Methods to accelerate protein structure determination by solution NMR

蛋白质骨架中或附着在蛋白质骨架上的核的化学位移对其所处的局部环境非常敏感。描述了一种名为Sparta的计算机程序，其在给定输入三维结构的情况下使用这种与局部结构的相关性来预测蛋白质主干化学位移，方法是在新生成的数据库中搜索在phi/psi/chi1扭转角和序列相似性方面与感兴趣的查询三元组提供最佳匹配的相邻残基的三元组。该数据库包含200种蛋白质的15N，1HN，1HA，13Ca，13Cb和13C‘化学位移，其中有高分辨率X射线(&#8804；2.4)结构可用。对phi/psi/chi1角和序列相似性的权重因子的相对重要性进行了经验优化。在包含最近邻、环电流和氢键效应后，20个最佳匹配三联体中中心残基的加权平均二级位移被用来预测已知结构的蛋白质的化学位移。验证表明，Sparta预测的位移与实验结果吻合良好，15N、1HN、1HN、13Ca、13Cb和13C‘的标准偏差分别为2.52、0.51、0.27、0.98、1.07和1.08ppm，包括离群值。

Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in phi/psi/chi1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15N, 1HN, 1Ha, 13Ca, 13Cb and 13C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4) structure is available. The relative importance of the weighting factors for the phi/psi/chi1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15N, 1HN, 1HN, 13Ca, 13Cb and 13C', respectively, including outliers.