Markwick Phineus R L, Bouvignies Guillaume, Blackledge Martin
Institute de Biologie Structurale Jean-Pierre Ebel, CNRS, CEA, UJF, UMR 5075, 41 rue Jules Horowitz, F-38027 Grenoble, Cedex, France.
J Am Chem Soc. 2007 Apr 18;129(15):4724-30. doi: 10.1021/ja0687668. Epub 2007 Mar 22.
Biological function relies on the complex spectrum of conformational dynamics occurring in biomolecules. We have combined Accelerated Molecular Dynamics (AMD) with experimental results derived from NMR to probe multiple time-scale motions in the third IgG-binding domain of Protein G (GB3). AMD is shown to accurately reproduce the amplitude and distribution of slow motional modes characterized using residual dipolar couplings, reporting on dynamics up to the millisecond timescale. In agreement with experiment, larger amplitude slower motions are localized in the beta-strand/loop motif spanning residues 14-24 and in loop 42-44. Principal component analysis shows these fluctuations participating in the primary mode, substantiating the existence of a correlated motion traversing the beta-sheet that culminates in maximum excursions at the active site of the molecule. Fast dynamics were simulated using extensive standard MD simulations and compared to order parameters extracted from 15N relaxation. Notably 60 2-ns fully solvated MD simulations exploring the different conformational substates sampled from AMD resulted in better reproduction of order parameters compared to the same number of simulations starting from the relaxed crystal structure. This illustrates the inherent dependence of protein dynamics on local conformational topology. The results provide rare insight into the complex hierarchy of dynamics present in GB3 and allow us to develop a model of the conformational landscape native to the protein, appearing as a steep sided potential well whose flat bottom comprises multiple similar but discrete conformational substates.
生物功能依赖于生物分子中发生的复杂构象动力学谱。我们将加速分子动力学（AMD）与源自核磁共振（NMR）的实验结果相结合，以探究蛋白G（GB3）的第三个IgG结合结构域中的多时间尺度运动。结果表明，AMD能够准确再现利用剩余偶极耦合表征的慢运动模式的幅度和分布，揭示长达毫秒时间尺度的动力学。与实验结果一致，较大幅度的慢运动集中在跨越14 - 24位残基的β链/环基序以及42 - 44环中。主成分分析表明，这些波动参与了主要模式，证实了存在一种贯穿β折叠的相关运动，该运动在分子的活性位点达到最大偏移。利用广泛的标准分子动力学模拟对快速动力学进行了模拟，并与从15N弛豫提取的序参数进行了比较。值得注意的是，与从松弛晶体结构开始的相同数量的模拟相比，探索从AMD采样的不同构象亚态的60次2纳秒全溶剂化分子动力学模拟能更好地再现序参数。这说明了蛋白质动力学对局部构象拓扑的内在依赖性。这些结果为GB3中存在的复杂动力学层次提供了难得的见解，并使我们能够建立该蛋白质天然构象景观的模型，其表现为一个陡峭的势阱，其平底包含多个相似但离散的构象亚态。
