Center for Biophysical Modeling and Simulation, and Department of Chemistry, University of Utah, Salt Lake City, Utah, USA.
Biophys J. 2010 Jan 6;98(1):18-26. doi: 10.1016/j.bpj.2009.09.049.
Coarse-grained models of the HIV-1 CA dimer are constructed based on all-atom molecular dynamics simulations. Coarse-grained representations of the capsid shell, which is composed of approximately 1500 copies of CA proteins, are constructed and their stability is examined. A key interaction between carboxyl and hexameric amino terminal domains is shown to generate the curvature of the capsid shell. It is demonstrated that variation of the strength of this interaction for different subunits in the lattice can cause formation of asymmetric, conical-shaped closed capsid shells, and it is proposed that variations, in the structure of the additional carboxyl-amino terminal binding interface during self-assembly, are important aspects of capsid cone formation. These results are in agreement with recent structural studies of the capsid hexamer subunit, which suggest that variability in the binding interface is a cause of the differences in subunit environments that exist in a conical structure.
基于全原子分子动力学模拟构建了 HIV-1 CA 二聚体的粗粒模型。构建了由大约 1500 个 CA 蛋白组成的衣壳壳的粗粒表示，并检查了它们的稳定性。显示羧基和六聚体氨基末端结构域之间的关键相互作用产生了衣壳壳的曲率。证明了晶格中不同亚基的这种相互作用强度的变化会导致不对称的锥形封闭衣壳壳的形成，并提出了在自组装过程中额外的羧基-氨基末端结合界面的结构变化是衣壳锥形成的重要方面。这些结果与最近对衣壳六聚体亚基的结构研究一致，表明结合界面的可变性是锥形结构中存在的亚基环境差异的原因。
