Camilloni C, Rocco A Guerini, Eberini I, Gianazza E, Broglia R A, Tiana G
Department of Physics, University of Milano and INFN, I-20133 Milan, Italy.
Biophys J. 2008 Jun;94(12):4654-61. doi: 10.1529/biophysj.107.125799. Epub 2008 Mar 13.
In performing protein-denaturation experiments, it is common to employ different kinds of denaturants interchangeably. We make use of molecular dynamics simulations of Protein L in water, in urea, and in guanidinium chloride (GdmCl) to ascertain if there are any structural differences in the associated unfolding processes. The simulation of proteins in solutions of GdmCl is complicated by the large number of charges involved, making it difficult to set up a realistic force field. Furthermore, at high concentrations of this denaturant, the motion of the solvent slows considerably. The simulations show that the unfolding mechanism depends on the denaturing agent: in urea the beta-sheet is destabilized first, whereas in GdmCl, it is the alpha-helix. Moreover, whereas urea interacts with the protein accumulating in the first solvation shell, GdmCl displays a longer-range electrostatic effect that does not perturb the structure of the solvent close to the protein.
在进行蛋白质变性实验时，通常会交替使用不同种类的变性剂。我们利用蛋白质L在水中、尿素中以及氯化胍（GdmCl）中的分子动力学模拟，来确定相关的展开过程中是否存在任何结构差异。在GdmCl溶液中对蛋白质进行模拟因涉及大量电荷而变得复杂，这使得难以建立一个逼真的力场。此外，在这种变性剂的高浓度下，溶剂的运动显著减慢。模拟结果表明，展开机制取决于变性剂：在尿素中，β-折叠首先失稳，而在GdmCl中，是α-螺旋失稳。此外，尿素与积累在第一溶剂化层中的蛋白质相互作用，而GdmCl则表现出一种长程静电效应，这种效应不会扰乱靠近蛋白质的溶剂结构。
