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辅助因子的时间控制可防止逆转录病毒 Gag 晶格组装中的动力学捕获。

Temporal control by cofactors prevents kinetic trapping in retroviral Gag lattice assembly.

机构信息

TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.

Department of Physics, and Center for Cellular and Biomolecular Machines, University of California, Merced, California.

出版信息

Biophys J. 2023 Aug 8;122(15):3173-3190. doi: 10.1016/j.bpj.2023.06.021. Epub 2023 Jun 30.

Abstract

For retroviruses like HIV to proliferate, they must form virions shaped by the self-assembly of Gag polyproteins into a rigid lattice. This immature Gag lattice has been structurally characterized and reconstituted in vitro, revealing the sensitivity of lattice assembly to multiple cofactors. Due to this sensitivity, the energetic criterion for forming stable lattices is unknown, as are their corresponding rates. Here, we use a reaction-diffusion model designed from the cryo-ET structure of the immature Gag lattice to map a phase diagram of assembly outcomes controlled by experimentally constrained rates and free energies, over experimentally relevant timescales. We find that productive assembly of complete lattices in bulk solution is extraordinarily difficult due to the large size of this ∼3700 monomer complex. Multiple Gag lattices nucleate before growth can complete, resulting in loss of free monomers and frequent kinetic trapping. We therefore derive a time-dependent protocol to titrate or "activate" the Gag monomers slowly within the solution volume, mimicking the biological roles of cofactors. This general strategy works remarkably well, yielding productive growth of self-assembled lattices for multiple interaction strengths and binding rates. By comparing to the in vitro assembly kinetics, we can estimate bounds on rates of Gag binding to Gag and the cellular cofactor IP6. Our results show that Gag binding to IP6 can provide the additional time delay necessary to support smooth growth of the immature lattice with relatively fast assembly kinetics, mostly avoiding kinetic traps. Our work provides a foundation for predicting and disrupting formation of the immature Gag lattice via targeting specific protein-protein binding interactions.

摘要

为了使 HIV 等逆转录病毒增殖,它们必须形成由 Gag 多聚蛋白自我组装成刚性晶格的病毒粒子。这种不成熟的 Gag 晶格已经在结构上进行了表征,并在体外进行了重建,揭示了晶格组装对多种辅助因子的敏感性。由于这种敏感性,形成稳定晶格的能量标准是未知的,它们的相应速率也是未知的。在这里,我们使用从不成熟的 Gag 晶格的低温电子断层扫描结构设计的反应-扩散模型,来绘制由实验约束的速率和自由能控制的组装结果的相图,这些速率和自由能跨越了实验相关的时间尺度。我们发现,由于这个大约 3700 个单体复合物的巨大尺寸,在大量溶液中完整晶格的有效组装是极其困难的。在生长完成之前,多个 Gag 晶格会发生成核,导致游离单体的损失和频繁的动力学捕获。因此,我们推导出了一种时间依赖性的方案,可以在溶液体积中缓慢滴定或“激活”Gag 单体,模拟辅助因子的生物学作用。这种通用策略非常有效,为多种相互作用强度和结合速率产生了自组装晶格的有效生长。通过与体外组装动力学进行比较,我们可以估计 Gag 与 Gag 和细胞辅助因子 IP6 结合的速率的边界。我们的结果表明,Gag 与 IP6 的结合可以提供额外的时间延迟,以支持具有相对较快组装动力学的不成熟晶格的平滑生长,从而在很大程度上避免动力学陷阱。我们的工作为通过靶向特定的蛋白质-蛋白质结合相互作用来预测和破坏不成熟的 Gag 晶格的形成提供了基础。

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