Laboratory of Cellular Biophysics, Rockefeller University, New York, New York, United States of America.
Department of Physics and Astronomy, Hofstra University, 151 Hofstra University, Hempstead, New York, United States of America.
PLoS One. 2018 Apr 20;13(4):e0196133. doi: 10.1371/journal.pone.0196133. eCollection 2018.
We report a computational model for the assembly of HIV-1 Gag into immature viral particles at the plasma membrane. To reproduce experimental structural and kinetic properties of assembly, a process occurring on the order of minutes, a coarse-grained representation consisting of a single particle per Gag molecule is developed. The model uses information relating the functional interfaces implicated in Gag assembly, results from cryo electron-tomography, and biophysical measurements from fluorescence microscopy, such as the dynamics of Gag assembly at single virions. These experimental constraints eliminated many classes of potential interactions, and narrowed the model to a single interaction scheme with two non-equivalent interfaces acting to form Gags into a hexamer, and a third interface acting to link hexamers together. This model was able to form into a hexameric structure with correct lattice spacing and reproduced biologically relevant growth rates. We explored the effect of genomic RNA seeding punctum growth, finding that RNA may be a factor in locally concentrating Gags to initiate assembly. The simulation results infer that completion of assembly cannot be governed simply by Gag binding kinetics. However the addition of membrane curvature suggests that budding of the virion from the plasma membrane could factor into slowing incorporation of Gag at an assembly site resulting in virions of the same size and number of Gag molecules independent of Gag concentration or the time taken to complete assembly. To corroborate the results of our simulation model, we developed an analytic model for Gag assembly finding good agreement with the simulation results.
我们报告了一个 HIV-1 Gag 在质膜上组装成不成熟病毒颗粒的计算模型。为了重现组装的实验结构和动力学特性，即发生在几分钟内的过程，开发了一种由每个 Gag 分子一个粒子组成的粗粒度表示。该模型使用了与 Gag 组装中涉及的功能界面相关的信息、冷冻电子断层扫描的结果以及荧光显微镜的生物物理测量结果，例如单个病毒颗粒上 Gag 组装的动力学。这些实验约束排除了许多潜在相互作用的类别，并将模型缩小到一个单一的相互作用方案，其中两个不等效的界面作用将 Gag 组装成六聚体，第三个界面作用将六聚体连接在一起。该模型能够形成具有正确晶格间距的六聚体结构，并复制了具有生物学相关性的生长速率。我们探讨了基因组 RNA 接种点生长对组装的影响，发现 RNA 可能是局部浓缩 Gag 以启动组装的一个因素。模拟结果推断，组装的完成不能仅仅由 Gag 结合动力学来控制。然而，膜曲率的增加表明，病毒从质膜出芽可能会影响组装部位 Gag 的掺入速度，从而导致相同大小和相同数量 Gag 分子的病毒，而与 Gag 浓度或完成组装所需的时间无关。为了证实我们的模拟模型的结果，我们开发了一个 Gag 组装的分析模型，发现与模拟结果吻合良好。
