Biophysical Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden.
J Am Chem Soc. 2013 Jun 12;135(23):8735-48. doi: 10.1021/ja403405d. Epub 2013 May 29.
Many proteins rely on rare structural fluctuations for their function, whereby solvent and other small molecules gain transient access to internal cavities. In magnetic relaxation dispersion (MRD) experiments, water molecules buried in such cavities are used as intrinsic probes of the intermittent protein motions that govern their exchange with external solvent. While this has allowed a detailed characterization of exchange kinetics for several proteins, little is known about the exchange mechanism. Here, we use a millisecond all-atom MD trajectory produced by Shaw et al. (Science2010, 330, 341) to characterize water exchange from the four internal hydration sites in the protein bovine pancreatic trypsin inhibitor. Using a recently developed stochastic point process approach, we compute the survival correlation function probed by MRD experiments as well as other quantities designed to validate the exchange-mediated orientational randomization (EMOR) model used to interpret the MRD data. The EMOR model is found to be quantitatively accurate, and the simulation reproduces the experimental mean survival times for all four sites with activation energy discrepancies in the range 0-3 kBT. On the other hand, the simulated hydration sites are somewhat too flexible, and the water flip barrier is underestimated by up to 6 kBT. The simulation reveals that water molecules gain access to the internal sites by a transient aqueduct mechanism, migrating as single-file water chains through transient (<5 ns) tunnels or pores. The present study illustrates the power of state-of-the-art molecular dynamics simulations in validating and extending experimental results.
许多蛋白质依赖于罕见的结构波动来发挥其功能，溶剂和其他小分子可以借此短暂进入内部腔室。在磁共振弛豫分散（MRD）实验中，埋藏在这些腔室中的水分子被用作内部探针，用于探测控制蛋白质与外部溶剂交换的间歇性蛋白质运动。虽然这已经允许对几种蛋白质的交换动力学进行详细的描述，但对交换机制知之甚少。在这里，我们使用 Shaw 等人（Science 2010, 330, 341）生成的毫秒级全原子 MD 轨迹，来描述蛋白质牛胰蛋白酶抑制剂中四个内部水合位点的水分子交换。我们使用最近开发的随机点过程方法，计算出 MRD 实验探测的生存相关函数以及其他旨在验证用于解释 MRD 数据的交换介导的取向随机化（EMOR）模型的数量。发现 EMOR 模型在定量上是准确的，模拟再现了所有四个位点的实验平均生存时间，其激活能差异在 0-3 kBT 范围内。另一方面，模拟的水合位点有点过于灵活，水翻转势垒被低估了 6 kBT。模拟表明，水分子通过瞬态导水机制进入内部位点，作为单分子水链通过瞬态（<5ns）隧道或孔隙迁移。本研究说明了最先进的分子动力学模拟在验证和扩展实验结果方面的强大功能。
