Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Building, Stanford, CA 94305, USA.
Proc Natl Acad Sci U S A. 2011 Aug 30;108(35):14455-60. doi: 10.1073/pnas.1110626108. Epub 2011 Aug 15.
Accurate description of water structure affects simulation of protein folding, substrate binding, macromolecular recognition, and complex formation. We study the hydration of buckminsterfullerene, the smallest hydrophobic nanosphere, by molecular dynamics simulations using a state-of-the-art quantum mechanical polarizable force field (QMPFF3), derived from quantum mechanical data at the MP2/aug-cc-pVTZ(-hp) level augmented by CCSD(T). QMPFF3 calculation of the hydrophobic effect is compared to that obtained with empirical force fields. Using a novel and highly sensitive method, we see polarization increases ordered water structure so that the imprint of the hydrophobic surface atoms on the surrounding waters is stronger and extends to long-range. We see less water order for empirical force fields. The greater order seen with QMPFF3 will affect biological processes through a stronger hydrophobic effect.
准确描述水的结构会影响蛋白质折叠、底物结合、大分子识别和复合物形成的模拟。我们通过分子动力学模拟研究了富勒烯，即最小的疏水纳米球的水合作用，使用了一种最先进的量子力学极化力场（QMPFF3），该力场源自 MP2/aug-cc-pVTZ(-hp) 水平的量子力学数据，并通过 CCSD(T) 进行了扩充。将 QMPFF3 计算的疏水效应与经验力场的结果进行了比较。使用一种新颖且高度灵敏的方法，我们发现极化增加了有序水结构，使得疏水表面原子对周围水的影响更强烈，并延伸到远程。我们发现经验力场的水有序性较低。与经验力场相比，QMPFF3 中观察到的更大的有序性将通过更强的疏水效应影响生物过程。
