Biomedical Engineering Reference
In-Depth Information
simply not sufficiently time-efficient. Other complementary methods of
obtaining structural information have been successfully demonstrated for
membrane proteins using a combination of a smaller number of NOE
restraints together with other distance restraints such as RDCs, PREs, PCSs
and isotropic chemical shift information, leading to the efficient determination
of high-quality NMR structures. 16,17,192 Such methods result in adequate
determination of the backbone conformation, while information on side-chain
orientations may have to rely on database-generated side-chain-packing
information. In the following sections, we assess these restraints. Unlike the
relatively short-distance NOEs which, when summed over the whole structure,
can result in significant propagation of errors, all these types of restraints
greatly reduce this problem.
12.5.1
Paramagnetic Effects
Methods which have shown considerable promise for providing additional
structural information involve restraints obtained from interactions with a
paramagnetic centre. The presence of a paramagnetic centre in the form of an
unpaired electron can lead to PRE. A number of additional effects can arise if
the paramagnetic centre consists of a transition metal. Typically lanthanide
ions are used which allow the additional observation of PCS, RDC (see also
Section 12.5.2) and cross-correlated relaxation effects. 193 So far, for membrane
protein structure determination, information from PREs and RDCs has been
used quite frequently. The PRE arises due to dipolar coupling between the
unpaired electron and nuclear spins, resulting in an additional contribution to
transverse relaxation of the spins, with a similar dependence on distance as the
NOE. However, the larger value of the electronic g-factor greatly increases the
range over which an effect can be observed. Longitudinal spin relaxation is
also affected but for most cases studied, the distance information is derived
from the effects on the transverse relaxation rate constants of the amide
protons:
2
c I g 2 m B S(Sz1)r {6
1
15
m 0
4p
3t c
1z(v H t c ) 2
C 2 ~
4t c z
ð 12 : 1 Þ
where r is the distance between the paramagnetic atom and the observed
nucleus; m 0 the vacuum permittivity; c I , the gyromagnetic ratio of the observed
nucleus; g, the electron g-factor; m B , the electron Bohr magneton; S, the
electron spin quantum-number; t c , the PRE correlation time typically
approximated by t r , the rotational correlation time; and v H /2p, the nuclear
Larmor frequency. As a result of the r 26 dependence, protons in the proximity
of the paramagnetic atom will experience a significant increase in their
relaxation rate. The protons closest to the paramagnetic centre are typically
broadened beyond detection, however, nuclei between 15 and 20 ˚ from the
centre
can
still
be
observed.
Comparison
with
a
diamagnetic
reference
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