Biomedical Engineering Reference
In-Depth Information
principal 'island' in the GLE plot, while realistic upper and lower limits are
deduced from the maximum width of the island in each dimension. This
approach provides a straightforward way of identifying residues with chemical
shifts that are consistent with multiple conformations [Figure 3.5(d)].
Degeneracy of this sort may be accidental, implying that several conformations
are capable of inducing similar electronic environments at multiple nucleus
sites within the fragment; alternatively, degeneracy could be related to
chemical shift averaging due to conformational flexibility. Filtering out the
estimates from such sites yields predictions of w and y that are more realistic,
with significant improvements for remaining glycine and pre-proline resi-
dues.
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The Real-SPINE 3.0 server is able to estimate backbone dihedral angles
from sequence information alone;
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remarkably, in 55% of cases it can return
Figure 3.5
Global likelihood estimate (GLE) diagrams produced by the DANGLE
algorithm
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for residues from the origin binding domain of the SV40 T-
antigen: PDB code, 2FUF; BMRB code, 4127. (a) Tyr-162, a b-strand
conformation; (b) Ala-169, an a-helical conformation; (c) Gly-250, a left-
handed turn conformation; and (d) Val-181, an ambiguous site showing
three possible conformations. 10u610u bins with probability scores below
the
threshold
value
are
in
white;
other
bins
are
shaded
from
red
(threshold value) to black (maximum probability).
