Computer-aided assignment of the 1H-NMR spectrum of the viral-protein-genome-linked polypeptide from cowpea mosaic virus

The 1H-NMR spectrum of the viral-protein-genome-linked (VPg) polypeptide from cowpea mosaic virus, has been interpreted via application of 2-dimensional (2D) NMR techniques. The interpretation of the data was performed by a computer program called 'PROSPECT' (PROtein SPECTra), which detects the cross-peak patterns of the amino acid residues in the spectra, assigns these patterns to amino acid types, and finally performs the sequential assignments using the well-known 'sequential walks' obtained from the NOE spectrum. Due to the severe overlap of resonances in the NMR spectrum of the VPg polypeptide, several ways of performing these walks existed. The program detected six alternatives for the sequential assignments of backbone N alpha H-C beta H-C beta H moieties.