Qu Youxing, Guo Jun-tao, Olman Victor, Xu Ying
Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
Nucleic Acids Res. 2004 Jan 26;32(2):551-61. doi: 10.1093/nar/gkh204. Print 2004.
Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for protein structure studies. However, solving a protein structure using RDC data alone is still a highly challenging problem. We report here a computer program, RDC-PROSPECT, for protein structure prediction based on a structural homolog or analog of the target protein in the Protein Data Bank (PDB), which best aligns with the (15)N-(1)H RDC data of the protein recorded in a single ordering medium. Since RDC-PROSPECT uses only RDC data and predicted secondary structure information, its performance is virtually independent of sequence similarity between a target protein and its structural homolog/analog, making it applicable to protein targets beyond the scope of current protein threading techniques. We have tested RDC-PROSPECT on all (15)N-(1)H RDC data (representing 43 proteins) deposited in the BioMagResBank (BMRB) database. The program correctly identified structural folds for 83.7% of the target proteins, and achieved an average alignment accuracy of 98.1% residues within a four-residue shift.
剩余偶极耦合（RDC）是蛋白质结构研究中最令人兴奋的新兴核磁共振技术之一。然而，仅使用RDC数据解析蛋白质结构仍然是一个极具挑战性的问题。我们在此报告一个计算机程序RDC - PROSPECT，用于基于蛋白质数据库（PDB）中目标蛋白质的结构同源物或类似物进行蛋白质结构预测，该同源物或类似物与在单一有序介质中记录的蛋白质的（15）N - （1）H RDC数据最佳匹配。由于RDC - PROSPECT仅使用RDC数据和预测的二级结构信息，其性能实际上与目标蛋白质与其结构同源物/类似物之间的序列相似性无关，这使得它适用于当前蛋白质穿线技术范围之外的蛋白质目标。我们已在BioMagResBank（BMRB）数据库中存入的所有（15）N - （1）H RDC数据（代表43种蛋白质）上测试了RDC - PROSPECT。该程序正确识别了83.7%的目标蛋白质的结构折叠，并在四个残基位移范围内实现了平均98.1%残基的比对准确性。
