Investigating substrate binding mechanism in prolyl oligopeptidase through molecular dynamics.

Prolyl oligopeptidase (PREP) has gained attention for its role in neurodegenerative diseases, particularly through protein-protein interactions with amyloid proteins such as alpha-synuclein and Tau. Although significant research has focused on PPIs, the substrate-binding dynamics within the catalytic pocket of PREP is less understood. This study combines molecular docking and molecular dynamics simulations to investigate the behavior of known PREP substrates, including thyrotropin-releasing hormone. Our simulations reveal that TRH transitions between three preferred regions within the binding pocket, one of which is favorable for catalytic activity. The absence of a single fixed binding site near the catalytic triad region may suggest a dynamic substrate-processing mechanism. Additionally, the potential of the TRH precursor as a substrate is evaluated. Our findings highlight the utility of computational methods in the analysis of protein dynamics and enzymatic mechanisms, offering insights into the functional versatility of PREP.