Ulmer Tobias S, Ramirez Benjamin E, Delaglio Frank, Bax Ad
Contribution from the Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
J Am Chem Soc. 2003 Jul 30;125(30):9179-91. doi: 10.1021/ja0350684.
NMR measurements of a large set of protein backbone one-bond dipolar couplings have been carried out to refine the structure of the third IgG-binding domain of Protein G (GB3), previously solved by X-ray crystallography at a resolution of 1.1 A. Besides the commonly used bicelle, poly(ethylene glycol), and filamentous phage liquid crystalline media, dipolar couplings were also measured when the protein was aligned inside either positively or negatively charged stretched acrylamide gels. Refinement of the GB3 crystal structure against the (13)C(alpha)-(13)C' and (13)C'-(15)N dipolar couplings improves the agreement between experimental and predicted (15)N-(1)H(N) as well as (13)C(alpha)-(1)H(alpha) dipolar couplings. Evaluation of the peptide bond N-H orientations shows a weak anticorrelation between the deviation of the peptide bond torsion angle omega from 180 degrees and the angle between the N-H vector and the C'-N-C(alpha) plane. The slope of this correlation is -1, indicating that, on average, pyramidalization of the peptide N contributes to small deviations from peptide bond planarity (
已对大量蛋白质主链一键偶极耦合进行了核磁共振测量,以优化蛋白G的第三个IgG结合结构域(GB3)的结构,该结构先前通过X射线晶体学在1.1埃的分辨率下解析得到。除了常用的双分子层、聚乙二醇和丝状噬菌体液晶介质外,当蛋白质在带正电或带负电的拉伸丙烯酰胺凝胶中排列时,也测量了偶极耦合。根据(13)Cα-(13)C′和(13)C′-(15)N偶极耦合对GB3晶体结构进行优化,提高了实验和预测的(15)N-(1)H(N)以及(13)Cα-(1)Hα偶极耦合之间的一致性。对肽键N-H取向的评估表明,肽键扭转角ω与180度的偏差与N-H向量和C′-N-Cα平面之间的夹角呈弱反相关。这种相关性的斜率为-1,表明平均而言,肽N的锥体化对肽键平面度的小偏差(<ω>=179.3±3.1度)的贡献程度与围绕C′-N键的真实扭转相同。尽管在构建晶体结构时通常假设N-H向量方向落在平分C′-N-Cα角的直线上,但更好的近似是将Cα-C′-N-H扭转角调整为-2度。(15)N-(1)H(N)偶极数据与普遍接受的运动模型并不矛盾,在该模型中,与肽平面正交的N-H键的角波动大于平面内运动,但与Cα(i-1)-N(i)-Cα(i)平面正交的角波动幅度最多比平面内运动大10-15度。偶极耦合分析表明,对于大多数GB3主链,酰胺序参数S高度均匀,变化小于±7%。对Hα质子位置的评估表明,平均Cα-Hα向量方向与与Cα-Cβ和Cα-N向量形成理想四面体角的方向偏差小于1度。