Implementation of the main chain directed assignment strategy. Computer assisted approach.

A computer-assisted procedure has been developed to apply the main chain directed (MCD) assignment strategy to the analysis of 1H NMR spectra of proteins. The underlying mathematical foundation of this procedure, termed MCDPAT, is presented. MCDPAT is based upon the expanded library of MCD patterns defined previously (A.J. Wand and S.J. Nelson. 1991. Biophys. J. 59:1101-1112), and has been evaluated with both simulated and experimental data from the protein ubiquitin. The influence of the precision, spectral variation, and inherent degeneracy upon the design of the procedure is explored. Several approaches have been taken to overcome the uncertainty introduced by these variables. These include a hierarchical approach to both primary pattern recognition and subsequent construction of MCD-defined units of secondary structure. It is shown that the MCDPAT procedure, in conjunction with automated statistically based spectral analysis, leads to the successful MCD assignment of the protein ubiquitin. The implications and limitations of this approach are discussed.