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X射线晶体学及其对理解细菌细胞壁重塑过程的影响。

X-ray crystallography and its impact on understanding bacterial cell wall remodeling processes.

作者信息

Büttner Felix Michael, Renner-Schneck Michaela, Stehle Thilo

机构信息

Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Straße 4, 72076 Tübingen, Germany.

Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Straße 4, 72076 Tübingen, Germany; Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA.

出版信息

Int J Med Microbiol. 2015 Feb;305(2):209-16. doi: 10.1016/j.ijmm.2014.12.018. Epub 2014 Dec 24.

Abstract

The molecular structure of matter defines its properties and function. This is especially true for biological macromolecules such as proteins, which participate in virtually all biochemical processes. A three dimensional structural model of a protein is thus essential for the detailed understanding of its physiological function and the characterization of essential properties such as ligand binding and reaction mechanism. X-ray crystallography is a well-established technique that has been used for many years, but it is still by far the most widely used method for structure determination. A particular strength of this technique is the elucidation of atomic details of molecular interactions, thus providing an invaluable tool for a multitude of scientific projects ranging from the structural classification of macromolecules over the validation of enzymatic mechanisms or the understanding of host-pathogen interactions to structure-guided drug design. In the first part of this review, we describe essential methodological and practical aspects of X-ray crystallography. We provide some pointers that should allow researchers without a background in structural biology to assess the overall quality and reliability of a crystal structure. To highlight its potential, we then survey the impact X-ray crystallography has had on advancing an understanding of a class of enzymes that modify the bacterial cell wall. A substantial number of different bacterial amidase structures have been solved, mostly by X-ray crystallography. Comparison of these structures highlights conserved as well as divergent features. In combination with functional analyses, structural information on these enzymes has therefore proven to be a valuable template not only for understanding their mechanism of catalysis, but also for targeted interference with substrate binding.

摘要

物质的分子结构决定其性质和功能。对于蛋白质等生物大分子而言尤其如此,蛋白质几乎参与了所有的生物化学过程。因此,蛋白质的三维结构模型对于详细理解其生理功能以及表征诸如配体结合和反应机制等基本特性至关重要。X射线晶体学是一项已确立多年的技术,但它至今仍是最广泛用于结构测定的方法。该技术的一个特别优势在于能够阐明分子相互作用的原子细节,从而为众多科学项目提供了一种极具价值的工具,这些项目涵盖从大分子的结构分类、酶促机制的验证、宿主-病原体相互作用的理解到基于结构的药物设计等各个方面。在本综述的第一部分,我们描述了X射线晶体学的基本方法和实际操作方面。我们提供了一些要点,应该能让没有结构生物学背景的研究人员评估晶体结构的整体质量和可靠性。为了突出其潜力,我们随后考察了X射线晶体学在推动对一类修饰细菌细胞壁的酶的理解方面所产生的影响。大量不同的细菌酰胺酶结构已被解析,其中大部分是通过X射线晶体学解析的。这些结构的比较突出了保守特征和差异特征。因此,结合功能分析,这些酶的结构信息已被证明不仅是理解其催化机制的宝贵模板,也是对底物结合进行靶向干扰的宝贵模板。

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