Encounter-State Over-Anchoring Governs Productive PETase Binding on PET Surfaces

Abstract

Polyethylene terephthalate (PET) hydrolysis by Ideonella sakaiensis PETase (IsPETase) begins at a heterogeneous solid–liquid interface, yet the molecular basis of productive surface recognition remains poorly resolved. Here, we combined a Martini 3 coarse-grained PET model with Go̅Martini protein dynamics to investigate IsPETase binding to an extended PET surface. A four-state kinetic model, comprising unbound, encounter, docked, and precatalytic states, shows that productive binding is not limited by adsorption itself but by a postadsorption reregistration step that converts surface-bound encounter complexes into productively aligned configurations. The simulations reveal a stage-dependent role of conformational flexibility: flexible surface loops facilitate early capture, whereas excessive flexibility promotes misregistered hydrophobic contacts, overstabilizes nonproductive encounter states, and lowers the overall probability of productive commitment. Route analysis on the contact landscape further shows that successful trajectories either commit directly to a product-like basin or undergo reregistration through encounter/transition basins. Comparative simulations of engineered PETase variants uncover a flexibility-driven speed–yield trade-off in which increased flexibility accelerates successful binding events but reduces productive yield through encounter-state over-anchoring. Guided by this mechanism, we formulated a landscape-based design strategy that either weakens encounter-specific anchors or reinforces product-like contacts, leading to mutations that improve productive-binding yield. These results identify postadsorption alignment as the key kinetic bottleneck in PETase surface recognition and provide a mechanistic framework for designing enzymes that operate at heterogeneous polymer interfaces.