PROTEIN BACKBONE DYNAMICS REVEALED BY QUASI SPECTRAL DENSITY-FUNCTION ANALYSIS OF AMIDE N-15 NUCLEI
PROTEIN BACKBONE DYNAMICS REVEALED BY QUASI SPECTRAL DENSITY-FUNCTION ANALYSIS OF AMIDE N-15 NUCLEI
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DOI：
10.1021/bi00010a005
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发表时间：
1995-03-14
期刊：
影响因子：
2.9
通讯作者：
NAGAYAMA, K
中科院分区：
文献类型：
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作者：
ISHIMA, R;NAGAYAMA, K
蛋白质中各个酰胺 N-15 核的谱密度函数 J(0)、J(omega(N)) 和 J(omega(H)+omega(N)) 通过准谱密度函数 (QSDF) 进行近似。使用该函数，对已发表数据的七个蛋白质系统的主链动力学进行了分析。我们将 J(0; omega(N)) 定义为 J(0) 和 J(omega(N)) 值之间的差值，它描述了慢于 50（或 60）MHz 的运动，而 J(omega(N); omega(H+N)) 定义为 J(omega(N)) 和 J((omega)(H)+omega(N)) 值之间的差，它描述了慢于 450（或 540）MHz 的运动。 QSDF 分析可以轻松提取蛋白质主链的 J(0; omega(N))，这通常与生物学相关反应有一定关系。与其他区域相比，eglin c 和葡萄糖通透酶 IIA 中的柔性 N 末端区域以及eglin c 中的环区域显示 J(0; omega(N)) 和 J(omega(N); omega(H+N)) 的值更小，表明运动增加速度快于纳秒。 FK506 结合蛋白主链的 J(0; omega(N)) 值在脱辅基蛋白中显示出很大的变化，但在 FK506 结合后落在非常窄的范围内。在位于二级结构之间的两个或三个残基中观察到 J(0) 和 J(omega(N)) 值的特征性增加或减少。
Spectral density functions J(0), J(omega(N)), and J(omega(H)+omega(N)) Of individual amide N-15 nuclei in proteins were approximated by a quasi spectral density function (QSDF). Using this function, the backbone dynamics were analyzed for seven protein systems on which data have been published. We defined J(0; omega(N)) as the difference between the J(0) and the J(omega(N)) values, which describes motions slower than 50 (or 60) MHz, and J(omega(N); omega(H+N)) as the difference between the J(omega(N)) and the J((omega)(H)+omega(N)) values, which describes motions slower than 450 (or 540) MHz. The QSDF analysis can easily extract the J(0; omega(N)) of protein backbones, which have often some relation to biologically relevant reactions. Flexible N-terminal regions in eglin c and glucose permease IIA and a loop region in eglin c showed smaller values of both the J(0; omega(N)) and the J(omega(N); omega(H+N)) as compared with the other regions, indicating increases in motions faster than nanosecond. The values of the J(0; omega(N)) for the backbone of the FK506 binding protein showed a large variation in the apoprotein but fell in a very narrow range after the binding of FK506. Characteristic increase or decrease in the values of J(0) and J(omega(N)) was observed in two or three residues located between secondary structures.