Geller M, Miller M, Swanson S M, Maizel J
Laboratory of Mathematical Biology, NCI-Frederick Cancer Research Facility and Development Center, MD 21702, USA.
Proteins. 1997 Feb;27(2):195-203.
Six models of the catalytic site of HIV-1 protease complexed with a reduced peptide inhibitor, MVT-101, were investigated. These studies focused on the details of protonation of the active site, its total net charge and hydrogen bonding pattern, which was consistent with both the observed coplanar configuration of the acidic groups of the catalytic aspartates (Asp-25 and Asp-125) and the observed binding mode of the inhibitor. Molecular dynamic simulations using AMBER 4.0 indicated that the active site should be neutral. The planarity of the aspartate dyad may be due to the formation of two hydrogen bonds: one between the inner O delta 1 oxygen atoms of the two catalytic aspartates and another between the O delta 2 atom of Asp-125 and the nitrogen atom of the reduced peptide bond of the bound inhibitor. This would require two additional protonations, either of both aspartates, or of one Asp and the amido nitrogen atom of Nle-204. Our results favor the Asp-inhibitor protonation but the other one is not excluded. Implications of these findings for the mechanism of enzymatic catalysis are discussed. Dynamic properties of the hydrogen bond network in the active site and an analysis of the interaction energy between the inhibitor and the protease are presented.
研究了六种与还原肽抑制剂MVT - 101复合的HIV - 1蛋白酶催化位点模型。这些研究聚焦于活性位点质子化的细节、其总净电荷和氢键模式，这与催化天冬氨酸（Asp - 25和Asp - 125）酸性基团观察到的共面构型以及抑制剂观察到的结合模式均一致。使用AMBER 4.0进行的分子动力学模拟表明活性位点应为中性。天冬氨酸二元组的平面性可能归因于两个氢键的形成：一个在两个催化天冬氨酸的内Oδ1氧原子之间，另一个在Asp - 125的Oδ2原子与结合抑制剂的还原肽键的氮原子之间。这将需要另外两个质子化，要么是两个天冬氨酸都质子化，要么是一个Asp和Nle - 204的酰胺氮原子质子化。我们的结果支持Asp - 抑制剂质子化，但另一种情况也不能排除。讨论了这些发现对酶催化机制的影响。还介绍了活性位点氢键网络的动态特性以及抑制剂与蛋白酶之间相互作用能的分析。
