REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.
J Phys Chem B. 2010 Feb 25;114(7):2525-32. doi: 10.1021/jp910958u.
HIV-1 protease is a crucial enzyme for the life cycle of the human immunodeficiency virus, the retrovirus that triggers AIDS. It is well documented that HIV-1 protease mediates the cleavage of Gag, Gag-Pol, and Nef precursor polyproteins and is highly selective concerning the set of 12 different amino acid sequences that cleaves. However, the governing principles and physical parameters, which determine substrate recognition and specificity, remain poorly understood despite the many speculative proposals that abound in the literature. In fact, it has been difficult so far to circumvent the fact that protease's substrates share little sequence identity and lack an obvious consensus binding motif. We have used microsecond time scale MD simulations to quantitatively show that some sequences of the polyprotein Gag-Pol that are not cleaved (nonsubstrates) have in fact a higher affinity to the active site of HIV-1 protease than a substrate; i.e., recognition is not governed by affinity to the active site. On the basis of a detailed analysis of the results and experimental data, we propose that the recognition is based on the geometric specificity of PR:Gag and PR:Gag-Pol multiprotein complex, that selects which residues lie in the specific position that makes them accessible to the active site for cleavage.
HIV-1 蛋白酶是人类免疫缺陷病毒（HIV）生命周期中至关重要的酶，HIV 是引发艾滋病的逆转录病毒。有充分的文献记载表明，HIV-1 蛋白酶介导 Gag、Gag-Pol 和 Nef 前体多蛋白的切割，并且对切割的 12 种不同氨基酸序列具有高度的选择性。然而，尽管文献中充斥着许多推测性的建议，但决定底物识别和特异性的基本原则和物理参数仍未得到很好的理解。事实上，迄今为止，我们很难回避这样一个事实，即蛋白酶的底物几乎没有共享的序列同一性，也缺乏明显的共识结合基序。我们已经使用微秒时间尺度的 MD 模拟来定量地表明，一些未被切割的多蛋白 Gag-Pol 序列（非底物）实际上比底物对 HIV-1 蛋白酶的活性位点具有更高的亲和力；即，识别不受与活性位点亲和力的控制。基于对结果和实验数据的详细分析，我们提出，识别是基于 PR：Gag 和 PR：Gag-Pol 多蛋白复合物的几何特异性，它选择使哪些残基位于特定位置，从而使其可用于活性位点进行切割。
