University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Biophys J. 2012 Mar 7;102(5):1108-17. doi: 10.1016/j.bpj.2012.01.002. Epub 2012 Mar 6.
Protein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the ~1-100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion's contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins.
蛋白质的功能通常需要大规模的结构域运动。在蛋白质结构域运动的实验表征方面，一个令人兴奋的新进展是中子自旋回波谱（NSE）的应用。NSE 直接探测在~1-100 ns 时间尺度上相干（即，对关联）散射。在这里，我们报告了一种蛋白质——磷酸甘油酸激酶的全原子分子动力学（MD）模拟，我们从该模拟中计算出小角度中子散射（SANS）和 NSE 散射性质。模拟衍生的和实验溶液 SANS 结果非常吻合。考察了平移和旋转全分子扩散对模拟衍生的 NSE 的贡献及其估计中的潜在问题。主成分分析确定了主导内部运动对 NSE 信号贡献的结构域运动类型，其中最大的是经典的铰链弯曲。相关的自由能分布是准谐的，摩擦特性对应于高度过阻尼运动。通过 MD 得出的运动幅度小于通过实验分析得出的运动幅度，并且讨论了这种差异的可能原因。MD 结果证实 NSE 的一个重要组成部分来自内部动力学。它们还表明，NSE 与 MD 的结合可能有助于确定蛋白质中功能结构域运动的形式、平均力势和时间依赖性。
