Characterization of protein-protein interaction interfaces from a single species.
Characterization of protein-protein interaction interfaces from a single species.
复制标题
DOI：
10.1371/journal.pone.0021053
复制
发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Lovell SC
中科院分区：
文献类型：
--
作者：
Talavera D;Robertson DL;Lovell SC
大多数蛋白质通过与其他蛋白质的特定相互作用来实现其生物学功能。因此，研究蛋白质之间的相互作用以及调节这些相互作用的界面对于理解生物功能是非常重要的。特别是，结合特异性的确切决定因素及其对蛋白质界面内结合能的贡献还没有被很好地理解。为了更好地理解这些决定因素，需要对相互作用面进行适当的描述。来自酿酒酵母的现有数据使我们能够专注于单个物种，并使用所有可用的结构，校正冗余，而不是使用结构代表。这使我们能够控制可能影响序列倾向的潜在混杂因素。我们发现主链原子对蛋白质-蛋白质相互作用有显著的贡献。这包括与相互作用链上的其他主链和侧链原子的相互作用。我们发现，相互作用的类型取决于接触中涉及的氨基酸和二级结构类型。例如，α-螺旋和大氨基酸中的残基最有可能通过其侧链原子参与相互作用。当我们计算蛋白质表面不同区域的平均溶剂化能时，我们发现了一个有趣的同质性。出乎意料的是，同系和杂系化合物在所有分析中都有非常相似的结果。我们的发现表明，蛋白质-蛋白质相互作用的形成方式由残基类型和界面上发现的二级结构决定。然而，尽管界面性质不同，但去溶能的均匀性表明界面组成和结合能之间存在复杂的关系。
Most proteins attain their biological functions through specific interactions with other proteins. Thus, the study of protein-protein interactions and the interfaces that mediate these interactions is of prime importance for the understanding of biological function. In particular the precise determinants of binding specificity and their contributions to binding energy within protein interfaces are not well understood. In order to better understand these determinants an appropriate description of the interaction surface is needed. Available data from the yeast Saccharomyces cerevisiae allow us to focus on a single species and to use all the available structures, correcting for redundancy, instead of using structural representatives. This allows us to control for potentially confounding factors that may affect sequence propensities. We find a significant contribution of main-chain atoms to protein-protein interactions. These include interactions both with other main-chain and side-chain atoms on the interacting chain. We find that the type of interaction depends on both amino acid and secondary structure type involved in the contact. For example, residues in α-helices and large amino acids are the most likely to be involved in interactions through their side-chain atoms. We find an intriguing homogeneity when calculating the average solvation energy of different areas of the protein surface. Unexpectedly, homo- and hetero-complexes have quite similar results for all analyses. Our findings demonstrate that the manner in which protein-protein interactions are formed is determined by the residue type and the secondary structure found in the interface. However the homogeneity of the desolvation energy despite heterogeneity of interface properties suggests a complex relationship between interface composition and binding energy.
登录
查看更多内容
影响因子：
5.6
作者：
LEE, B;RICHARDS, FM
通讯作者：
RICHARDS, FM
影响因子：
64.8
作者：
Gavin, AC;Bösche, M;Superti-Furga, G
通讯作者：
Superti-Furga, G
DOI：
10.1002/prot.340230412
发表时间：
1995-12-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
Frishman, D;Argos, P
通讯作者：
Argos, P
影响因子：
64.8
作者：
Gavin, AC;Aloy, P;Superti-Furga, G
通讯作者：
Superti-Furga, G
DOI：
10.1073/pnas.092147999
发表时间：
2002-04-30
影响因子：
11.1
作者：
Aloy, P;Russell, RB
通讯作者：
Russell, RB