Karunaweera Sadish, Gee Moon Bae, Weerasinghe Samantha, Smith Paul E
Department of Chemistry, Kansas State University, Manhattan, Kansas 66506.
J Chem Theory Comput. 2012 May 28;8(10):3493-3503. doi: 10.1021/ct300079v. Epub 2012 Oct 9.
Most cellular processes occur in systems containing a variety of components many of which are open to material exchange. However, computer simulations of biological systems are almost exclusively performed in systems closed to material exchange. In principle, the behavior of biomolecules in open and closed systems will be different. Here, we provide a rigorous framework for the analysis of experimental and simulation data concerning open and closed multicomponent systems using the Kirkwood-Buff (KB) theory of solutions. The results are illustrated using computer simulations for various concentrations of the solutes Gly, Gly(2) and Gly(3) in both open and closed systems, and in the absence or presence of NaCl as a cosolvent. In addition, KB theory is used to help rationalize the aggregation properties of the solutes. Here one observes that the picture of solute association described by the KB integrals, which are directly related to the solution thermodynamics, and that provided by more physical clustering approaches are different. It is argued that the combination of KB theory and simulation data provides a simple and powerful tool for the analysis of complex multicomponent open and closed systems.
大多数细胞过程发生在包含多种成分的系统中,其中许多成分可进行物质交换。然而,生物系统的计算机模拟几乎都是在物质交换封闭的系统中进行的。原则上,生物分子在开放和封闭系统中的行为会有所不同。在此,我们提供了一个严格的框架,用于使用柯克伍德 - 布夫(KB)溶液理论分析关于开放和封闭多组分系统的实验和模拟数据。通过计算机模拟展示了结果,模拟对象为开放和封闭系统中不同浓度的溶质甘氨酸(Gly)、二聚甘氨酸(Gly(2))和三聚甘氨酸(Gly(3)),以及有无作为共溶剂的氯化钠(NaCl)的情况。此外,KB理论用于帮助解释溶质的聚集特性。在此可以观察到,与溶液热力学直接相关的KB积分所描述的溶质缔合情况,与更多基于物理聚集方法所提供的情况不同。有人认为,KB理论与模拟数据的结合为分析复杂的多组分开放和封闭系统提供了一个简单而强大的工具。