Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR
Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR
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DOI：
10.1023/a:1016359412284
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发表时间：
2002-06-01
影响因子：
2.7
通讯作者：
Pons, M
中科院分区：
文献类型：
--
作者：
Bernadó, P;de la Torre, JG;Pons, M
HYDROMR 是最先进的流体动力学建模的实现，用于从原子级表示开始计算刚性蛋白质结构中 NH 或 C-α-H 向量的谱密度函数。因此，HYDROMR 可用于根据刚性模型预测 NMR 弛豫时间，并将其与实验结果进行比较。 HYDROMR 包含一个可调参数，即原子元素半径。描述了确定计算值和实验 T-1/T-2 值之间最佳一致性的值的协议。对于大多数蛋白质，原子元素半径的值范围在 2.8 埃到 3.8 埃之间，分布集中在 3.3 埃。从通常范围向较大值的偏差与几种蛋白质的聚集有关。较低值的偏差可能与大规模运动或不适当的模型结构有关。如果平均结构正确，实验 T-1/T-2 值与 HYDROMR 计算值之间的偏差可用于区分受各向异性运动影响的残基和参与化学交换的残基。
HYDRONMR is an implementation of state of the art hydrodynamic modeling to calculate the spectral density functions for NH or C-alpha-H vectors in a rigid protein structure starting from an atomic level representation. Thus HYDRONMR can be used to predict NMR relaxation times from a rigid model and to compare them with the experimental results. HYDRONMR contains a single adjustable parameter, the atomic element radius. A protocol to determine the value that gives the best agreement between calculated and experimental T-1/T-2 values is described. For most proteins, the value of the atomic element radius ranges between 2.8 Angstrom and 3.8 Angstrom with a distribution centered at 3.3 Angstrom. Deviations from the usual range towards larger values are associated to aggregation in several proteins. Deviations to lower values may be related to large-scale motions or inappropriate model structures.If the average structure is correct, deviations between experimental T-1/T-2 values and those calculated with HYDRONMR can be used to distinguish residues affected by anisotropic motion from those that are involved in chemical exchange.