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).