Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, United States of America.
Departamento de Física, Universidad Autónoma Metropolitana, Iztapalapa, Ciudad de México, México.
PLoS One. 2019 Aug 22;14(8):e0221256. doi: 10.1371/journal.pone.0221256. eCollection 2019.
HIV-1 Gag is a large multidomain poly-protein with flexible unstructured linkers connecting its globular subdomains. It is compact when in solution but assumes an extended conformation when assembled within the immature HIV-1 virion. Here, we use molecular dynamics (MD) simulations to quantitatively characterize the intra-domain interactions of HIV-1 Gag. We find that the matrix (MA) domain and the C-terminal subdomain CActd of the CA capsid domain can form a bound state. The bound state, which is held together primarily by interactions between complementary charged and polar residues, stabilizes the compact state of HIV-1 Gag. We calculate the depth of the attractive free energy potential between the MA/ CActd sites and find it to be about three times larger than the dimerization interaction between the CActd domains. Sequence analysis shows high conservation within the newly-found intra-Gag MA/CActd binding site, as well as its spatial proximity to other well known elements of Gag -such as CActd's SP1 helix region, its inositol hexaphosphate (IP6) binding site and major homology region (MHR), as well as the MA trimerization site. Our results point to a high, but yet undetermined, functional significance of the intra-Gag binding site. Recent biophysical experiments that address the binding specificity of Gag are interpreted in the context of the MA/CActd bound state, suggesting an important role in selective packaging of genomic RNA by Gag.
HIV-1 Gag 是一种具有灵活无规连接的大型多结构域聚蛋白，连接其球状亚结构域。在溶液中时，它是紧凑的，但在组装到不成熟的 HIV-1 病毒粒子中时，它会呈现出伸展构象。在这里，我们使用分子动力学（MD）模拟来定量表征 HIV-1 Gag 的域内相互作用。我们发现基质（MA）域和 CA 衣壳域的 C 末端亚域 CActd 可以形成一个结合状态。该结合状态主要由互补带电和极性残基之间的相互作用来稳定，稳定了 HIV-1 Gag 的紧凑状态。我们计算了 MA/ CActd 结合位点之间的吸引力自由能势的深度，发现它比 CActd 域之间的二聚化相互作用大约大三倍。序列分析表明，在新发现的 Gag 内 MA/CActd 结合位点内具有高度保守性，并且与 Gag 的其他已知元素（如 CActd 的 SP1 螺旋区、其六磷酸肌醇（IP6）结合位点和主要同源区（MHR）以及 MA 三聚化位点）的空间接近。我们的结果表明，该结合位点具有较高但尚未确定的功能意义。最近的生物物理实验解决了 Gag 结合特异性的问题，我们根据 MA/CActd 结合状态对其进行了解释，表明其在 Gag 对基因组 RNA 的选择性包装中具有重要作用。
