ANALYSIS OF PACKING CONTACTS IN PROTEIN CRYSTALS

这个项目的目标是确定包装的共同特点 蛋白质晶体中的相互作用， 布鲁克海文蛋白质数据库 我们将考虑剩余类型 参与，具体的成对相互作用，并检查的关系， 包装接触晶体习性。 我们在PKB中使用了新的功能 用于识别蛋白质数据中非冗余结构子集的套件 具有有效晶体对称性信息的银行。 对于这些结构 我们已经按残基和残基对类型列出了原子接触， 进行了初步的统计分析。最有趣的功能 迄今为止确定的是赖氨酸、精氨酸和 谷氨酸侧链在包装接触。 盐桥包括 这些残基在蛋白质三级结构中很重要，但似乎 较小的不带电侧链的相互作用在晶体中占主导地位， 打包 详细分析这些数据的统计方法已经 开发这些将用于精确量化参与 包装相互作用中的不同残基，同时调整其 丰度，在蛋白质表面上的出现，以及特定的 立体化学本项目将对以下方面进行实证描述： 预期在蛋白质-蛋白质界面处的非键合相互作用。 这可能 证明可用于鉴定具有生物学重要性的对接位点。 它还可能建议改变对接相互作用强度的方法， 一种改善蛋白质晶体有序性的方法，或者作为一种识别 对接点的生物学功能。

The goal of this project is to identify common features of packing interactionsin protein crystals, by statistical survey of structures in the Brookhaven Protein Data Bank. We will consider residue types involved, specific pairwise interactions, and examine the relationship of packing contacts to crystal habit. We have used new functions in the PKB suite to identify a non-redundant subset of structures in the Protein Data Bank which have valid crystal symmetry information. For these structure we have tabulated atomic contacts by residue and residue-pair type, and conducted a preliminary statistical analyses. The most interesting feature identified to date is the low participation of lysine, arginine and glutamic acid side chains in packing contacts. Salt bridges involving these residues are important in protein tertiary structure, but it appears that interactions of smaller, uncharged side chains predominate in crystal packing. Statistical methods for detailed analysis of these datahave been developed. These will be used to quantitate precisely the participation different residues in packing interactions, while adjusting for their abundance, occurrence on the protein surface, and specific stereochemistry. This project will develop an empirical description of nonbonded interactions expected at protein-protein interfaces. This may prove useful in identification of docking sites of biological importance. It may also suggest ways to alter the strength of docking interactions, as a means to improve ordering in protein crystals, or as a means to identify the biological function of docking sites.