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Antidistance Restraints
The absence of a detectable nuclear Overhauser effect (NOE) between
two protons may be interpreted as the protons being far apart in
space. Thus, a repulsive potential can be implemented during molecular
dynamics calculations to discourage proton-proton association. Such
non-NOE or “antidistance constraint” (ADC) can be formulated in terms
of the probability of NOE observation as a function of distance
;
a decaying function that, when directly implemented as a potential,
biases the proton pair to assume distances corresponding to low
values. The XADC energy term is a place holder for such type of
one-dimensional potentials.
The
profile should be provided by the user as it depends on the
particular experimental conditions affecting the NOE intensities
(NOESY mixing time, rotational correlation time, INEPT delays in
NOESY-HSQC experiments, sample deuteration). In addition, different
curves could be provided for different types of proton pairs (H
-
H, H-CH
, etc.). For an example of the derivation of
curves, as well as a practical application of the energy term see
Bermejo and Llinás (2008).
Subsections
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