Norin M, Haeffner F, Hult K, Edholm O
Royal Institute of Technology, Stockholm, Sweden.
Biophys J. 1994 Aug;67(2):548-59. doi: 10.1016/S0006-3495(94)80515-6.
We report on molecular dynamics simulations of a medium-sized protein, a lipase from Rhizomucor miehei, in vacuum, in water, and in a nonpolar solvent, methyl hexanoate. Depending on force field and solvent, the molecular dynamics structures obtained as averages over 150 ps had root-mean-square deviations in the range of 1.9 to 3.6 A from the crystal structure. The largest differences between the structures were in hydrogen bonding and exposed surface areas of the protein. The surface area increased in both solvents and became smaller in vacuum. The change of surface exposure varied greatly between different residues and occurred in accordance with the hydrophobicity of the residue and the nature of the solvent. The fluctuations of the atoms were largest in the external loops and agreed well with crystallographic temperature factors. Root-mean-square fluctuations were significantly smaller in the nonpolar solvents than they were in water, which is in accordance with the notion that proteins become more rigid in nonpolar solvents. In methyl hexanoate a partial opening of the lid covering the active site occurred, letting a methyl hexanoate molecule approach the active site.
我们报告了对一种中等大小的蛋白质——米黑根毛霉脂肪酶，在真空、水和非极性溶剂己酸甲酯中的分子动力学模拟。根据力场和溶剂的不同，在150皮秒内得到的平均分子动力学结构与晶体结构的均方根偏差在1.9至3.6埃范围内。结构之间最大的差异在于蛋白质的氢键和暴露表面积。在两种溶剂中表面积都增加了，而在真空中变小。不同残基的表面暴露变化差异很大，并且与残基的疏水性和溶剂的性质有关。原子的波动在外部环中最大，这与晶体学温度因子吻合得很好。在非极性溶剂中的均方根波动明显小于在水中的，这与蛋白质在非极性溶剂中变得更刚性的观点一致。在己酸甲酯中，覆盖活性位点的盖子部分打开，使一个己酸甲酯分子接近活性位点。
