为设计高特异性底物而对蛋白酶3结合位点的研究。
Inspection of the binding sites of proteinase3 for the design of a highly specific substrate.
作者信息
Hajjar Eric, Korkmaz Brice, Gauthier Francis, Brandsdal Bjørn Olav, Witko-Sarsat Véronique, Reuter Nathalie
机构信息
Computational Biology Unit, BCCS, University of Bergen, N-5008 Bergen, Norway.
出版信息
J Med Chem. 2006 Feb 23;49(4):1248-60. doi: 10.1021/jm051018t.
Proteinase3 (PR3) and human neutrophil elastase (HNE) are homologous proteases from the polymorphonuclear neutrophils and have been thought for a long time to have close enzymatic specificity. We have used molecular dynamics simulations to investigate and compare the interactions between different peptides and the two enzymes. The important role played especially by the C-terminal part of the peptides is confirmed. We provide a map of the subsites of PR3 and a description of the interaction scheme for six ligands. The main difference between HNE and PR3 concerns S2, S1', S2', and S3'. The recognition subsites in PR3 are interconnected; in particular, Lys99 participates to a hydrophobic (S4) and a polar (S2) pocket. On the basis of the simulations, we suggest that VADVKDR is a highly specific sequence for PR3; enzymatic assays confirm that it is cleaved by PR3 with a high specificity constant (k(cat)/K(m) = 3,400,000 M(-1) s(-1)) and not by HNE.
蛋白酶3（PR3）和人中性粒细胞弹性蛋白酶（HNE）是来自多形核中性粒细胞的同源蛋白酶，长期以来人们一直认为它们具有相似的酶特异性。我们使用分子动力学模拟来研究和比较不同肽与这两种酶之间的相互作用。肽的C末端部分所起的重要作用得到了证实。我们提供了PR3的亚位点图谱以及六种配体的相互作用方案描述。HNE和PR3之间的主要差异在于S2、S1'、S2'和S3'。PR3中的识别亚位点相互连接；特别是，赖氨酸99参与一个疏水（S4）口袋和一个极性（S2）口袋。基于模拟结果，我们认为VADVKDR是PR3的高度特异性序列；酶活性测定证实它被PR3以高特异性常数（k(cat)/K(m)=3,400,000 M(-1) s(-1)）切割，而不被HNE切割。
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