PACES: Protein sequential assignment by computer-assisted exhaustive search.

Abstract

A crucial step in determining solution structures of proteins using nuclear magnetic resonance (NMR) spectroscopy is the process of sequential assignment, which correlates backbone resonances to corresponding residues in the primary sequence of a protein, today, typically using data from triple-resonance NMR experiments. Although the development of automated approaches for sequential assignment has greatly facilitated this process, the performance of these programs is usually less satisfactory for large proteins, especially in the cases of missing connectivity or severe chemical shift degeneracy. Here, we report the development of a novel computer-assisted method for sequential assignment, using an algorithm that conducts an exhaustive search of all spin systems both for establishing sequential connectivities and then for assignment. By running the program iteratively with user intervention after each cycle, ambiguities in the assignments can be eliminated efficiently and backbone resonances can be assigned rapidly. The efficiency and robustness of this approach have been tested with 27 proteins of sizes varying from 76 amino acids to 723 amino acids, and with data of varying qualities, using experimental data for three proteins, and published assignments modified with simulated noise for the other 24. The complexity of sequential assignment with regard to the size of the protein, the completeness of NMR data sets, and the uncertainty in resonance positions has been examined.