BCMB/CHEM 8190
Problem Set 6
1) A NOESY experiment is conducted on a small protein using a short mixing time (50ms). Crosspeaks are
observed and integrated for a glycine residue. Using the distance between the two alpha protons in this amino
acid (0.175nm) as a distance standard, and the following crosspeak intensity data, estimate the dihedral angle
phi (N-Cα bond) for this amino acid. Use other standard bond and angle geometries as necessary.
Ha1 - Ha2 28.0
Ha1 - HN 1.6
Ha2 - HN 0.5
2) The following are planes from HNCA and NHCO experiments taken at the same 15N chemical shift.
a) add the residue number to
the peaks in the HNCA
spectrum
b) why are the upfield peaks
in each pair weaker?
c) will the weaker peaks
always be upfield?
2) Below we show some plots for 15N T1s and T2s for a 21 kDa protein collected at 600 MHz for protons and
25º C.
a) Using the simple formulas given in class estimate the correlation time for the protein using some of the data
around residues 30-60.
b) Given that the dipolar interaction constant for a H-N pair (dd/4) is 5.85 x 109, calculate the order parameter
S for these residues
c) If S were 0.8 and the fast motions of the H-N vector were associated with wobbling around the surface of a
cone, what would be the cone angle?
T2 (ms)
T1 (ms)
Sequence
Sequence