Re-evaluation of the model-free analysis of fast internal motion in proteins using NMR relaxation
Re-evaluation of the model-free analysis of fast internal motion in proteins using NMR relaxation
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DOI：
10.1021/jp8038576
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发表时间：
2008-09-25
影响因子：
3.3
通讯作者：
Wand, A. Joshua
中科院分区：
文献类型：
--
作者：
Frederick, Kendra King;Sharp, Kim A.;Wand, A. Joshua
NMR自旋弛豫在蛋白质及其复合物的快速内部运动的表征中保持着核心作用。氨基酸侧链运动的分布和幅度的知识对于解释蛋白质的残余构象熵的动力学代理是至关重要的，这可能对蛋白质功能的熵有潜在的显着贡献。溶解在液体中的大分子中的NMR弛豫现象的流行处理是Lipari和Szabo的所谓无模型方法。无模式方法的鲁棒性最近受到强烈批评，蛋白质内部运动的显著范围和结构背景，其特征在于这种NMR弛豫技术，归因于无模式治疗产生的伪影，特别是相对于基本运动的对称性。我们开发了一个客观的量化运动的空间和时间的不对称性，并重新检查的基础上的无模型治疗。关于非对称运动的无模型方法的鲁棒性的担忧似乎通常是没有根据的。广义序参量的鲁棒恢复。无模型处理对不对称运动的敏感性限于有效相关时间，其根据定义是归一化量而不是真实的时间常数，因此在此上下文中不太感兴趣。在无模型方法中重新获得信心，然后我们研究了钙饱和钙调素和内皮型一氧化氮合酶的钙调素结合结构域之间的复合物中侧链运动的微观分布。氘弛豫被用来表征在复杂的甲基基团的运动。一个显着的范围内的Lipari-Szabo模型的自由广义序参数被认为与基本的结构参数，如埋深的相关性很小。这些结果与神经元型一氧化氮合酶钙调素结合结构域的同源复合物形成对比，该结构域具有明显不同的高亲和力结合的热力学起源。
NMR spin relaxation retains a central role in the characterization of the fast internal motion of proteins and their complexes. Knowledge of the distribution and amplitude of the motion of amino acid side chains is critical for the interpretation of the dynamical proxy for the residual conformational entropy of proteins, which can potentially significantly contribute to the entropy of protein function. A popular treatment of NMR relaxation phenomena in macromolecules dissolved in liquids is the so-called model-free approach of Lipari and Szabo. The robustness of the mode-free approach has recently been strongly criticized and the remarkable range and structural context of the internal motion of proteins, characterized by such NMR relaxation techniques, attributed to artifacts arising from the model-free treatment, particularly with respect to the symmetry of the underlying motion. We develop an objective quantification of both spatial and temporal asymmetry of motion and re-examine the foundation of the model-free treatment. Concerns regarding the robustness of the model-free approach to asymmetric motion appear to be generally unwarranted. The generalized order parameter is robustly recovered. The sensitivity of the model-free treatment to asymmetric motion is restricted to the effective correlation time, which is by definition a normalized quantity and not a true time constant and therefore of much less interest in this context. With renewed confidence in the model-free approach, we then examine the microscopic distribution of side chain motion in the complex between calcium-saturated calmodulin and the calmodulin-binding domain of the endothelial nitric oxide synthase. Deuterium relaxation is used to characterize the motion of methyl groups in the complex. A remarkable range of Lipari-Szabo model-free generalized order parameters are seen with little correlation with basic structural parameters such as the depth of burial. These results are contrasted with the homologous complex with the neuronal nitric oxide synthase calmodulin-binding domain, which has distinctly different thermodynamic origins for high affinity binding.