Cation–pi interaction in protein structures（2）

一对原子i和j之间的范德华能量由下式给出
vdw=4ɛij(σij12/rij12−σij6/rij6),
where σij = (σiiσjj)1/2 and ɛij = (ɛiiɛjj)1/2; and ɛ are, respectively, the van der Waals radius and well depth.
In identifying the cation-π interactions, all cation-π pairs (K or R with F, Y, or W) within 10 Å of each other are considered. If there is a gap large enough to insert a water molecule at closest contact, the structure is rejected, and the residues are considered “noninteracting.” For the remaining “interacting pairs,” the OPLS electrostatic energy, Ees, is evaluated. If Ees ≤ −2.0 kcal/mol, the pair is counted as a cation-π interaction. If Ees > −1.0 kcal/mol, the structure is rejected. If −2.0 < Ees ≤ −1.0 kcal/mol, the structure is retained only if EvdW ≤ −1.0 kcal/mol (Gallivan and Dougherty, 1999).
The influence of cation-π interaction varies in different classes of proteins, such asglobular, membrane, DNA binding, mesophilic, and thermophilic proteins (Wintjens etal.