Venkatraman Prasanna, Balakrishnan Satish, Rao Shashidhar, Hooda Yogesh, Pol Suyog
Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India.
PLoS One. 2009 May 27;4(5):e5700. doi: 10.1371/journal.pone.0005700.
Proteases play a central role in cellular homeostasis and are responsible for the spatio-temporal regulation of function. Many putative proteases have been recently identified through genomic approaches, leading to a surge in global profiling attempts to characterize their function. Through such efforts and others it has become evident that many proteases play non-traditional roles. Accordingly, the number and the variety of the substrate repertoire of proteases are expected to be much larger than previously assumed. In line with such global profiling attempts, we present here a method for the prediction of natural substrates of endo proteases (human proteases used as an example) by employing short peptide sequences as specificity determinants.
METHODOLOGY/PRINCIPAL FINDINGS: Our method incorporates specificity determinants unique to individual enzymes and physiologically relevant dual filters namely, solvent accessible surface area--a parameter dependent on protein three-dimensional structure and subcellular localization. By incorporating such hitherto unused principles in prediction methods, a novel ligand docking strategy to mimic substrate binding at the active site of the enzyme, and GO functions, we identify and perform subjective validation on putative substrates of matriptase and highlight new functions of the enzyme. Using relative solvent accessibility to rank order we show how new protease regulatory networks and enzyme cascades can be created.
We believe that our physiologically relevant computational approach would be a very useful complementary method in the current day attempts to profile proteases (endo proteases in particular) and their substrates. In addition, by using functional annotations, we have demonstrated how normal and unknown functions of a protease can be envisaged. We have developed a network which can be integrated to create a proteolytic world. This network can in turn be extended to integrate other regulatory networks to build a system wide knowledge of the proteome.
蛋白酶在细胞内稳态中发挥核心作用,负责功能的时空调节。最近通过基因组学方法鉴定出了许多假定的蛋白酶,这导致全球范围内对其功能进行表征的分析尝试激增。通过这些努力以及其他研究,已明显发现许多蛋白酶发挥着非传统作用。因此,蛋白酶底物库的数量和种类预计比以前设想的要多得多。与这种全球分析尝试一致,我们在此提出一种方法,通过使用短肽序列作为特异性决定因素来预测内切蛋白酶(以人类蛋白酶为例)的天然底物。
方法/主要发现:我们的方法纳入了各个酶特有的特异性决定因素以及生理相关的双重筛选标准,即溶剂可及表面积——一个取决于蛋白质三维结构和亚细胞定位的参数。通过在预测方法中纳入这些迄今未使用的原则、一种模拟底物在酶活性位点结合的新型配体对接策略以及基因本体(GO)功能,我们鉴定了matriptase的假定底物并进行了主观验证,突出了该酶的新功能。利用相对溶剂可及性进行排序,我们展示了如何构建新的蛋白酶调节网络和酶级联反应。
我们认为,我们基于生理学的计算方法在当前分析蛋白酶(特别是内切蛋白酶)及其底物的尝试中,将是一种非常有用的补充方法。此外,通过使用功能注释,我们展示了如何设想蛋白酶的正常和未知功能。我们开发了一个可以整合的网络,以创建一个蛋白水解世界。这个网络反过来可以扩展,以整合其他调节网络,从而建立全系统的蛋白质组知识。