Peng J W, Wagner G
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.
Biochemistry. 1992 Sep 15;31(36):8571-86. doi: 10.1021/bi00151a027.
A new strategy is used for studying the internal motions of proteins based on measurements of NMR relaxation parameters. The strategy yields values of the so-called spectral density functions J(omega) for N-H bond vectors. The spectral density functions are related to the distribution of frequencies contained in the rotational (overall and internal) motions of these NH bond vectors. No a priori model assumptions about the dynamics are required in this approach. The method involves measurements of six relaxation parameters consisting of 15N longitudinal relaxation rates, transverse relaxation rates of in-phase and antiphase coherence, the relaxation rates of heteronuclear 1H-15N two-spin order, the heteronuclear 1H-15N nuclear Overhauser effects, and longitudinal relaxation rates of the amide protons. The values of the spectral density functions at the five frequencies 0, omega N, omega H + omega N, omega H, and omega H - omega N are determined from the relaxation parameters using analytical relations derived previously [Peng & Wagner (1992) J. Magn. Reson. 98, 308-332]. Here, the method is applied to characterize the backbone dynamics of the 15N-enriched proteinase inhibitor eglin c, a protein of 70 residues. The values for J(0) and J(omega N = 50 MHz) vary significantly with the amino acid sequence, whereas the spectral densities at higher frequencies, J(450 MHz), J(500 MHz), and J(550 MHz), are typically much smaller and show no significant variation with the sequence. The collective behavior of the J(omega) values indicate greater internal motion for the proteinase binding loop residues and the first eight N-terminal residues. The additional internal motion in these regions is in the rate range below 450 MHz. The values of J(omega) are also compared with root mean square deviations (rmsds) of backbone atoms as obtained in NMR structure determinations. Low values of J(0) and J(omega N) are correlated with high rmsds. Spectral densities at higher frequencies, J(450 MHz), J(500 MHz), and J(550 MHz), are small and show no correlation with rmsds. A comparison with the spectral density functions obtained by fitting the experimental data to the functional dependence of the Lipari and Szabo formalism [Lipari & Szabo (1982a) J. Am. Chem. Soc. 104, 4546-4559] is made.
一种基于核磁共振弛豫参数测量来研究蛋白质内部运动的新策略被采用。该策略可得出所谓的N-H键向量的光谱密度函数J(ω)的值。光谱密度函数与这些NH键向量的旋转（整体和内部）运动中所含频率的分布相关。在这种方法中，无需对动力学做先验模型假设。该方法涉及测量六个弛豫参数，包括15N纵向弛豫率、同相和反相相干的横向弛豫率、异核1H-15N双自旋序的弛豫率、异核1H-15N核Overhauser效应以及酰胺质子的纵向弛豫率。利用先前推导的解析关系[Peng & Wagner (1992) J. Magn. Reson. 98, 308 - 332]，从弛豫参数确定五个频率0、ωN、ωH + ωN、ωH和ωH - ωN处的光谱密度函数值。在此，该方法被应用于表征富含15N的蛋白酶抑制剂eglin c（一种70个残基的蛋白质）的主链动力学。J(0)和J(ωN = 50 MHz)的值随氨基酸序列有显著变化，而较高频率处的光谱密度J(450 MHz)、J(500 MHz)和J(550 MHz)通常要小得多，且随序列无显著变化。J(ω)值的集体行为表明蛋白酶结合环残基和前八个N端残基有更大的内部运动。这些区域额外的内部运动处于低于450 MHz的速率范围内。J(ω)的值还与核磁共振结构测定中获得的主链原子的均方根偏差（rmsds）进行了比较。J(0)和J(ωN)的低值与高rmsds相关。较高频率处的光谱密度J(450 MHz)、J(500 MHz)和J(550 MHz)较小，且与rmsds无相关性。还与通过将实验数据拟合到Lipari和Szabo形式体系的函数依赖关系[Lipari & Szabo (1982a) J. Am. Chem. Soc. 104, 4546 - 4559]所获得的光谱密度函数进行了比较。
