Pizzitutti Francesco, Marchi Massimo, Sterpone Fabio, Rossky Peter J
Commissariat a l'Energie Atomique, DSV-DBJC-SBFM, Centre d'Etudes, Saclay, 91191 Gif-sur-Yvette Cedex, France.
J Phys Chem B. 2007 Jul 5;111(26):7584-90. doi: 10.1021/jp0717185. Epub 2007 Jun 12.
Water around biomolecules slows down with respect to pure water, and both rotation and translation exhibit anomalous time dependence in the hydration shell. The origin of such behavior remains elusive. We use molecular dynamics simulations of water dynamics around several designed protein models to establish the connection between the appearance of the anomalous dynamics and water-protein interactions. For the first time we quantify the separate effect of protein topological and energetic disorder on the hydration water dynamics. When a static protein structure is simulated, we show that both types of disorder contribute to slow down water diffusion, and that allowing for protein motion, increasing the spatial dimensionality of the interface, reduces the anomalous character of hydration water. The rotation of water is, instead, altered by the energetic disorder only; indeed, when electrostatic interactions between the protein and water are switched off, water reorients even faster than in the bulk. The dynamics of water is also related to the collective structure--à voir the hydrogen bond (H-bond) network--formed by the solvent enclosing the protein surface. We show that, as expected for a full hydrated protein, when the protein surface offers pinning sites (charged or polar sites), the superficial water-water H-bond network percolates throughout the whole surface, hindering the water diffusion, whereas it does not when the protein surface lacks electrostatic interactions with water and the water diffusion is enhanced.
生物分子周围的水相对于纯水而言流动性减慢,并且在水化层中,水分子的转动和平动都表现出异常的时间依赖性。这种行为的起源仍然难以捉摸。我们通过对几个设计好的蛋白质模型周围的水动力学进行分子动力学模拟,来建立异常动力学的出现与水 - 蛋白质相互作用之间的联系。我们首次量化了蛋白质拓扑无序和能量无序对水化水动力学的单独影响。当模拟静态蛋白质结构时,我们发现这两种无序类型都会导致水扩散减慢,并且允许蛋白质运动、增加界面的空间维度会降低水化水的异常特性。相反,水的转动仅受能量无序的影响;实际上,当蛋白质与水之间的静电相互作用关闭时,水重新定向的速度甚至比在本体中还要快。水的动力学还与由包围蛋白质表面的溶剂形成的集体结构(即氢键网络)有关。我们表明,正如对完全水合蛋白质所预期的那样,当蛋白质表面提供固定位点(带电或极性位点)时,表面水 - 水氢键网络贯穿整个表面,阻碍水的扩散,而当蛋白质表面缺乏与水的静电相互作用且水扩散增强时则不会出现这种情况。