The Binding Behavior of Peptide Ligands to Human Osteoclast-Stimulating Factor SH3 Domain Shifted by a Rationally Designed π-Stacking System

Human osteoclast-stimulating factor (OSF) induces osteoclast formation and bone resorption in osteoporosis by recruiting multiple signaling complexes with downstream partners. Protein contains a peptide-recognition Src homology 3 (SH3) domain that can recognize and bind class II linear motif [Formula: see text] to its partner proteins. The motif is defined by two prolines at positions [Formula: see text]1 and [Formula: see text]2, which are the primary anchor residues required for the domain recognition, and a positively charged amino acid at position [Formula: see text]4, which is the secondary anchor residue and determines the binding orientation of the motif peptides on the domain surface. In this study, we systematically examined the intermolecular interaction of OSF SH3 domain with a high-affinity decapeptide segment derived from its partner protein Sam68 at structural and energetic levels. It was found that, in addition to the primary and secondary anchor residues, the residue at peptide position [Formula: see text]1 is also important, which can form a [Formula: see text]-stacking system (consisting of multiple cation-[Formula: see text] or [Formula: see text]–[Formula: see text] stacking interactions) with its vicinal aromatic residues Phe23, Trp49 and Tyr65 of OSF SH3 domain, thus, largely stabilizing the domain–peptide complex. Here, we assigned the position [Formula: see text]1 as the third anchor residue and investigated the stacking effect by systematically substituting the position [Formula: see text]1 residue with six charged/aromatic amino acids (Arg, Lys, His, Phe, Tyr and Trp) and one neutral amino acid (Ala), as well as their impacts on the domain–peptide binding. A strong stacking effect was observed in association with charged/aromatic substitutions relative to neutral substitution, conferring substantial stability to the complex formation. A further fluorescence-based assay also substantiated the computational findings; the lysine and tyrosine substitutions ([Formula: see text] and [Formula: see text]) were observed to significantly and moderately improve peptide affinity by 4.7-fold and 1.4-fold relative to wild-type Sam68 decapeptide ([Formula: see text]), respectively.