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Acta crystallographica. Section F, Structural biology communications最新文献

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IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-05-03
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引用次数: 0
Crystal structure of the long Rib domain of the LPXTG-anchored surface protein from Limosilactobacillus reuteri 雷特氏乳酸菌 LPXTG 表面锚定蛋白长 Rib 结构域的晶体结构。
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-05-03 DOI: 10.1107/S2053230X24003868
Yi Xue, Zhen Wu, Xue Kang

The Rib domain, which is often found as tandem-repeat structural modules in surface proteins of Gram-positive bacteria, plays important roles in mediating interactions of bacteria with their environments and hosts. A comprehensive structural analysis of various Rib domains is essential to fully understand their impact on the structure and functionality of these bacterial adhesins. To date, structural information has been limited for this expansive group of domains. In this study, the high-resolution crystal structure of the second member of the long Rib domain, a unique subclass within the Rib-domain family, derived from Limosilactobacillus reuteri is presented. The data not only demonstrate a highly conserved structure within the long Rib domain, but also highlight an evolutionary convergence in structural architecture with other modular domains found in cell-adhesion molecules.

Rib 结构域通常以串联重复结构模块的形式存在于革兰氏阳性细菌的表面蛋白中,在介导细菌与其环境和宿主的相互作用方面发挥着重要作用。要全面了解各种 Rib 结构域对这些细菌粘附蛋白的结构和功能的影响,就必须对它们进行全面的结构分析。迄今为止,关于这组结构域的结构信息还很有限。本研究展示了长 Rib 结构域第二成员的高分辨率晶体结构,该结构域是 Rib 结构域家族中的一个独特亚类,来自于Limosilactobacillus reuteri。这些数据不仅证明了长 Rib 结构域内高度保守的结构,而且还强调了与细胞粘附分子中发现的其他模块化结构域在结构架构上的进化趋同性。
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引用次数: 0
Structural and biochemical characterization of the M405S variant of Desulfovibrio vulgaris formate dehydrogenase. 低俗脱硫弧菌甲酸脱氢酶 M405S 变体的结构和生物化学特征。
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-05-01 DOI: 10.1107/S2053230X24003911
Guilherme Vilela-Alves, Rita Rebelo Manuel, Neide Pedrosa, Inês A Cardoso Pereira, Maria João Romão, Cristiano Mota

Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO2 to formate, with biotechnological applications envisaged in climate-change mitigation. The role of Met405 in the active site of Desulfovibrio vulgaris formate dehydrogenase AB (DvFdhAB) has remained elusive. However, its proximity to the metal site and the conformational change that it undergoes between the resting and active forms suggests a functional role. In this work, the M405S variant was engineered, which allowed the active-site geometry in the absence of methionine Sδ interactions with the metal site to be revealed and the role of Met405 in catalysis to be probed. This variant displayed reduced activity in both formate oxidation and CO2 reduction, together with an increased sensitivity to oxygen inactivation.

依赖钼或钨的甲酸脱氢酶已成为将二氧化碳化学还原为甲酸盐的重要催化剂,其生物技术应用有望缓解气候变化。Met405 在脱硫弧菌甲酸脱氢酶 AB(DvFdhAB)活性位点中的作用一直难以确定。不过,它与金属位点的接近程度以及在静态和活性形式之间发生的构象变化表明了它的功能性作用。在这项工作中,我们设计了 M405S 变体,从而揭示了在没有蛋氨酸 Sδ 与金属位点相互作用的情况下活性位点的几何形状,并探究了 Met405 在催化过程中的作用。这种变体在甲酸氧化和二氧化碳还原中的活性都有所降低,对氧气失活的敏感性也有所提高。
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引用次数: 0
X-ray crystal structure of a designed rigidified imaging scaffold in the ligand-free conformation. 设计的无配体构象刚性成像支架的 X 射线晶体结构。
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-05-01 Epub Date: 2024-05-20 DOI: 10.1107/S2053230X2400414X
Matthew P Agdanowski, Roger Castells-Graells, Michael R Sawaya, Duilio Cascio, Todd O Yeates, Mark A Arbing

Imaging scaffolds composed of designed protein cages fused to designed ankyrin repeat proteins (DARPins) have enabled the structure determination of small proteins by cryogenic electron microscopy (cryo-EM). One particularly well characterized scaffold type is a symmetric tetrahedral assembly composed of 24 subunits, 12 A and 12 B, which has three cargo-binding DARPins positioned on each vertex. Here, the X-ray crystal structure of a representative tetrahedral scaffold in the apo state is reported at 3.8 Å resolution. The X-ray crystal structure complements recent cryo-EM findings on a closely related scaffold, while also suggesting potential utility for crystallographic investigations. As observed in this crystal structure, one of the three DARPins, which serve as modular adaptors for binding diverse `cargo' proteins, present on each of the vertices is oriented towards a large solvent channel. The crystal lattice is unusually porous, suggesting that it may be possible to soak crystals of the scaffold with small (≤30 kDa) protein cargo ligands and subsequently determine cage-cargo structures via X-ray crystallography. The results suggest the possibility that cryo-EM scaffolds may be repurposed for structure determination by X-ray crystallography, thus extending the utility of electron-microscopy scaffold designs for alternative structural biology applications.

通过低温电子显微镜(cryo-EM)测定小分子蛋白质的结构,可以利用由设计的蛋白质笼与设计的杏仁蛋白重复蛋白(DARPins)融合而成的成像支架。其中一种特征特别明显的支架类型是由 24 个亚基(12 个 A 和 12 个 B)组成的对称四面体组装体,每个顶点上都有三个与货物结合的 DARPins。在此,我们以 3.8 Å 的分辨率报道了一个具有代表性的四面体支架在 apo 状态下的 X 射线晶体结构。该 X 射线晶体结构补充了最近对一个密切相关支架的低温电子显微镜研究结果,同时也表明了晶体学研究的潜在用途。正如在该晶体结构中所观察到的,存在于每个顶点上的三个 DARPins(作为模块化适配器用于结合各种 "货物 "蛋白)中的一个面向一个大的溶剂通道。晶格异常多孔,这表明有可能用小型(≤30 kDa)蛋白质货物配体浸泡支架晶体,然后通过 X 射线晶体学确定笼-货结构。这些结果表明,低温电子显微镜支架有可能被重新用于通过 X 射线晶体学确定结构,从而将电子显微镜支架设计的用途扩展到其他结构生物学应用领域。
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引用次数: 0
Cryo-EM sample preparation for high-resolution structure studies 用于高分辨率结构研究的低温电子显微镜样品制备。
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-04-30 DOI: 10.1107/S2053230X24002553
Liguo Wang, Christina M. Zimanyi

High-resolution structures of biomolecules can be obtained using single-particle cryo-electron microscopy (SPA cryo-EM), and the rapidly growing number of structures solved by this method is encouraging more researchers to utilize this technique. As with other structural biology methods, sample preparation for an SPA cryo-EM data collection requires some expertise and an understanding of the strengths and limitations of the technique in order to make sensible decisions in the sample-preparation process. In this article, common strategies and pitfalls are described and practical advice is given to increase the chances of success when starting an SPA cryo-EM project.

利用单颗粒冷冻电镜(SPA cryo-EM)可以获得生物大分子的高分辨率结构,而且利用这种方法解决的结构数量正在迅速增加,这鼓励了更多的研究人员利用这种技术。与其他结构生物学方法一样,为收集 SPA 冷冻电子显微镜数据而进行的样品制备也需要一定的专业知识以及对该技术优势和局限性的了解,以便在样品制备过程中做出合理的决定。本文将介绍常见的策略和误区,并给出实用建议,以增加启动 SPA Cryo-EM 项目的成功机会。
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引用次数: 0
Structural and functional characterization of FabG4 from Mycolicibacterium smegmatis 烟曲霉分枝杆菌 FabG4 的结构和功能表征
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-04-30 DOI: 10.1107/S2053230X2400356X
Xinping Ran, Prashit Parikh, Jan Abendroth, Tracy L. Arakaki, Matthew C. Clifton, Thomas E. Edwards, Donald D. Lorimer, Stephen Mayclin, Bart L. Staker, Peter Myler, Krystle J. McLaughlin

The rise in antimicrobial resistance is a global health crisis and necessitates the development of novel strategies to treat infections. For example, in 2022 tuberculosis (TB) was the second leading infectious killer after COVID-19, with multi-drug-resistant strains of TB having an ∼40% fatality rate. Targeting essential biosynthetic pathways in pathogens has proven to be successful for the development of novel antimicrobial treatments. Fatty-acid synthesis (FAS) in bacteria proceeds via the type II pathway, which is substantially different from the type I pathway utilized in animals. This makes bacterial fatty-acid biosynthesis (Fab) enzymes appealing as drug targets. FabG is an essential FASII enzyme, and some bacteria, such as Mycobacterium tuberculosis, the causative agent of TB, harbor multiple homologs. FabG4 is a conserved, high-molecular-weight FabG (HMwFabG) that was first identified in M. tuberculosis and is distinct from the canonical low-molecular-weight FabG. Here, structural and functional analyses of Mycolicibacterium smegmatis FabG4, the third HMwFabG studied to date, are reported. Crystal structures of NAD+ and apo MsFabG4, along with kinetic analyses, show that MsFabG4 preferentially binds and uses NADH when reducing CoA substrates. As M. smegmatis is often used as a model organism for M. tuberculosis, these studies may aid the development of drugs to treat TB and add to the growing body of research that distinguish HMwFabGs from the archetypal low-molecular-weight FabG.

抗菌药耐药性的增加是一个全球性的健康危机,因此有必要开发治疗感染的新策略。例如,在 2022 年,结核病(TB)是仅次于 COVID-19 的第二大传染病杀手,耐多药结核菌株的致死率高达 40%。事实证明,针对病原体的重要生物合成途径开发新型抗菌治疗方法是成功的。细菌中的脂肪酸合成(FAS)是通过 II 型途径进行的,与动物体内的 I 型途径有很大不同。这使得细菌脂肪酸生物合成(Fab)酶成为有吸引力的药物靶点。FabG 是一种重要的 FASII 酶,某些细菌(如结核病的致病菌结核分枝杆菌)含有多种同源物。FabG4 是一种保守的高分子量 FabG(HMwFabG),最早在结核分枝杆菌中被发现,它与典型的低分子量 FabG 不同。 本文报告了迄今为止研究的第三种 HMwFabG--烟草分枝杆菌 FabG4 的结构和功能分析。NAD+和apo MsFabG4的晶体结构以及动力学分析表明,MsFabG4在还原CoA底物时优先结合并使用NADH。由于M. smegmatis经常被用作结核杆菌的模式生物,这些研究可能有助于开发治疗结核病的药物,并为越来越多的研究增添了新的内容,这些研究将HMwFabGs与典型的低分子量FabG区分开来。
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引用次数: 0
Beyond publishing: introducing Interviews with authors 出版之外:介绍作者访谈。
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-04-30 DOI: 10.1107/S2053230X24003339
Maria Cristina Nonato, Mark J. van Raaij, Jon Agirre

To find out what lies behind the articles published in Acta Cryst. F – Structural Biology Communications the journal now publishes interviews with its authors.

为了了解《Acta Cryst.F - Structural Biology Communications》发表的文章背后的故事。
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引用次数: 0
The unbearable burden of peer review? 难以承受的同行评审负担?
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-03-04 DOI: 10.1107/S2053230X24002024
Mark J. van Raaij

The current situation of scientific manuscript peer review is discussed, both generally and as applied to Acta Crystallographica F – Biological Research Communications.

本文讨论了科学手稿同行评审的现状,既有一般性的,也有适用于《晶体学报》--《生物研究通讯》的。
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引用次数: 0
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-03-04
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引用次数: 0
Crystallization and biochemical studies of the NYN domain of human KHNYN 人类 KHNYN NYN 结构域的结晶和生化研究。
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-03-04 DOI: 10.1107/S2053230X24000943
Sunho Hong, Jungwoo Choe

KHNYN is composed of an N-terminal KH-like RNA-binding domain and a C-terminal PIN/NYN endoribonuclease domain. It forms a complex with zinc-finger antiviral protein (ZAP), leading to the degradation of viral or cellular RNAs depending on the ZAP isoform. Here, the production, crystallization and biochemical analysis of the NYN domain (residues 477–636) of human KHNYN are presented. The NYN domain was crystallized with a heptameric single-stranded RNA from the AU-rich elements of the 3′-UTR of interferon lambda 3. The crystal belonged to space group P4132, with unit-cell parameters a = b = c = 111.3 Å, and diffacted to 1.72 Å resolution. The RNase activity of the NYN domain was demonstrated using different single-stranded RNAs, together with the binding between the NYN domain of KHNYN and the zinc-finger domain of ZAP.

KHNYN 由一个 N 端 KH 样 RNA 结合结构域和一个 C 端 PIN/NYN 内切酶结构域组成。它与锌指抗病毒蛋白(ZAP)形成复合物,根据 ZAP 异构体的不同导致病毒或细胞 RNA 的降解。本文介绍了人类 KHNYN 的 NYN 结构域(残基 477-636)的制作、结晶和生化分析。该 NYN 结构域与来自干扰素 lambda 3 的 3'-UTR 中富含 AU 元素的七聚单链 RNA 一起结晶。晶体属于空间群 P4132,单位晶胞参数为 a = b = c = 111.3 Å,衍射分辨率为 1.72 Å。利用不同的单链 RNA 验证了 NYN 结构域的 RNase 活性,以及 KHNYN 的 NYN 结构域与 ZAP 的锌指结构域之间的结合。
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引用次数: 0
期刊
Acta crystallographica. Section F, Structural biology communications
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