We are refining the structure of a recombinant fragment of syrian hamster PrP gene product using 3 dimensional heteronuclear NMR. This prion protein is known to exist in at least two different conformations. One solution form that is predominantly alpha helical (PrPc) and another, aggregated beta-sheet form (PrP Scrapie). The structural dimorphism in itself is interesting since it demonstrates that amino acid sequences can encode more than one structure, but more importantly, the sequence has significance in human pathology because it is involved in prion diseases. Prions can cause scrapie in sheep, mad cow disease, and kuru, Cruetzfeld- Jakob, Gerstmann-Staussler-Scheinker disease, and fatal familial insomnia in humans. This project is significant for both drug design, and, on a more fundamental level, our ability to understand protein folding. In the structure refinement process, we constantly use MidasPlus to check the results of our calculations, and display the NMR constraints with the program noeshow. The interactive process of examining the sructure and adding in restraints is heavily dependent on graphics since we have such a great deal of spectral overlap. In addition to molecular graphics, we use the NMR spectral analysis and database management program SPARKY to manage the data from about 1000 proton resonances and over 3000 NOES.
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