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 $P_{\mbox{\scriptsize noe}}$; a decaying function that, when directly implemented as a potential, biases the proton pair to assume distances corresponding to low $P_{\mbox{\scriptsize noe}}$ values. The XADC energy term is a place holder for such type of one-dimensional potentials.

The $P_{\mbox{\scriptsize noe}}$ 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 $P_{\mbox{\scriptsize noe}}$ curves could be provided for different types of proton pairs (H$^N$- H$^N$, H$^N$-CH$_3$, etc.). For an example of the derivation of $P_{\mbox{\scriptsize noe}}$ curves, as well as a practical application of the energy term see Bermejo and Llinás (2008).

Xplor-NIH 2023-11-10