Structural Dissection and Optimization of a Cation–π–π Stacking System in Human Pregnancy-Related Serine Protease–Peptide Complex

Abstract

Human pregnancy-related serine protease (PRSP) belongs to the high temperature requirement A (HTRA) family of homo-oligomeric and ATP-independent serine proteases, which plays an important role in human placental development and has been recognized as a potential therapeutic target for diverse diseases. Previously, we have successfully obtained the halogenated versions of HTRA peptide ligands via a rational design approach. In this study, we systematically investigate the solution complex structure of PRSP PDZ domain with its phage-displayed peptide ligand and identify a cation–π–π stacking system across the domain–peptide complex interface. The structural configuration, energetic property and molecular basis of the stacking system are examined in detail by using theoretical calculations and affinity assays. It is revealed that the stacking system is a noncovalent unit independent of other regions of the domain–peptide complex, which plays crucial role in conferring affinity and specificity to the complex binding. In addition, a coupled effect between cation–π and π–π interactions in the stacking system is observed; breaking of one interaction can influence another interaction substantially. As compared to other aromatic amino acids such as Tyr, Phe and His as well as neutral amino acid Ala, the wild-type peptide residue Trp is found as the best choice that can effectively stabilize the domain–peptide complex architecture.