What can we learn by computing 13Cα chemical shifts for X-ray protein models?
What can we learn by computing 13Cα chemical shifts for X-ray protein models?
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DOI：
10.1107/s0907444909012086
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发表时间：
2009-07-01
影响因子：
2.2
通讯作者：
Scheraga, Harold A.
中科院分区：
文献类型：
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作者：
Arnautova, Yelena A.;Vila, Jorge A.;Scheraga, Harold A.
利用分别在1.8埃和1.9埃分辨率下解析的泛素（PDB编码1ubq）和甲型流感病毒非结构蛋白1 rna结合域（PDB编码1ail）的室温x射线结构，研究一组构象是否比单一x射线结构更符合x射线数据和溶液中观察到的C-13（α）化学位移。为此，通过将这些蛋白质与沉积在PDB中的实验x射线数据相匹配，生成了这些蛋白质的一组新构象。对于每一个生成的结构，都显示出与沉积的x射线结构相似的R和R-free因子，在理论的DFT水平上计算了序列中所有残基的C-13（α）化学位移。然后利用构象平均均方根偏差（ca-r.m.s.d）来评估这些构象组再现所观察到的C-13（α）化学位移的能力。对于泛素，计算得到的构象集更好地代表了观察到的C-13（α）化学位移。而不是单一的x射线衍生结构。然而，对于甲型流感病毒非结构蛋白1的rna结合域，考虑构象集合并不能改善与观察到的C-13（α）化学位移的一致性。对于晶体中的蛋白质结构以及所观察到的C-13（α）化学位移，是否一组构象的集合比任何单一结构更准确地表示，这取决于坐标的色散，根据所生成模型中的全原子r.m.s.d.；生成的模型满足实验x射线数据，精度与PDB结构相当。因此，系综的生成是确定单一结构是否足以准确表示实验x射线数据和观察到的溶液中C-13（α）化学位移的必要步骤。
The room-temperature X-ray structures of ubiquitin (PDB code 1ubq) and of the RNA-binding domain of nonstructural protein 1 of influenza A virus (PDB code 1ail) solved at 1.8 and 1.9 angstrom resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed C-13(alpha) chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and R-free factors similar to those of the deposited X-ray structure, the C-13(alpha) chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed C-13(alpha) chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed C-13(alpha) chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed C-13(alpha) chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed C-13(alpha) chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with accuracy as good as the PDB structure. Therefore, generation of an ensemble is a necessary step to determine whether or not a single structure is sufficient for an accurate representation of both experimental X-ray data and observed C-13(alpha) chemical shifts in solution.