Figure 1.
The overlap of ligand and protein binding sites within protein families.
(A) The distribution of overlap scores (Eqn 1) is shown for all families that bind both ligands and proteins (grey; n = 1,028), and the subsets of families with a statistically significant overlap (p0.01; solid; n = 197) or non-overlap (p
0.01; dashed; n = 113). The highest overlap score observed is 10.83 (not shown). (B) The residue type propensity (Eqn 3) and (C) conservation (Eqn 4) at alignment positions that bind both ligands and proteins (black; n = 102,436), bind ligands (cyan; n = 46,610), bind proteins (orange; n = 491,723) in comparison to all solvent-exposed residues (grey; n = 1,147,882). The statistical significance of the residue propensities was estimated by a bootstrap resampling procedure (Table S5).
Figure 2.
Ligand-protein binding site overlap observed at protein–protein interactions as a function of sequence identity.
The maximum observed ligand binding site overlap (y-axis) for (A) inter-molecular domain–domain and (B) domain–peptide interactions, as a function of the ligand binding site sequence identity (x-axis). The densities in these plots are represented by colors that range from yellow (no density) to blue (maximum density). The (C) maximal and (D) cumulative overlap profile is shown at a minimum ligand binding site identity threshold of 30% for inter-molecular (black), intra-molecular (orange) domain–domain, and domain–peptide (cyan) interactions. Tick marks indicate interfaces that exhibit a particular level of interface coverage. The overlap score refers to the fraction of interface residues aligned to ligand binding site residues (Eqn 2).
Table 1.
Examples of ligand binding sites that align to protein–protein interfaces with identical or nearly identical sequences.
Figure 3.
Small molecule binding sites overlapped with four broad classes of protein–protein interfaces.
(A) Enzyme – protein inhibitors: eg, 3′-phosphothymidine (3′–5′)-pyrophosphate adenosine 3′-phosphate (PDB 1U1B:PAX) overlapped with the ribonuclease (orange, 2Q4G)–inhibitor (purple, 2Q4G) interface. (B) Enzyme–protein substrate: eg, Kni-577 (cyan, 1MRW:K47) bound to the HIV-protease dimer (grey backbone, 1MRW:A,B; orange, 1A8K:A,B) at the same positions as its peptide substrate (purple, 1A8K:C). (C) Structural or regulatory interfaces: eg, kabiramide-C (cyan, 1QZ5:KAB) bound to Actin (grey backbone, 1QZ5:A; orange, 1H1V:A) at the same position as Gelsolin (purple, 1H1V:G). (D) Several ligands complemented protein interfaces: eg, bepridil (cyan, 1lxf:BEP) bound at the interface between troponin C (orange, 1LXF:C) and troponin I (purple, 1LXF:I). Figure produced by PyMOL (http://pymol.org).
Figure 4.
Overlapping binding sites suggest structural mechanisms for observed small molecule effects.
(A) Sanglifehrin (cyan, PDB 1NMK:SFM) binds to cyclophilin A (grey, 1NMK; orange, 1AK4:A) at the same position that binds the HIV Gag capsid protein (purple, 1AK4:D). (B) Fusicoccin (cyan, 1O9E:FSC) binds to a region of the plant 14-3-3 protein (grey, 1O9E) that is homologous to the 14-3-3- (orange, 1A38:A) binding site for phosphopeptides (purple, 1A38:P). (C) Bepridil (cyan and blue, 1LXF:BEP) binds to Troponin C (grey, 1LXF:C) at positions that are homologous to the calmodulin (orange, 1K93:D) interface for anthrax edema factor (purple, 1K93:A). Troponin C aligns to both EF-hand motifs in calmodulin: The binding site aligned with EF-motif 2 (cyan) exhibits greater overlap with the anthrax edema factor interface than EF-motif 1 (blue).