ja9535524_si_002.pdf (1.18 MB)
Determination of the Backbone Dihedral Angles φ in Human Ubiquitin from Reparametrized Empirical Karplus Equations
journal contribution
posted on 1996-03-13, 00:00 authored by Andy C. Wang, Ad BaxThe backbone dihedral angle φ in polypeptides is characterized
by four different J couplings:
3JHNHα,
3JHNC‘,
3JHNCβ,
and
3JHαC‘.
E.COSY and quantitative J correlation techniques have
been used to measure these couplings
in the protein human ubiquitin, uniformly enriched in 13C
and 15N. Assuming that the dihedral backbone angles
in
solution are identical to those in the X-ray structure of this protein
and that HN is located in the C‘−N−Cα
plane,
Karplus relations for
3JHNHα,
3JHαC‘,
and
3JHNCβ,
have been reparametrized. The root-mean-square (rms)
difference
between measured values of
3JHNHα,
3JHαC‘,
3JHNCβ,
and
3JHNC‘
and their corresponding Karplus curves are 0.53, 0.25,
0.24, and 0.36 Hz, respectively, whereas the precision of these
measurements is considerably better. For any given
residue, the differences between the four measured J
couplings and values predicted by their Karplus curves on
the
basis of the X-ray structure-derived φ angle are highly correlated
with one another. On average, a root-mean-square
change of 5.7° in the X-ray derived φ angles is needed to obtain
optimal agreement with all four measured J
couplings.
There is no clear correlation between the φ angle correction
needed and the out-of-plane position of the amide
proton predicted by ab initio calculations. The small
differences in φ angles therefore presumably result from
small
uncertainties in the atomic positions of the 1.8 Å X-ray structure.
However, they may also be caused by genuine
differences between the structure of the protein in solution and in the
crystalline state or contain a contribution
resulting from deviations from the assumption that the
HN−N−Cα−Hα dihedral angle
equals φ − 60°.