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首页> 外文期刊>IUCrJ >Do we see what we should see? Describing non-covalent interactions in protein structures including precision
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Do we see what we should see? Describing non-covalent interactions in protein structures including precision

机译：我们看到了应该看到的东西吗？描述蛋白质结构中的非共价相互作用，包括精度

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摘要

The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and α-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.
机译：X射线晶体结构分析作为一种技术的功能是“查看原子在哪里”。结果被广泛的研究团体广泛使用。但是，这种“看原子在哪里”可能会给人一种错误的安全感，除非已经考虑了原子放置的精度。实际上，以不正确的精度（即到太多的小数位）表示键距和角度是司空见惯的。本文有三个主题。首先，详细介绍了蛋白质晶体结构结果的正确表示基础，并针对蛋白质数据库条目进行了分析。建立蛋白质晶体结构中每个原子的放置精度的基础是不平凡的。其次，提出了利用这种精度描述符的知识库。在此将其应用于蛋白质结构中的盐桥即离子对的情况;这是从这种结构精确表示开始的最基本的地方，因为盐桥是蛋白质结构稳定性的宗旨之一。离子对在蛋白质寡聚，配体和底物的分子识别，变构调节，结构域运动和α-螺旋加帽中也起着核心作用。新的知识库SBPS（蛋白质结构中的盐桥）考虑了这些结构精度，并且是同类中的第一个。本文的第三个主题是表明对这种精度描述的需求的自然扩展，例如涉及金属蛋白的那些描述以及可电离氨基酸的质子化状态的确定。总体而言，还应注意的是，这项工作和这些示例也与蛋白质三维结构分子图形软件有关。

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