Exact Distances and Internal Dynamics of Perdeuterated Ubiquitin from NOE Buildups
Exact Distances and Internal Dynamics of Perdeuterated Ubiquitin from NOE Buildups
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DOI：
10.1021/ja905366h
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发表时间：
2009-12-02
影响因子：
15
通讯作者：
Riek, Roland
中科院分区：
文献类型：
--
作者：
Voegeli, Beat;Segawa, Takuya F.;Riek, Roland
提出将核Overhauser效应（NOES）转化为相对精确的距离，用于蛋白质的详细结构研究。为此，我们证明了使用设计的N-15分辨HMQC-NOESY实验测量过氘化人泛素中酰胺质子之间的NOE积累，能够以高精度和精密度测定H-1(N)-H-1(N)距离达5埃。这些noe导出的距离具有类似于0.07埃的实验随机误差，小于从核磁共振或x射线结构（pdb代码：1D3Z和1UBQ）中提取的相应距离获得的成对rmsd（均方根偏差）0.24埃，也小于x射线和核磁共振结构距离的成对rmsd（0.15埃）。由于NOE包含结构和动态信息，因此将三维结构与NOE导出的距离进行比较也可以深入了解空间动力学。与x射线结构或核磁共振结构相比，从NOES中提取运动信息似乎具有挑战性，因为运动可能被结构的质量所掩盖。尽管如此，详细的分析表明-链之间的运动和泛素α -螺旋中的大型复杂运动。然而，noe衍生的运动幅度较小，可能与使用GROMOS力场进行的水中泛素20 ns分子动力学模拟中的运动具有不同的特征。此外，最近发表的一组表示时间尺度为毫秒（pdb: 2K39）的构象分布的结构并不比单个x射线结构更好地满足NOES。因此，在整个蛋白质中测量可能数千个精确的NOES可以作为正确表示蛋白质结构和动力学的绝佳探针。
It is proposed to convert nuclear Overhauser effects (NOES) into relatively precise distances for detailed structural studies of proteins. To this purpose, it is demonstrated that the measurement of NOE buildups between amide protons in perdeuterated human ubiquitin using a designed N-15-resolved HMQC-NOESY experiment enables the determination of H-1(N)-H-1(N) distances up to 5 angstrom with high accuracy and precision. These NOE-derived distances have an experimental random error of similar to 0.07 angstrom, which is smaller than the pairwise rmsd (root-mean-square deviation) of 0.24 angstrom obtained with corresponding distances extracted from either an NMR or an X-ray structure (pdb codes: 1D3Z and 1UBQ), and also smaller than the pairwise rmsd between distances from X-ray and NMR structures (0.15 angstrom). Because the NOE contains both structural and dynamical information, a comparison between the 3D structures and NOE-derived distances may also give insights into through-space dynamics. It appears that the extraction of motional information from NOES by comparison to the X-ray structure or the NMR structure is challenging because the motion may be masked by the quality of the structures. Nonetheless, a detailed analysis thereof suggests motions between beta-strands and large complex motions in the alpha-helix of ubiquitin. The NOE-derived motions are, however, of smaller amplitude and possibly of a different character than those present in a 20 ns molecular dynamic simulation of ubiquitin in water using the GROMOS force field. Furthermore, a recently published set of structures representing the conformational distribution over time scales up to milliseconds (pdb: 2K39) does not satisfy the NOES better than the single X-ray structure. Hence, the measurement of possibly thousands of exact NOES throughout the protein may serve as an excellent probe toward a correct representation of both structure and dynamics of proteins.