Schwartz R, Shor P W, Prevelige P E, Berger B
Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Biophys J. 1998 Dec;75(6):2626-36. doi: 10.1016/S0006-3495(98)77708-2.
A computer model is described for studying the kinetics of the self-assembly of icosahedral viral capsids. Solution of this problem is crucial to an understanding of the viral life cycle, which currently cannot be adequately addressed through laboratory techniques. The abstract simulation model employed to address this is based on the local rules theory of. Proc. Natl. Acad. Sci. USA. 91:7732-7736). It is shown that the principle of local rules, generalized with a model of kinetics and other extensions, can be used to simulate complicated problems in self-assembly. This approach allows for a computationally tractable molecular dynamics-like simulation of coat protein interactions while retaining many relevant features of capsid self-assembly. Three simple simulation experiments are presented to illustrate the use of this model. These show the dependence of growth and malformation rates on the energetics of binding interactions, the tolerance of errors in binding positions, and the concentration of subunits in the examples. These experiments demonstrate a tradeoff within the model between growth rate and fidelity of assembly for the three parameters. A detailed discussion of the computational model is also provided.
描述了一种用于研究二十面体病毒衣壳自组装动力学的计算机模型。解决这个问题对于理解病毒生命周期至关重要，而目前通过实验室技术无法充分解决这一问题。用于解决此问题的抽象模拟模型基于《美国国家科学院院刊》91:7732 - 7736中提出的局部规则理论。结果表明，通过动力学模型及其他扩展进行推广的局部规则原理，可用于模拟自组装中的复杂问题。这种方法允许在保留衣壳自组装许多相关特征的同时，对衣壳蛋白相互作用进行计算上易于处理的类似分子动力学的模拟。给出了三个简单的模拟实验来说明该模型的使用。这些实验表明了生长和畸形率对结合相互作用能量学、结合位置误差容忍度以及示例中亚基浓度的依赖性。这些实验证明了模型中这三个参数在生长速率和组装保真度之间的权衡。还提供了对计算模型的详细讨论。
