López-Méndez Blanca, Güntert Peter
Tatsuo Miyazawa Memorial Program, RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan.
J Am Chem Soc. 2006 Oct 11;128(40):13112-22. doi: 10.1021/ja061136l.
Fully automated structure determination of proteins in solution (FLYA) yields, without human intervention, three-dimensional protein structures starting from a set of multidimensional NMR spectra. Integrating existing and new software, automated peak picking over all spectra is followed by peak list filtering, the generation of an ensemble of initial chemical shift assignments, the determination of consensus chemical shift assignments for all (1)H, (13)C, and (15)N nuclei, the assignment of NOESY cross-peaks, the generation of distance restraints, and the calculation of the three-dimensional structure by torsion angle dynamics. The resulting, preliminary structure serves as additional input to the second stage of the procedure, in which a new ensemble of chemical shift assignments and a refined structure are calculated. The three-dimensional structures of three 12-16 kDa proteins computed with the FLYA algorithm coincided closely with the conventionally determined structures. Deviations were below 0.95 A for the backbone atom positions, excluding the flexible chain termini. 96-97% of all backbone and side-chain chemical shifts in the structured regions were assigned to the correct residues. The purely computational FLYA method is suitable for substituting all manual spectra analysis and thus overcomes a main efficiency limitation of the NMR method for protein structure determination.
溶液中蛋白质的全自动结构测定（FLYA）无需人工干预，就能从一组多维核磁共振谱中得出蛋白质的三维结构。整合现有软件和新软件后，首先对所有谱图进行自动峰检测，随后进行峰列表过滤、生成初始化学位移归属集合、确定所有氢、碳-13和氮-15原子核的一致性化学位移归属、指定核欧沃豪斯效应（NOESY）交叉峰、生成距离限制，并通过扭转角动力学计算三维结构。所得的初步结构作为该程序第二阶段的额外输入，在该阶段会计算新的化学位移归属集合和优化后的结构。用FLYA算法计算出的三种12 - 16 kDa蛋白质的三维结构与传统方法测定的结构非常吻合。除了柔性链末端外，主链原子位置的偏差低于0.95埃。结构化区域中所有主链和侧链化学位移的96 - 97%都被正确归属到相应残基上。纯计算的FLYA方法适用于替代所有人工谱图分析，从而克服了核磁共振方法在蛋白质结构测定中的一个主要效率限制。
