Larsen T A, Olson A J, Goodsell D S
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
Structure. 1998 Apr 15;6(4):421-7. doi: 10.1016/s0969-2126(98)00044-6.
Most soluble proteins are active as low-number oligomers. Statistical surveys of oligomeric proteins have defined the roles of hydrophobicity and complementarity in the stability of protein interfaces, but tend to average structural features over a diverse set of protein-protein interfaces, blurring information on how individual interfaces are stabilized.
We report a visual survey of 136 homodimeric proteins from the Brookhaven Protein Data Bank, with images that highlight the major structural features of each protein-protein interaction surface. Nearly all of these proteins have interfaces formed between two globular subunits. Surprisingly, the pattern of hydrophilicity over the surface of these interfaces is quite variable. Approximately one-third of the interfaces show a recognizable hydrophobic core, with a single large, contiguous, hydrophobic patch surrounded by a ring of intersubunit polar interactions. The remaining two-thirds of the proteins show a varied mixture of small hydrophobic patches, polar interactions and water molecules scattered over the entire interfacial area. Ten proteins in the survey have intertwined interfaces formed by extensive interdigitation of the two subunit chains. These interfaces are very hydrophobic and are associated with proteins that require both stability and internal symmetry.
The archetypal protein interface, with a defined hydrophobic core, is present in only a minority of the surveyed homodimeric proteins. Most homodimeric proteins are stabilized by a combination of small hydrophobic patches, polar interactions and a considerable number of bridging water molecules. The presence or absence of a hydrophobic core within these interfaces does not correlate with specific protein functions.
大多数可溶性蛋白质以低聚体形式具有活性。对寡聚蛋白质的统计调查已经确定了疏水性和互补性在蛋白质界面稳定性中的作用，但往往会对各种蛋白质 - 蛋白质界面的结构特征进行平均，从而模糊了关于单个界面如何稳定的信息。
我们对来自布鲁克海文蛋白质数据库的136种同二聚体蛋白质进行了可视化调查，所生成的图像突出了每个蛋白质 - 蛋白质相互作用表面的主要结构特征。几乎所有这些蛋白质都具有在两个球状亚基之间形成的界面。令人惊讶的是，这些界面表面的亲水性模式差异很大。大约三分之一的界面显示出可识别的疏水核心，有一个单一的大的、连续的疏水斑块，周围环绕着亚基间极性相互作用的环。其余三分之二的蛋白质显示出小的疏水斑块、极性相互作用和散布在整个界面区域的水分子的各种混合。调查中的10种蛋白质具有由两条亚基链广泛交叉形成的交织界面。这些界面非常疏水，并且与需要稳定性和内部对称性的蛋白质相关。
具有明确疏水核心的典型蛋白质界面仅存在于少数被调查的同二聚体蛋白质中。大多数同二聚体蛋白质通过小的疏水斑块、极性相互作用和相当数量的桥连水分子的组合来稳定。这些界面中疏水核心的存在与否与特定的蛋白质功能无关。
