We report the free-energy landscape and thermodynamics of the protein-protein association responsible for the drug-induced multimerization of HIV-1 integrase (IN). Allosteric HIV-1 integrase inhibitors promote aberrant IN multimerization by bridging IN-IN intermolecular interactions. However, the thermodynamic driving forces and kinetics of the multimerization remain largely unknown. Here, we explore the early steps in the IN multimerization by using umbrella sampling and unbiased molecular dynamics simulations in explicit solvent. In direct simulations, the two initially separated dimers spontaneously associate to form near-native complexes that resemble the crystal structure of the aberrant tetramer. Most strikingly, the effective interaction of the protein-protein association is very short-ranged: the two dimers associate rapidly within tens of nanoseconds when their binding surfaces are separated by d ≤ 4.3 Å (less than two water diameters). Beyond this distance, the oligomerization kinetics appears to be diffusion controlled with a much longer association time. The free-energy profile also captured the crucial role of allosteric IN inhibitors in promoting multimerization and explained why several C-terminal domain mutations are remarkably resistant to the drug-induced multimerization. The results also show that at small separation, the protein-protein binding process contains two consecutive phases with distinct thermodynamic signatures. First, interprotein water molecules are expelled to the bulk, resulting in a small increase in entropy, as the solvent entropy gain from the water release is nearly cancelled by the loss of side-chain entropies as the two proteins approach each other. At shorter distances, the two dry binding surfaces adapt to each other to optimize their interaction energy at the expense of further protein configurational entropy loss. Although the binding interfaces feature clusters of hydrophobic residues, overall, the protein-protein association in this system is driven by enthalpy and opposed by entropy.

中文翻译：

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探索蛋白质-蛋白质结合的自由能景观和热力学：变构抑制剂诱导的 HIV-1 整合酶多聚化

我们报告了负责药物诱导 HIV-1 整合酶 (IN) 多聚化的蛋白质-蛋白质协会的自由能景观和热力学。变构 HIV-1 整合酶抑制剂通过桥接 IN-IN 分子间相互作用促进异常的 IN 多聚化。然而，多聚化的热力学驱动力和动力学仍然很大程度上未知。在这里，我们通过在显式溶剂中使用伞形采样和无偏分子动力学模拟来探索 IN 多聚化的早期步骤。在直接模拟中，两个最初分离的二聚体自发地结合形成近乎天然的复合物，类似于异常四聚体的晶体结构。最引人注目的是，蛋白质-蛋白质关联的有效相互作用是非常短程的：当它们的结合表面相隔 d ≤ 4.3 Å（小于两个水的直径）时，这两个二聚体在几十纳秒内迅速结合。超过这个距离，低聚动力学似乎受扩散控制，结合时间要长得多。自由能谱还捕捉到变构 IN 抑制剂在促进多聚化中的关键作用，并解释了为什么几个 C 端结构域突变对药物诱导的多聚化具有显着抗性。结果还表明，在小分离时，蛋白质-蛋白质结合过程包含具有不同热力学特征的两个连续相。首先，蛋白间水分子被排出到本体中，导致熵的小幅增加，因为当两种蛋白质相互接近时，从水释放中获得的溶剂熵几乎被侧链熵的损失抵消了。在较短的距离上，两个干燥的结合表面相互适应以优化它们的相互作用能，但代价是进一步的蛋白质构型熵损失。尽管结合界面具有疏水残基簇，但总体而言，该系统中的蛋白质-蛋白质结合受焓驱动，受熵反。