Soares Rosemberg O, Torres Pedro H M, da Silva Manuela L, Pascutti Pedro G
Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Diretoria de Metrologia Aplicada às Ciências da Vida (DIMAV), Instituto Nacional de Metrologia Qualidade e Tecnologia (INMETRO), Xerém, Brazil.
Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
J Struct Biol. 2016 Aug;195(2):216-226. doi: 10.1016/j.jsb.2016.06.006. Epub 2016 Jun 10.
The active site of HIV protease (HIV-PR) is covered by two flaps. These flaps are known to be essential for the catalytic activity of the HIV-PR, but their exact conformations at the different stages of the enzymatic pathway remain subject to debate. Understanding the correct functional dynamics of the flaps might aid the development of new HIV-PR inhibitors. It is known that, the HIV-PR catalytic efficiency is pH-dependent, likely due to the influence of processes such as charge transfer and protonation/deprotonation of ionizable residues. Several Molecular Dynamics (MD) simulations have reported information about the HIV-PR flaps. However, in MD simulations the protonation of a residue is fixed and thus it is not possible to study the correlation between conformation and protonation state. To address this shortcoming, this work attempts to capture, through Constant pH Molecular Dynamics (CpHMD), the conformations of the apo, substrate-bound and inhibitor-bound HIV-PR, which differ drastically in their flap arrangements. The results show that the HIV-PR flaps conformations are defined by the protonation of the catalytic residues Asp25/Asp25' and that these residues are sensitive to pH changes. This study suggests that the catalytic aspartates can modulate the opening of the active site and substrate binding.
HIV蛋白酶（HIV-PR）的活性位点被两个侧翼覆盖。已知这些侧翼对于HIV-PR的催化活性至关重要，但它们在酶促途径不同阶段的确切构象仍存在争议。了解侧翼正确的功能动态可能有助于开发新型HIV-PR抑制剂。已知HIV-PR的催化效率依赖于pH值，这可能是由于诸如电荷转移以及可电离残基的质子化/去质子化等过程的影响。一些分子动力学（MD）模拟报告了有关HIV-PR侧翼的信息。然而，在MD模拟中，残基的质子化是固定的，因此无法研究构象与质子化状态之间的相关性。为了解决这一缺点，本研究试图通过恒定pH分子动力学（CpHMD）捕捉无配体、底物结合和抑制剂结合的HIV-PR的构象，这些构象在侧翼排列上有很大差异。结果表明，HIV-PR侧翼构象由催化残基Asp25/Asp25'的质子化决定，并且这些残基对pH变化敏感。这项研究表明，催化天冬氨酸可以调节活性位点的开放和底物结合。
