A Motif-Based Method for Predicting Interfacial Residues in Both the RNA and Protein Components of Protein-RNA Complexes
A Motif-Based Method for Predicting Interfacial Residues in Both the RNA and Protein Components of Protein-RNA Complexes
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DOI：
10.1142/9789814749411_0041
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发表时间：
2016
影响因子：
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通讯作者：
Usha Muppirala;Benjamin A. Lewis;Carla M. Mann;D. Dobbs
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文献类型：
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作者：
Usha Muppirala;Benjamin A. Lewis;Carla M. Mann;D. Dobbs
预测蛋白质-RNA复合物中的界面残基的努力主要集中在预测蛋白质中的RNA结合残基。然而，用于预测RNA序列中蛋白质结合残基的计算方法是迄今为止相对较少关注的问题。虽然序列基序的分类和注释蛋白质序列的价值是公认的，序列基序还没有被广泛应用于预测大分子复合物中的界面残基。在这里，我们提出了一种新的序列基序为基础的方法“特定的合作伙伴”的界面残留预测。给定特定的蛋白质-RNA对，目标是同时预测蛋白质序列中的RNA结合残基和RNA序列中的蛋白质结合残基。在5倍交叉验证实验中，我们的方法，PS-PRIP，达到92%的特异性和61%的灵敏度，与马修斯相关系数（MCC）为0.58，在预测蛋白质中的RNA结合位点。该方法实现了69%的特异性和75%的灵敏度，但在预测RNA中的蛋白质结合位点时具有0.13的低MCC。当在实验验证的蛋白质- RNA相互作用的两个独立的“盲”数据集上测试PS-PRIP时，获得了类似的性能结果，这表明该方法对于鉴定结构信息不可用的蛋白质-RNA复合物中的潜在界面残基应该是广泛适用的和有价值的。PS-PRIP网络服务器和数据集可在http://pridb.gdcb.iastate.edu/PSPRIP/上获得。
Efforts to predict interfacial residues in protein-RNA complexes have largely focused on predicting RNA-binding residues in proteins. Computational methods for predicting protein-binding residues in RNA sequences, however, are a problem that has received relatively little attention to date. Although the value of sequence motifs for classifying and annotating protein sequences is well established, sequence motifs have not been widely applied to predicting interfacial residues in macromolecular complexes. Here, we propose a novel sequence motif-based method for "partner-specific" interfacial residue prediction. Given a specific protein-RNA pair, the goal is to simultaneously predict RNA binding residues in the protein sequence and protein-binding residues in the RNA sequence. In 5-fold cross validation experiments, our method, PS-PRIP, achieved 92% Specificity and 61% Sensitivity, with a Matthews correlation coefficient (MCC) of 0.58 in predicting RNA-binding sites in proteins. The method achieved 69% Specificity and 75% Sensitivity, but with a low MCC of 0.13 in predicting protein binding sites in RNAs. Similar performance results were obtained when PS-PRIP was tested on two independent "blind" datasets of experimentally validated protein- RNA interactions, suggesting the method should be widely applicable and valuable for identifying potential interfacial residues in protein-RNA complexes for which structural information is not available. The PS-PRIP webserver and datasets are available at: http://pridb.gdcb.iastate.edu/PSPRIP/.