Hydrogens and hydrogen-bond networks in macromolecular MicroED data

IF 3.5 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Structural Biology: X Pub Date : 2022-01-01 DOI:10.1016/j.yjsbx.2022.100078
Max T.B. Clabbers , Michael W. Martynowycz , Johan Hattne , Tamir Gonen
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引用次数: 3

Abstract

Microcrystal electron diffraction (MicroED) is a powerful technique utilizing electron cryo-microscopy (cryo-EM) for protein structure determination of crystalline samples too small for X-ray crystallography. Electrons interact with the electrostatic potential of the sample, which means that the scattered electrons carry information about the charged state of atoms and provide relatively stronger contrast for visualizing hydrogen atoms. Accurately identifying the positions of hydrogen atoms, and by extension the hydrogen bonding networks, is of importance for understanding protein structure and function, in particular for drug discovery. However, identification of individual hydrogen atom positions typically requires atomic resolution data, and has thus far remained elusive for macromolecular MicroED. Recently, we presented the ab initio structure of triclinic hen egg-white lysozyme at 0.87 Å resolution. The corresponding data were recorded under low exposure conditions using an electron-counting detector from thin crystalline lamellae. Here, using these subatomic resolution MicroED data, we identified over a third of all hydrogen atom positions based on strong difference peaks, and directly visualize hydrogen bonding interactions and the charged states of residues. Furthermore, we find that the hydrogen bond lengths are more accurately described by the inter-nuclei distances than the centers of mass of the corresponding electron clouds. We anticipate that MicroED, coupled with ongoing advances in data collection and refinement, can open further avenues for structural biology by uncovering the hydrogen atoms and hydrogen bonding interactions underlying protein structure and function.

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大分子MicroED数据中的氢和氢键网络
微晶电子衍射(MicroED)是一种利用电子冷冻显微镜(cryo-EM)测定蛋白质结构的强大技术,用于对x射线晶体学太小的晶体样品进行蛋白质结构测定。电子与样品的静电势相互作用,这意味着散射的电子携带有关原子带电状态的信息,并为可视化氢原子提供相对较强的对比。准确识别氢原子的位置,进而确定氢键网络,对于理解蛋白质的结构和功能,特别是药物的发现具有重要意义。然而,单个氢原子位置的识别通常需要原子分辨率数据,到目前为止,对于大分子MicroED来说仍然是难以捉摸的。最近,我们以0.87 Å的分辨率提出了三斜蛋清溶菌酶的从头计算结构。在低曝光条件下,利用薄晶片上的电子计数检测器记录了相应的数据。在这里,利用这些亚原子分辨率MicroED数据,我们根据强差峰确定了超过三分之一的氢原子位置,并直接可视化氢键相互作用和残基的带电状态。此外,我们发现原子核间距离比相应电子云的质心更准确地描述了氢键长度。我们预计MicroED,加上数据收集和改进的持续进步,可以通过揭示蛋白质结构和功能背后的氢原子和氢键相互作用,为结构生物学开辟进一步的途径。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Journal of Structural Biology: X
Journal of Structural Biology: X Biochemistry, Genetics and Molecular Biology-Structural Biology
CiteScore
6.50
自引率
0.00%
发文量
20
审稿时长
62 days
期刊最新文献
Corrigendum to “Minimizing ice contamination during specimen preparation for cryo-soft X-ray tomography and cryo-electron tomography” [J. Struct. Biol.: X 10(2024) 100113] Editorial by Natalie Reznikov [for Buss et al., “Hierarchical organization of bone in three dimensions: A twist of twists” (2022)] Structural analysis of the stable form of fibroblast growth factor 2 – FGF2-STAB Localization of albumin with correlative super resolution light- and electron microscopy in the kidney Minimizing ice contamination during specimen preparation for cryo-soft X-ray tomography and cryo-electron tomography
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