Idiyatullin Djaudat, Nesmelova Irina, Daragan Vladimir A, Mayo Kevin H
Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.
Protein Sci. 2003 May;12(5):914-22. doi: 10.1110/ps.0228703.
This study presents a site-resolved experimental view of backbone C(alpha)H and NH internal motions in the 56-residue immunoglobulin-binding domain of streptococcal protein G, GB1. Using (13)C(alpha)H and (15)NH NMR relaxation data [T(1), T(2), and NOE] acquired at three resonance frequencies ((1)H frequencies of 500, 600, and 800 MHz), spectral density functions were calculated as F(omega) = 2omegaJ(omega) to provide a model-independent way to visualize and analyze internal motional correlation time distributions for backbone groups in GB1. Line broadening in F(omega) curves indicates the presence of nanosecond time scale internal motions (0.8 to 5 nsec) for all C(alpha)H and NH groups. Deconvolution of F(omega) curves effectively separates overall tumbling and internal motional correlation time distributions to yield more accurate order parameters than determined by using standard model free approaches. Compared to NH groups, C(alpha)H internal motions are more broadly distributed on the nanosecond time scale, and larger C(alpha)H order parameters are related to correlated bond rotations for C(alpha)H fluctuations. Motional parameters for NH groups are more structurally correlated, with NH order parameters, for example, being larger for residues in more structured regions of beta-sheet and helix and generally smaller for residues in the loop and turns. This is most likely related to the observation that NH order parameters are correlated to hydrogen bonding. This study contributes to the general understanding of protein dynamics and exemplifies an alternative and easier way to analyze NMR relaxation data.
本研究展示了链球菌蛋白G的56个残基免疫球蛋白结合结构域GB1中主链CαH和NH内部运动的位点解析实验视图。利用在三个共振频率（1H频率分别为500、600和800 MHz）下获取的13CαH和15NH NMR弛豫数据（T1、T2和NOE），计算光谱密度函数F(ω) = 2ωJ(ω)，以提供一种独立于模型的方法来可视化和分析GB1中主链基团的内部运动相关时间分布。F(ω)曲线中的线宽表明所有CαH和NH基团存在纳秒时间尺度的内部运动（0.8至5纳秒）。F(ω)曲线的去卷积有效地分离了整体翻滚和内部运动相关时间分布，从而产生比使用标准无模型方法确定的更准确的序参量。与NH基团相比，CαH内部运动在纳秒时间尺度上分布更广泛，并且较大的CαH序参量与CαH波动的相关键旋转有关。NH基团的运动参数在结构上相关性更强，例如，在β折叠和螺旋的更结构化区域中的残基的NH序参量较大，而在环和转角中的残基的NH序参量通常较小。这很可能与NH序参量与氢键相关的观察结果有关。本研究有助于对蛋白质动力学的总体理解，并举例说明了一种分析NMR弛豫数据的替代且更简便的方法。
