Specific interactions between the alkaline protease of P. aeruginosa and its natural peptide inhibitor: ab initio molecular simulations

Abstract

Alkaline protease aeruginolysin (APR) is an important virulence factor in the evasion of the immune system by Pseudomonas aeruginosa (P. aeruginosa). The P. aeruginosa genome also encodes the highly potent and specifc APR peptide inhibitor (APRin). However, the structural reason for the signifcant inhibition has not been revealed. Using ab initio molecular simulations, we here investigated the specifc interactions between APR and APRin to elucidate which amino acid residues of APRin and APR contribute strongest to the inhibition. Since APR has a Zn2+ ion at the ligand-binding site and histidine and glutamic acid residues are coordinated with Zn2+, it is essential to precisely describe these coordination bonds to elucidate the specifc interactions between APR and APRin. Therefore, we employed the ab initio fragment molecular orbital method to investigate the specifc interactions at an electronic level. The results revealed that Ser1 and Ser2 at the N-terminus of APRin signifcantly contribute to the binding between APRin and APR. In particular, Ser1 binds strongly to Zn2+ as well as to the sidechains of His176(Hid), His180(Hid), and His186(Hid) in APR. This is the main reason for the strong interaction between APR and APRin. The results also elucidated signifcant contributions of the positively charged Arg83 and Arg90 residues of APRin to the binding with APR. These fndings may provide information useful for the design of novel small agents as potent APR inhibitors.