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原子核的化学位移对它们的局部环境非常敏感。一个计算机程序，斯巴达，描述了使用这种相关性与局部结构来预测蛋白质骨架化学位移，给定一个输入的三维结构，通过搜索一个新生成的数据库为三个相邻的残基，提供最佳匹配的phi/psi/chi 1扭转角和序列相似性的查询三重感兴趣。 该数据库包含200种蛋白质的15 N、1HN、1Ha、13 Ca、13 Cb和13 C '化学位移，这些蛋白质具有高分辨率的X射线（2.4）结构。加权因子的phi/psi/chi 1角度和序列相似性的相对重要性进行了经验优化。 加权，平均二级位移的中心残基在20个最匹配的三联体，包括最近的邻居，环电流，和氢键的影响后，被用来预测已知结构的蛋白质的化学位移。验证表明SPARTA预测和实验位移之间具有良好的一致性，15 N、1HN、1HN、13 Ca、13 Cb和13 C '的标准偏差分别为2.52、0.51、0.27、0.98、1.07和1.08 ppm，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.