Biomedical Engineering Reference
In-Depth Information
Figure 3.3
Secondary chemical shifts and secondary structure elements for human
ubiquitin: PDB code, 1D3Z; BMRB code, 17769. All histograms are
plotted as a function of residue number: (a) secondary
13
C
a
shifts,
Dd(
13
C
a
); (b) secondary
13
C
b
shifts, Dd(
13
C
b
); (c) the DCAB index,
[Dd(
13
C
a
)-Dd(
13
C
b
)] after three-point smoothing;
67
and (d) three-state
classification of secondary structure according to DSSP.
83
'helix' class; sites with Dd (
1
H
a
) . +0.1 ppm are classed as 'strand'; and all
remaining sites are labelled 'coil'. The majority decision over all recorded
nuclei yields a consensus prediction for the residue that is more reliable than
using the Dd (
1
H
a
) value alone.
75
Consensus CSI analyses provide residue-
specific information about secondary structure, which can be contrasted with
the global content or structural class estimates that result from Fourier-
transform infrared, circular dichroism spectroscopy or low-resolution NMR
estimation methods.
5,76
This per-residue secondary structure classification can
facilitate manual resonance assignment, protein visualisation, fold categorisa-
tion, homology modelling and sequence alignment.
77
