CAVITIES AND PACKING AT PROTEIN INTERFACES
CAVITIES AND PACKING AT PROTEIN INTERFACES
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DOI：
10.1002/pro.5560031205
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发表时间：
1994-12-01
期刊：
影响因子：
8
通讯作者：
ARGOS, P
中科院分区：
文献类型：
--
作者：
HUBBARD, SJ;ARGOS, P
对蛋白质结构中的内部堆积缺陷或“空洞”(包括空的和含水的)进行了分析，包括3个空洞类别：结构域内、结构域间和蛋白质亚单位之间。我们确认了所有空洞类型共有的几个基本特征，但也发现了一些新的特征，包括那些区分类别的特征。总的空腔体积只占总蛋白质体积的一小部分，但随着蛋白质大小的增加而增加。充满水的“空洞”拥有一个更极地的表面，而且通常更大。它们的组成水是满足局部氢键潜力所必需的。据观察，平均而言，空腔周围的原子比它们所处的环境更不灵活。亚基间和域间空穴平均比域内空穴大，占据其驻留表面的更大比例，并且更频繁地充满水。我们观察到与剪切型磁区运动有关的磁区-磁区界面处的空腔体积增加。将讨论界面空穴对亚单位和结构域形状互补的意义和蛋白质对接问题，以及它们在寡聚蛋白质中的结构和功能作用。关于空腔大小、极性、溶剂化、一般丰度和残基类型的结果应该为蛋白质建模和设计提供有用的指导。
An analysis of internal packing defects or ''cavities'' (both empty and water-containing) within protein structures has been undertaken and includes 3 cavity classes: within domains, between domains, and between protein subunits. We confirm several basic features common to all cavity types but also find a number of new characteristics, including those that distinguish the classes. The total cavity volume remains only a small fraction of the total protein volume and yet increases with protein size. Water-filled ''cavities'' possess a more polar surface and are typically larger. Their constituent waters are necessary to satisfy the local hydrogen bonding potential. Cavity-surrounding atoms are observed to be, on average, less flexible than their environments. Intersubunit and interdomain cavities are on average larger than the intradomain cavities, occupy a larger fraction of their resident surfaces, and are more frequently water-filled. We observe increased cavity volume at domain-domain interfaces involved with shear type domain motions. The significance of interfacial cavities upon subunit and domain shape complementarity and the protein docking problem, as well as in their structural and functional role in oligomeric proteins, will be discussed. The results concerning cavity size, polarity, solvation, general abundance, and residue type constituency should provide useful guidelines for protein modeling and design.