Protein complex compositions predicted by structural similarity.
Protein complex compositions predicted by structural similarity.
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DOI：
10.1093/nar/gkl353
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发表时间：
2006
影响因子：
14.9
通讯作者：
Madhusudhan MS
中科院分区：
文献类型：
--
作者：
Davis FP;Braberg H;Shen MY;Pieper U;Sali A;Madhusudhan MS
蛋白质通过与其他分子的相互作用发挥作用。因此，蛋白质之间的物理相互作用网络引起了实验生物学家和计算生物学家的极大兴趣。在这里，我们提出了酿酒酵母中3387个二元和1234个高阶蛋白质复合体的结构预测，分别涉及924和195个蛋白质。为了生成候选复合体，建立了单个蛋白质的比较模型，并以已知结构的复合体为模板组合在一起。然后使用从PIBASE()中的二元结构域界面得出的统计势来评估这些候选配合物。统计潜力从一组序列随机化的阴性样本中区分出100个界面结构的基准集合，假阳性率为3%，真阳性率为97%。此外，还利用功能注释和亚细胞定位数据对预测的复合体进行了筛选。在三个骆驼VHH结构域-猪α-淀粉酶的相互作用中，证明了该方法能够在备选方案中选择正确的结合模式。我们还强调了模板络合物中不存在的共络合结构域超家族的预测。通过与MODBASE的集成，将该方法应用于特性不如酿酒酵母的蛋白质组，将有助于扩大蛋白质相互作用空间的结构和功能覆盖范围。预测的络合物存放在MODBASE()中。
Proteins function through interactions with other molecules. Thus, the network of physical interactions among proteins is of great interest to both experimental and computational biologists. Here we present structure-based predictions of 3387 binary and 1234 higher order protein complexes in Saccharomyces cerevisiae involving 924 and 195 proteins, respectively. To generate candidate complexes, comparative models of individual proteins were built and combined together using complexes of known structure as templates. These candidate complexes were then assessed using a statistical potential, derived from binary domain interfaces in PIBASE (). The statistical potential discriminated a benchmark set of 100 interface structures from a set of sequence-randomized negative examples with a false positive rate of 3% and a true positive rate of 97%. Moreover, the predicted complexes were also filtered using functional annotation and sub-cellular localization data. The ability of the method to select the correct binding mode among alternates is demonstrated for three camelid VHH domain—porcine α–amylase interactions. We also highlight the prediction of co-complexed domain superfamilies that are not present in template complexes. Through integration with MODBASE, the application of the method to proteomes that are less well characterized than that of S.cerevisiae will contribute to expansion of the structural and functional coverage of protein interaction space. The predicted complexes are deposited in MODBASE ().
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影响因子：
14.9
作者：
Eswar, N;John, B;Sali, A
通讯作者：
Sali, A
影响因子：
64.8
作者：
Gavin, AC;Bösche, M;Superti-Furga, G
通讯作者：
Superti-Furga, G
影响因子：
64.8
作者：
Gavin, AC;Aloy, P;Superti-Furga, G
通讯作者：
Superti-Furga, G
影响因子：
5.8
作者：
Davis, FP;Sali, A
通讯作者：
Sali, A
影响因子：
3
作者：
Bader, GD;Hogue, CW
通讯作者：
Hogue, CW