Molecular design of orthogonal stacking system at the complex interface of HtrA PDZ domain with its peptide ligands

The high temperature requirement A (HtrA) protease plays a crucial role in protein quality control and cell fate. The enzyme contains a catalytic protease domain and a regulatory PDZ domain; the latter determines the substrate specificity of the former by specifically binding to the C-terminal hydrophobic stretch of its partner proteins. Previously, a pentapeptide ligand H3C1 was identified as the potential binder of HtrA PDZ domain using phage display technique. Here, an orthogonal pi-cation-pi stacking system at the crystal domain-peptide complex interface was analysed by integrating theoretical calculations and experimental assays. It was demonstrated that there is a strong (positive) synergistic effect between the two wings of the stacking system; breaking of cation-pi interaction in one wing can largely impair the interaction strength of another wing. The pi-electron contributes primarily to the synergistic effect, although geometric property is also (marginally) responsible for it. Next, the systematic combinations between the four aromatic amino acids (Phe, Tyr, Trp and His) plus one non-aromatic amino acid (Ala) at the two wings of pi-cation-pi stacking were investigated. It was found that two aromatic substitutions (Phe-4Tyr and Phe-4Trp) at a wing can considerably and moderately improve peptide affinity by 3.2- and 1.5-fold, respectively, whereas the non-aromatic mutations at each wing and at both of them can significantly reduce the affinity with K-d increase from 1.8 (wild type) to 34 mu M and 160 mu M (single-point mutations), as well as 210 mu M (double-point mutation), suggesting that just breaking of one wing can substantially undermine the synergism of orthogonal pi-cation-pi stacking.