cryogenic electron micros copy. a The novel compound is the ﬁ rst natural product antibiotic of unknown structure solved de novo by this approach (PDB 7T3H). It is a decapeptide of sequence W1 N 2 S3N4 V5H6 S7Y 8 R 9F10, which has two closed rings: 1) a carbon-carbon bond formed between the Trp1 C 6 and the β -carbon of Asn 4 (green box) and 2) an unusual nitrogen-carbon linkage between the His6 imidazole Nε2 and the β - carbon of Tyr8 (orange box). These connections create unfused 4-and 3-constituent rings respectively, resulting in a ﬂ exible peptide, contrasting the fused rings of darobactins. Dynobactin A is one example of natural -product antibiotics acting against the outer membrane protein of Gram - negative bacteria. This study demonstrates how electron microscope accelerates antibiotic discovery by providing unambiguous structures from submicron-sized crystals.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361467","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

Novel manganese halide 2D, 1D and 0D frameworks and their emission properties 新型卤化锰二维、一维和零维框架及其发射特性

Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323099825

M. Ozide, RayVen Gonzales, Tatiana Timofeeva, Raúl Castañeda

引用次数: 0

Reciprocal-space mapping for macromolecular crystallography 用于大分子晶体学的互易空间制图

Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323098212

S. Meisburger, N. Ando

{"title":"Reciprocal-space mapping for macromolecular crystallography","authors":"S. Meisburger, N. Ando","doi":"10.1107/s2053273323098212","DOIUrl":"https://doi.org/10.1107/s2053273323098212","url":null,"abstract":"Diﬀuse scattering can provide insight into protein dynamics from macromolecular crystallography (MX) experiments. In conventional MX, the protein’s average structure is determined by analyzing Bragg peak intensities. Diﬀuse scattering signals present in the same diﬀraction images contain a wealth of information about deviations from the average structure, including lattice disorder and protein breathing motions. We have shown that when diﬀraction data are measured carefully at room temperature, the diﬀuse scattering can be processed to obtain a three-dimensional reciprocal space map that is further analyzed to determine correlated motion. To make diﬀuse scattering techniques more widely available, we have created a python package mdx2 that is both convenient to use and simple to extend and modify. It is lightweight, relying on the scientiﬁc python ecosystem for numerical methods, dials and dxtbx for initial processing and data import, and NeXus format for data storage. Mdx2 can be run on the command line or imported as a package, for instance to encapsulate a complete workﬂow in a Jupyter notebook for reproducible computing and edu cation. Finally, I will discuss our recent eﬀorts to improve performance and scalability toward real-time data reduction at synchrotron beamlines.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361489","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

Further studies on copper cyanide networks 氰化铜网络的进一步研究

Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323097103

Peter W. R. Corfield, A. M. F. Varona, Tristan B. DaCunha, Nurul B. Eisha, Ahmed Elsayed

引用次数: 0

Integrated M and RELION pipeline in a Linux environment 在 Linux 环境中集成 M 和 RELION 管道

Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323097462

Zhihai Liu, Jinhong Wang, Hua Wang, Lin Mei

引用次数: 0