Structure‐based statistical modeling and analysis of peptide affinity and cross‐reactivity to human senile osteoporosis OSF SH3 domain

Abstract

Human osteoclast-stimulating factor (OSF) induces osteoclast formation and bone resorption in senile osteoporosis by recruiting multiple signaling complexes with cognate interacting partners through its N-terminal Src homology 3 (SH3) peptide-recognition domain. The domain can recognize and bind to the polyproline regions of its partner proteins, rendering a broad ligand specificity and cross-reactivity. Here, the structural basis and physicochemical property of peptide affinity and cross-reactivity to OSF SH3 domain were investigated systematically by using an integration of statistical analysis and molecular modeling. A structure-based quantitative structure-activity relationship method called cross-nonbonded interaction characterization and statistical regression was used to characterize the intermolecular interactions involved in computationally modeled domain-peptide complex structures and then to correlate the interactions with affinity for a panel of collected SH3-binding peptide samples. Both the structural stability and generalization ability of obtained quantitative structure-activity relationship regression models were examined rigorously via internal cross-validation and external test, confirming that the models can properly describe even single-residue mutations at domain-peptide complex interface and give a reasonable extrapolation for the mutation effect on peptide affinity. Subsequently, the best model was used to investigate the promiscuity and cross-reactivity of OSF SH3 domain binding to its various peptide ligands. It is found that few key residues in peptide ligands are primarily responsible for the domain affinity and selectivity, while most other residues only play a minor role in domain-peptide binding affinity and stability. The peptide residues can be classified into 3 groups in terms of their contribution to ligand selectivity: key, assistant, and marginal residues. Considering that the key residues are very few so that many domain interacting partners share a similar binding profile, additional factors such as in vivo environments and biological contexts would also contribute to the specificity and cross-reactivity of OSF SH3 domain.---