Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets

BMC Bioinformatics

Table 3 Conserved pockets in the IL-2 superfamily at the known IL2 receptor interfaces

Pocket prediction (ensemble scoring)	Highly conserved pocket residues at interface	Sensitivity	Specificity
PASS (Provar)	13	30.2	81.8
Ligsite pockets (Provar)	13	30.2	80.5
fpocket (Provar)	18	37.2	71.4
fpocket (MDpocket)	21	48.8	46.8

There are three distinct interfaces made between IL-2 and the subunits of the IL-2 receptor, which together involve 43 residues of the 120 residue IL2 protein (with only 1 residue that contacts two subunits). Investigation of pockets in 17 apo structures from the highly diverse IL-2 superfamily (pair wise sequence identities of 7.5-13.3%) using the Provar scoring methodology (Equation 4) shows that there are several relatively highly conserved pocket-lining residues which lie at the receptor interfaces (Figure 9). This is suggestive that these pockets are functionally significant in a substantial proportion of the family. Selecting the 25% of residues with the highest Provar scores from analyses with PASS, LIGSITE^-cs and fpocket prediction methods shows a similar pattern of high specificity (TN/(TN + FP)), but low sensitivity (TP/(TP + FN)) for interface residues. Scoring fpocket predictions with an alternative ensemble approach (MDPocket) that uses spatial averaging, and is thus sensitive to superposition error, has high scores in similar locations, but also scores more areas of the protein surface similarly highly and thus has lower specificity.

ISSN: 1471-2105