An nπ* Interaction in the Bound Substrate of Aspartic Proteases Replicates the Oxyanion Hole

ACS Catal. 2019 Feb 1;9(2):1464-1471. doi: 10.1021/acscatal.8b04142. Epub 2018 Nov 29.


Aspartic proteases regulate many biological processes and are prominent targets for therapeutic intervention. Structural studies have captured intermediates along the reaction pathway, including the Michaelis complex and tetrahedral intermediate. Using a Ramachandran analysis of these structures, we discovered that residues occupying the P1 and P1' positions (which flank the scissile peptide bond) adopt the dihedral angle of an inverse γ-turn and polyproline type-II helix, respectively. Computational analyses reveal that the polyproline type-II helix engenders an nπ* interaction in which the oxygen of the scissile peptide bond is the donor. This interaction stabilizes the negative charge that develops in the tetrahedral intermediate, much like the oxyanion hole of serine proteases. The inverse γ-turn serves to twist the scissile peptide bond, vacating the carbonyl π* orbital and facilitating its hydration. These previously unappreciated interactions entail a form of substrate-assisted catalysis and offer opportunities for drug design.

Keywords: HIV-1 protease; aspartic protease; inverse γ-turn; n→π* interaction; oxyanion hole; pepsin; renin; substrate-assisted catalysis.