Question

Physical Biochemistry

The peaks of a protein NMR spectrum carry a subtle, interesting signature: one side of a peak looks a little different from the other side. The differences offer clues about the internal structure of a protein 2.0 intensity I 0.0 0 50 LUUUUUUUUUUUUUU 10 20 30 40 Af (sec) Experience shows the following equation to be a robust model for the signature: I(Af)= B+(Af-4f.) Q: What are best values of A, B, and Af? Advice: Figure out Af, first. Then chase after A and B via guess-and-check. Best values of these three quantities will deliver a closely-matching plot of the signature.

Answer 1

Tcs(n) = mcs + (ucs - mcs).e=lecs. It decreases exponentially (see Fig. 1 ) from ucs to mcs with the size n of a, as the correct assignment of only a small number of peaks is likely to lead to a higher RMSD than the correct assignment of a high number of peaks. In addition, the CS-filter is applied only if the current assignment a contains a minimum number of five peaks. The 15N and 1HN chemical shifts have a range of about 30 and 3 ppm respectively, but the 1HN shifts are less well predicted and require therefore proportionally higher ucs and mcs parameter values. The parameters Ucs and mcs are set for the 1HN chemical shifts to 2 and 0.8 ppm, respectively. For the 15N

sitheo. The general idea is to reject only assignments a = [a1, d2, ...) of a set of peaks and not to reject a single peak assignment ap = (peak; , residueix), since this could introduce errors in the assignment result due to the imperfections of the predicted values 8theo. The RMSD for a current assignment a = [A1, A2, ..., an] is given by: RMSD, = with n being the actual number of assigned peaks, i.e. the depth of the backtracking search (see (Stratmann et al. 2009) for more details). The current assignment a along the backtracking search is rejected if RMSDa> Tcs(n). The empirically chosen RMSD threshold function