Roberts Victoria A
San Diego Supercomputer Center, University of California, San Diego , La Jolla, California 92093, United States.
J Chem Theory Comput. 2015 Sep 8;11(9):4500-11. doi: 10.1021/ct501125r. Epub 2015 Aug 6.
HIV integrase (HIV-IN), one of three HIV enzymes, is a target for the treatment of AIDS, but the full biological assembly has been difficult to characterize, hampering inhibitor design. The recent crystallographic structures of integrase from prototype foamy virus (PFV-IN) with bound DNA were a breakthrough, revealing how viral DNA organizes two integrase dimers into a tetramer that has the two active sites appropriately spaced for insertion of the viral DNA into host DNA. The organization of domains within each PFV-IN protein chain, however, varies significantly from that found in HIV-IN structures. With the goal of identifying shared structural characteristics, the interactions among components of the PFV-IN and HIV-IN assemblies were investigated with the macromolecular docking program DOT. DOT performs an exhaustive, rigid-body search between two macromolecules. Computational docking reproduced the crystallographic interactions of the PFV-IN catalytic and N-terminal domains with viral DNA and found similar viral DNA interactions for HIV-IN. Computational docking did not reproduce the crystallographic interactions of the PFV-IN C-terminal domain (CTD). Instead, two symmetry-related positions were found for the PFV-IN CTD that indicate formation of a CTD dimer between the two active sites. Our predicted CTD dimer is consistent with cross-linking studies showing interactions of the CTD with viral DNA that appear to be blocked in the PFV-IN structures. The CTD dimer can insert two arginine-rich loops between the two bound vDNA molecules and the host DNA, a region that is unoccupied in the PFV-IN crystallographic structures. The positive potential from these two loops would alleviate the large negative potential created by the close proximity of two viral vDNA ends, helping to bring together the two active sites and assisting host DNA binding. This study demonstrates the ability of computational docking to evaluate complex crystallographic assemblies, identify interactions that are influenced by the crystal environment, and provide plausible alternatives.
HIV整合酶（HIV-IN）是三种HIV酶之一，是治疗艾滋病的靶点，但完整的生物组装体一直难以表征，这阻碍了抑制剂的设计。近期原型泡沫病毒整合酶（PFV-IN）与结合DNA的晶体结构是一项突破，揭示了病毒DNA如何将两个整合酶二聚体组织成一个四聚体，该四聚体具有两个活性位点，其间距适合将病毒DNA插入宿主DNA。然而，每个PFV-IN蛋白链内结构域的组织与HIV-IN结构中的情况有显著差异。为了识别共同的结构特征，使用大分子对接程序DOT研究了PFV-IN和HIV-IN组装体各组分之间的相互作用。DOT在两个大分子之间进行详尽的刚体搜索。计算对接重现了PFV-IN催化结构域和N端结构域与病毒DNA的晶体相互作用，并发现HIV-IN也有类似的病毒DNA相互作用。计算对接没有重现PFV-IN C端结构域（CTD）的晶体相互作用。相反，发现PFV-IN CTD有两个对称相关的位置，这表明在两个活性位点之间形成了一个CTD二聚体。我们预测的CTD二聚体与交联研究一致，该研究表明CTD与病毒DNA的相互作用在PFV-IN结构中似乎被阻断。CTD二聚体可以在两个结合的病毒DNA分子和宿主DNA之间插入两个富含精氨酸的环，该区域在PFV-IN晶体结构中未被占据。这两个环的正电势将减轻两个病毒vDNA末端紧密靠近所产生的大的负电势，有助于使两个活性位点聚集在一起并协助宿主DNA结合。这项研究证明了计算对接能够评估复杂的晶体组装体，识别受晶体环境影响的相互作用，并提供合理的替代方案。
