Dissecting subunit interfaces in homodimeric proteins
Dissecting subunit interfaces in homodimeric proteins
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DOI：
10.1002/prot.10461
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发表时间：
2003-11-15
影响因子：
2.9
通讯作者：
Janin, J
中科院分区：
文献类型：
--
作者：
Bahadur, RP;Chakrabarti, P;Janin, J
对122个已知三维结构的同源二聚体的亚基界面进行了分析，并通过在界面聚集原子将其分解成多组表面片，其中70个界面是单一的片，其他的有多达6个片，通常是由不同的结构域贡献的。平均界面埋入每个单体表面的1,940埃(2)，包含一个或两个埋藏600-1,600埃(2)的斑块，65%是非极性的，包括18个氢键。然而，122个界面的大小和疏水性范围很大。每个界面都有一个由残基组成的核心，原子埋在二聚体中，周围是残基的边缘，原子仍然可以被溶剂访问。核心平均占界面的77%，除了精氨酸残基的存在外，其氨基酸组成与蛋白质内部相似，而边缘更像蛋白质表面。同源二聚体中的界面的这些属性是永久性的组装，与蛋白质-蛋白质复合体的这些属性进行比较，在蛋白质-蛋白质复合体中，组分在独立折叠后相互关联。平均而言，同二聚体中的亚基界面比复合体中的大两倍，而且由于核心的大部分属于核心，所以亚基的极性要小得多，尽管两种类型的接口中核心的氨基酸组成相似。(C)2003年Wiley-Liss，Inc.
The subunit interfaces of 122 homodimers of known three-dimensional structure are analyzed and dissected into sets of surface patches by clustering atoms at the interface; 70 interfaces are single-patch, the others have up to six patches, often contributed by different structural domains. The average interface buries 1,940 Angstrom(2) of the surface of each monomer, contains one or two patches burying 600-1,600 Angstrom(2), is 65% nonpolar and includes 18 hydrogen bonds. However, the range of size and of hydrophobicity is wide among the 122 interfaces. Each interface has a core made of residues with atoms buried in the dimer, surrounded by a rim of residues with atoms that remain accessible to solvent. The core, which constitutes 77% of the interface on average, has an amino acid composition that resembles the protein interior except for the presence of arginine residues, whereas the rim is more like the protein surface. These properties of the interfaces in homodimers, which are permanent assemblies, are compared to those of protein-protein complexes where the components associate after they have independently folded. On average, subunit interfaces in homodimers are twice larger than in complexes, and much less polar due to the large fraction belonging to the core, although the amino acid compositions of the cores are similar in the two types of interfaces. (C) 2003 Wiley-Liss, Inc.