JOURNAL OF MAGNETIC RESONANCE 125, 34–42 (1997) ARTICLE NO. MN971106 Protein Heteronuclear NMR Assignments Using Mean-Field Simulated Annealing

Abstract

A computational method for the assignment of the NMR spec- number of source NMR spectra. For a variety of reasons, tra of larger (21 kDa) proteins using a set of six of the most even modest increases in protein size greatly complicate the sensitive heteronuclear multidimensional nuclear magnetic resonance experiments is described. Connectivity data obtained from HNCa, HN(CO)Ca, HN(Ca)Ha, andHa(CaCO)NH and spin-system identification data obtained from CP-(H)CCH–TOCSY and CP-(H)C(CaCO)NH–TOCSY were used to perform sequence-specific assignments using a mean-field formalism and simulated annealing. This mean-field method reports the reso-nance assignments in a probabilistic fashion, displaying the cer-assignment process. First, the larger number of more poorly resolved resonances results in greater problems with spectral overlap. This situation is exacerbated by increased relaxation rates, which limit the source data to only those obtainable by the most sensitive experiments. Because of these limita-tions, any practical automated assignment method for proteins above 15 kDa must be able to work with data that are tainty of assignments in an unambiguous and quantitative man-limited, probabilistic, ambiguous, and sometimes missing or ner. This technique was applied to the NMR data of the 172- inaccurate. A further problem is the existence of an exponenresidue peptide-binding domain of the E. coli heat-shock protein, tially large number of ways of assigning N spin systems to DnaK. The method is demonstrated to be robust to significant amounts of missing, spurious, noisy, extraneous, and erroneous data. � 1997 Academic Press N residues in the protein, which eliminates any hope of performing an exhaustive search over all possible assign-ments, even using the fastest computers. In order to deal with this problem, many automated methods rely on som