Sowmya Gopichandran, Anita Sathyanarayanan, Kangueane Pandjassarame
Bioinformation. 2011 May 7;6(4):137-43. doi: 10.6026/97320630006137.
Protein heterodimer complexes are often involved in catalysis, regulation, assembly, immunity and inhibition. This involves the formation of stable interfaces between the interacting partners. Hence, it is of interest to describe heterodimer interfaces using known structural complexes. We use a non-redundant dataset of 192 heterodimer complex structures from the protein databank (PDB) to identify interface residues and describe their interfaces using amino-acids residue property preference. Analysis of the dataset shows that the heterodimer interfaces are often abundant in polar residues. The analysis also shows the presence of two classes of interfaces in heterodimer complexes. The first class of interfaces (class A) with more polar residues than core but less than surface is known. These interfaces are more hydrophobic than surfaces, where protein-protein binding is largely hydrophobic. The second class of interfaces (class B) with more polar residues than core and surface is shown. These interfaces are more polar than surfaces, where binding is mainly polar. Thus, these findings provide insights to the understanding of protein-protein interactions.
蛋白质异源二聚体复合物通常参与催化、调节、组装、免疫和抑制过程。这涉及到相互作用伙伴之间形成稳定的界面。因此，利用已知的结构复合物来描述异源二聚体界面是很有意义的。我们使用来自蛋白质数据库（PDB）的192个异源二聚体复合物结构的非冗余数据集来识别界面残基，并使用氨基酸残基性质偏好来描述它们的界面。对该数据集的分析表明，异源二聚体界面通常富含极性残基。分析还表明异源二聚体复合物中存在两类界面。第一类界面（A类）极性残基比核心区域多但比表面少，这是已知的。这些界面比表面更疏水，而蛋白质-蛋白质结合在很大程度上是疏水的。第二类界面（B类）极性残基比核心区域和表面都多。这些界面比表面更具极性，而表面结合主要是极性的。因此，这些发现为理解蛋白质-蛋白质相互作用提供了见解。
