Investigation of the binding specificity of Erbin-PDZ affinity clamp by molecular dynamics simulations

An exquisitely specific “affinity clamp” with nanomolar affinities was recently engineered via directed evolution strategy, which is composed of the human Erbin-PDZ domain and the fibronectin type III (FN3) domain. This high-specificity affinity clamp showed distinct binding affinity to two p120-related catenin peptides, δ-catenin and ARVCF. To investigate the interactions between the affinity clamp and these two peptides and probe the ligand binding specificity, here we performed the molecular dynamics (MD) simulations and free energy evaluations on the complexes. A hydrogen bond network was discovered between ligands δ-catenin, ARVCF and the affinity clamp. Compared with δ-catenin, ARVCF formed more hydrogen bonds with the affinity clamp. The binding free energies evaluated by the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) methodology successfully ranked the ligand binding free energies, which is in agreement with the surface plasmon resonance (SPR) experiment. The further decomposition of the binding free energy revealed that electrostatic interactions, Van der Waals and hydrophobic interactions are predominant to the binding affinity difference. Our MD simulation results will provide structural and mechanistic insights for further optimization of the interactions between the affinity clamp and catenin peptides.