Setny Piotr
Department of Biophysics, Institute of Experimental Physics, University of Warsaw, 02-089 Warsaw, Poland.
J Chem Phys. 2008 Mar 28;128(12):125105. doi: 10.1063/1.2839885.
We consider a model system of methane molecule and a hemispherical, hydrophobic pocket of an 8 A radius, remaining together in aqueous environment. A spatial map of potential of mean force acting on methane molecule due to presence of pocket is constructed, based on a series of explicit solvent molecular dynamics simulations. A relation between free energy variations associated with methane translocations and accompanying changes in solvent density distribution is analyzed. A funnel-like area where free energy is diminished with respect to bulk is present over the pocket entrance and extends up to 9 A toward the bulk solvent. In order to get into the pocket, however, methane has to cross a free energy barrier, which is more prominent around the circumferential part of pocket entrance, while achieving bulklike free energy values at the very center. As a methane molecule crosses this barrier, the pocket gets completely dehydrated, which leads to "hydrophobic collapse," manifested by a sharp decrease in free energy. We find that the observed free energy changes are closely related to interactions between the methane hydration shell and the surrounding solvent. Results presented here are a continuation of our previous studies of methane-pocket systems.
我们考虑一个模型系统,其中甲烷分子与一个半径为8埃的半球形疏水口袋在水环境中共存。基于一系列显式溶剂分子动力学模拟,构建了由于口袋的存在而作用于甲烷分子的平均力势的空间图。分析了与甲烷迁移相关的自由能变化与伴随的溶剂密度分布变化之间的关系。在口袋入口上方存在一个漏斗状区域,相对于本体,自由能在此区域减小,并向本体溶剂延伸9埃。然而,为了进入口袋,甲烷必须越过一个自由能垒,该自由能垒在口袋入口的圆周部分周围更为突出,而在口袋正中心达到类似本体的自由能值。当一个甲烷分子越过这个壁垒时,口袋会完全脱水,这会导致“疏水坍塌”,表现为自由能急剧下降。我们发现,观察到的自由能变化与甲烷水合壳层和周围溶剂之间的相互作用密切相关。这里呈现的结果是我们之前对甲烷 - 口袋系统研究的延续。