Prediction of Binding Sites in Receptor-Ligand Complexes with the Gaussian Network Model

Residues at the binding sites of the ligand and receptor of several enzyme-inhibitor and antibody-antigen complexes are predicted from the slowest (for the ligand) and fastest (for the receptor) modes of motion by the Gaussian Network Model applied to unbound molecules.

Figure 1

The enzyme (green)-ligand (blue) complex structure 1BRC. Binding residues are obtained from the model on unbound receptor and ligand, 1BRA, and 1AAP, respectively (see text for details).

Figure 2

Slowest mode relative fluctuations (a) $⟨\Delta R_{ij}^2⟩$ of residue $i$ with all other residues, for the native unbound ligand of the enzyme-inhibitor 1BRC, 1AAP, indicated by the dots along a column corresponding to the residue $i$, (b) $⟨\Delta R_{i,1}^2⟩$ and $⟨\Delta R_{i,n}^2⟩$ of residue $i$ with the first and the last ($n$th) residue of the ligand.

Figure 3

Total correlation, $C_{ij}(k)$, for (a) the ligand (1AAP) with the slowest mode, and (b) for the receptor (1BRA) with the fastest mode.