INTRAMOLECULAR CAVITIES IN GLOBULAR-PROTEINS
INTRAMOLECULAR CAVITIES IN GLOBULAR-PROTEINS
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DOI：
10.1093/protein/7.5.613
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发表时间：
1994-05-01
期刊：
影响因子：
--
通讯作者：
ARGOS, P
中科院分区：
文献类型：
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作者：
HUBBARD, SJ;GROSS, KH;ARGOS, P
121蛋白质链的内部空腔的分析已进行，以改善其发生，形态和蛋白质三级结构中的作用的表征，包括在其检测中使用的最佳探针大小的分析。阐明了一些基本的空腔特性。空洞是非人为的，显然与结构测定方法、分辨率和数据细化无关。总空腔体积随蛋白质大小而增加，但仅构成总蛋白质体积的一小部分，但空腔几乎总是存在于大小>100个残基的蛋白质中。它们最常见于蛋白质核心中。“空的”和含溶剂的空腔已被比较，发现溶剂化的空腔具有更极性的表面;这两类也被认为表现出不同的氨基酸类型和二级结构偏好。一般而言，封闭空腔的残基相对于其周围环境不显示任何额外的局部流动性。含水空腔不对它们的内部溶剂施加超过本体溶剂的体积限制，并且允许良好的氢键。这些结果应该被证明是有用的蛋白质建模和设计。
An analysis of internal cavities in 121 protein chains has been undertaken to improve the characterization of their occurrence, morphology and role in protein tertiary structure, including an analysis of the optimal probe size for use in their detection. A number of basic cavity characteristics were elucidated. Cavities are non-artefactual and apparently independent of the method of structure determination, resolution and refinement of the data. Overall cavity volume increases with protein size and yet constitutes only a small fraction of the total protein volume but cavities are nearly always present in proteins >100 residues in size. They are most commonly found in the protein core. 'Empty' and solvent-containing cavities have been compared and solvated cavities found to possess a more polar surface; the two classes are also seen to exhibit different amino acid type and secondary structural preferences. In general, residues that enclose cavities do not display any extra local mobility relative to their surrounding environments. Water-containing cavities do not impose volume restrictions upon their internal solvent beyond that of bulk solvent and permit good hydrogen bonding. These results should prove useful in protein modelling and design.