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.2000; Gromiha etal.2002a; Chakravarty and Varadarajan,2002;Gromiha, 2003; Gromiha et al. 2004a,b: Gromiha and Suwa, 2005). Furthermore, cation-π interaction has been used to calculate the interaction energy between amino acid residues (Shacham et al. 2004). Recently, cation-π interactions are used to understand the recognition mechanism of protein-protein complexes (Gromiha et al. 2009).
The concept of cation-π interactions is simple to develop a computer program for delineating such interactions and their interaction energies. However, Gallivan and Dougherty (1999)developed the program, CAPTURE, which is available on the Web for academic users. It is available at http://capture.caltech.edu/. It has the options to run for any structure available in the PDB or upload the file in the PDB format. The output for the protein human lysozyme is shown in Figure 3.9. It lists the amino acid composition of the cation-π interaction forming residues and the number of cation-π interactions for all the possible six pairs. Furthermore, the residues involved in cation-π interactions along with their respective cationinteraction energy are listed. This will be helpful to understand the strength of each cation-π interaction.
在确定阳离子-π相互作用时，考虑彼此之间的所有阳离子-π对（K或R与F，Y或W）。如果存在足够大的间隙以插入最接近的水分子，则结构被拒绝，并且残基被认为是“不相互作用的”。对于“相互作用的对”，评估OPLS静电能Ees。如果Ees≤-2.0千卡/摩尔，则该对被计为阳离子-π相互作用。如果Ees> -1.0千卡/摩尔，则结构被拒绝。如果-2.0