Supercomputer Education and Research Centre, Indian Institute of Science , Bangalore, Karnataka 560 012, India.
School of Chemistry, University of Manchester , Brunswick Street, Manchester M13 9PL, England.
IUCrJ. 2013 Dec 5;1(Pt 1):74-81. doi: 10.1107/S2052252513031485. eCollection 2014 Jan 1.
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.
X 射线晶体结构分析技术的强大之处在于“看到原子的位置”。研究人员广泛应用其结果。然而，除非考虑到原子位置的精度，否则这种“看到原子的位置”可能会产生一种错误的安全感。事实上，经常会出现将键距离和角度呈现为错误精度（即过多的小数位数）的情况。本文有三个主题。首先，详细介绍了一种正确表示蛋白质晶体结构结果的基础，并结合对蛋白质数据库条目的分析进行了演示。确定蛋白质晶体结构中每个原子位置精度的基础并不简单。其次，提出了一个利用这种精度描述符的知识库。在这里，它应用于蛋白质结构中的盐桥（即离子对）的情况；由于盐桥是蛋白质结构稳定性的基本原则之一，因此从这种结构精度表示开始是最基本的起点。离子对在蛋白质寡聚化、配体和底物的分子识别、变构调节、结构域运动和α-螺旋帽的形成中也起着核心作用。一个新的知识库 SBPS（蛋白质结构中的盐桥）考虑了这些结构精度，是同类知识库中的第一个。本文的第三个主题是指出需要这种精度描述的自然扩展，例如涉及金属蛋白和可电离氨基酸质子化状态的确定。总的来说，还指出这项工作和这些例子也与蛋白质三维结构分子图形软件相关。
