Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy
Figure 2
Conventional process of resonance assignments for a protein labeled with stable isotopes (13C and 15N).
Peaks observed in multidimensional spectra are matched to search for common frequencies. Some common frequencies identify atoms within a residue; others identify atoms in neighboring residues. The common visual aid in this process is a series of paired strip plots from complementary NMR experiments. Strips from CBCA(CO)NH (a and c) and HNCACB (b and d) experiments can be used here to assign the tripeptide Thr-Tyr-His. Starting with Cα (CA) and Cβ (CB) frequencies assumed to belong to Thr66 (strip a), a horizontal trace (line), arising from the common frequency of NH nuclei, is used to locate Cα and Cβ of Tyr67 in (strip b). To continue the process, the same peaks are located in (strip c), and the peaks are traced to strip d. In strip d, given the accepted tolerances across spectra (shown by boxes around the selected peaks), several alternative assignments are plausible for His68. These additional peaks may be artifacts (false peaks), or peaks from other nuclei with similar frequency. Depending on the starting point of the assignment process, the choice of experiments, the amount of conflicting information, or other factors, an exponentially expanding number of alternative assignments can arise, rendering a computational solution intractable. This difficulty has proved to be a major drawback for NMR structure determination, particularly for larger proteins.