Vander Zanden Crystal M, Carter Megan, Ho Pui Shing
Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, United States(1)Current address: Department of Biochemistry and Biophysics, Stockholm Univeristy SE-106 91 Stockholm, Sweden.
Methods. 2013 Nov;64(1):12-8. doi: 10.1016/j.ymeth.2013.07.039. Epub 2013 Aug 6.
The concept of single crystals of macromolecules as thermodynamic systems is not a common one. However, it should be possible to derive thermodynamic properties from single crystal structures, if the process of crystallization follows thermodynamic rules. We review here an example of how the stabilizing potentials of molecular interactions can be measured from studying the properties of DNA crystals. In this example, we describe an assay based on the four-stranded DNA junction to determine the stabilizing potentials of halogen bonds, a class of electrostatic interactions, analogous to hydrogen bonds, that are becoming increasing recognized as important for conferring specificity in protein-ligand complexes. The system demonstrates how crystallographic studies, when coupled with calorimetric methods, allow the geometries at the atomic level to be directly correlated with the stabilizing energies of molecular interactions. The approach can be generally applied to study the effects of DNA sequence and modifications of the thermodynamic stability of the Holliday junction and, by inference, on recombination and recombination dependent processes.
将大分子单晶视为热力学系统的概念并不常见。然而，如果结晶过程遵循热力学规则，那么从单晶结构推导热力学性质应该是可行的。在此，我们回顾一个例子，说明如何通过研究DNA晶体的性质来测量分子间相互作用的稳定势。在这个例子中，我们描述了一种基于四链DNA连接体的测定方法，以确定卤键的稳定势，卤键是一类静电相互作用，类似于氢键，越来越被认为对于赋予蛋白质-配体复合物特异性很重要。该系统展示了晶体学研究与量热法相结合时，如何使原子水平的几何结构与分子间相互作用的稳定能直接相关。该方法通常可用于研究DNA序列的影响以及对霍利迪连接体热力学稳定性的修饰，并由此推断对重组和依赖重组的过程的影响。
