CNR Institute for Interdisciplinary Applications of Physics, I-90146 Palermo, Italy.
Biophys J. 1999 Nov;77(5):2470-8. doi: 10.1016/S0006-3495(99)77083-9. Epub 2008 Nov 21.
Molecular dynamics simulations using a simple multielement model solute with internal degrees of freedom and accounting for solvent-induced interactions to all orders in explicit water are reported. The potential energy landscape of the solute is flat in vacuo. However, the sole untruncated solvent-induced interactions between apolar (hydrophobic) and charged elements generate a rich landscape of potential of mean force exhibiting typical features of protein landscapes. Despite the simplicity of our solute, the depth of minima in this landscape is not far in size from free energies that stabilize protein conformations. Dynamical coupling between configurational switching of the system and hydration reconfiguration is also elicited. Switching is seen to occur on a time scale two orders of magnitude longer than that of the reconfiguration time of the solute taken alone, or that of the unperturbed solvent. Qualitatively, these results are unaffected by a different choice of the water-water interaction potential. They show that already at an elementary level, solvent-induced interactions alone, when fully accounted for, can be responsible for configurational and dynamical features essential to protein folding and function.
本文报道了一种简单的多元素模型溶质的分子动力学模拟,该模型具有内部自由度,并考虑了溶剂诱导相互作用的所有阶次,以明确的水为溶剂。在真空中,溶质的位能景观是平坦的。然而,仅仅是无截短的溶剂诱导相互作用,在非极性(疏水性)和带电元素之间产生了丰富的平均力势能景观,表现出典型的蛋白质景观特征。尽管我们的溶质很简单,但这种景观中的最小深度与稳定蛋白质构象的自由能相差不大。系统构象切换和水合重新配置之间的动态耦合也被激发出来。可以看出,切换发生的时间尺度比单独考虑溶质的重新配置时间或未受干扰的溶剂的时间尺度长两个数量级。定性地说,这些结果不受不同的水分子间相互作用势的选择的影响。它们表明,即使在基本水平上,仅当完全考虑溶剂诱导相互作用时,它们就可以负责蛋白质折叠和功能所必需的构象和动力学特征。