Institut Jean Lamour, Département 1, CNRS, Nancy-Université, UPV-Metz, Vandoeuvre-lès-Nancy, France.
J Chem Phys. 2011 Feb 28;134(8):085107. doi: 10.1063/1.3554731.
First shells of hydration and bulk solvent play a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics approach. We formulate a hydration model where the hydrogen bonds between water molecules pertaining to the first shell of the protein conformation may be either mainly formed or broken. At thermal equilibrium, hydrogen bonds are formed at low temperature and are broken at high temperature. To explore the solvent effect, we follow the folding of a large sampling of protein chains, using a master-equation evolution. The dynamics shows a clear mechanism. Above the glass-transition temperature, a large ratio of chains fold very rapidly into the native structure irrespective of the temperature, following pathways of high transition rates through structures surrounded by the solvent with broken hydrogen bonds. Although these states have an infinitesimal probability, they act as strong dynamical attractors and fast folding proceeds along these routes rather than pathways with small transition rates between configurations of much higher equilibrium probabilities. At a given low temperature, a broad jump in the folding times is observed. Below this glass temperature, the pathways where hydrogen bonds are mainly formed become those of highest rates although with conformational changes of huge relaxation times. The present results reveal that folding obeys a double-funnel mechanism.
水合壳和主体溶剂在蛋白质折叠中起着至关重要的作用。在这里,我们使用理论蛋白质-溶剂模型和统计物理方法研究了水在蛋白质动力学中的作用。我们提出了一种水合模型,其中蛋白质构象第一层的水分子之间的氢键可以主要形成或断裂。在热平衡时,氢键在低温下形成,在高温下断裂。为了探索溶剂效应,我们使用主方程演化方法,对大量蛋白质链的折叠进行了研究。动力学显示出一种明确的机制。在玻璃化转变温度以上,很大比例的链无论温度如何都非常迅速地折叠成天然结构,遵循通过溶剂包围的结构的高转移率途径,这些结构中的氢键被打破。尽管这些状态的概率极小,但它们作为强动力学吸引子,快速折叠沿着这些途径进行,而不是沿着配置之间转移率较小的途径,这些配置的平衡概率要高得多。在给定的低温下,折叠时间会出现明显的跃升。在这个玻璃化温度以下,虽然构象变化的弛豫时间很大,但主要形成氢键的途径成为了转移率最高的途径。本研究结果表明,折叠遵循双漏斗机制。