Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Nagoya, Japan.
Proteins. 2011 Aug;79(8):2372-9. doi: 10.1002/prot.23084. Epub 2011 Jun 7.
We investigated fragmental sequences that were inserted into proteins during long molecular evolution and relevant to the association of homo-oligomers. Seventeen insertions in 12 SCOP (structure classification of proteins) families were examined and were classified into large and small insertions. The large insertions are composed of interface-like residues and effectively increase the interface area. In contrast, small insertions are composed of the residues that are not commonly found at the interfaces and have a small interface area: their roles in the oligomerization process are unclear. We found that the small insertions were located in the middle of protein sequences and therefore must involve residues with strong turn and less interface-like propensities. From a structural viewpoint, small insertions were found to mask hydrophobic patches or act as spacers to fill cavities present at interfaces. The presence or absence of small insertions coincides with the annotated oligomeric states for homologs in the SwissProt database, and the calculation of the association scores predicts that small insertions contribute to the stability of oligomers. These results support the significant role of small, nonhydrophobic insertions in protein oligomerization.
我们研究了在长分子进化过程中插入蛋白质中的片段序列，这些序列与同源寡聚物的结合有关。我们检查了 12 个 SCOP（蛋白质结构分类）家族中的 17 个插入，并将它们分为大插入和小插入。大插入由界面样残基组成，有效地增加了界面面积。相比之下，小插入由通常不在界面上发现的残基组成，具有较小的界面面积：它们在寡聚化过程中的作用尚不清楚。我们发现小插入位于蛋白质序列的中间，因此必须涉及具有强转角和较少界面倾向的残基。从结构的角度来看，小插入被发现可以掩盖疏水性补丁或充当间隔物以填充界面上存在的腔。在 SwissProt 数据库中，小插入的存在或不存在与同源物的注释寡聚状态一致，并且关联分数的计算预测小插入有助于寡聚物的稳定性。这些结果支持小的非疏水性插入在蛋白质寡聚化中具有重要作用。
