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Here, we combined a Martini 3 coarse-grained PET model with Go\u0305Martini 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\u2013yield 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.<\/jats:p>","DOI":"10.1021\/acs.jctc.6c00544","type":"journal-article","created":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T13:03:05Z","timestamp":1785934985000},"page":"8579-8594","source":"Crossref","is-referenced-by-count":0,"title":["Encounter-State\nOver-Anchoring Governs Productive\nPETase Binding on PET Surfaces"],"prefix":"10.1021","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-9550-7123","authenticated-orcid":true,"given":"Chengze","family":"Huo","sequence":"first","affiliation":[{"name":"The Hong Kong University of Science and Technology (Guangzhou) , , , ,","place":["Guangzhou, Guangdong, China, 511400"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4030-356X","authenticated-orcid":true,"given":"Jun","family":"Wang","sequence":"additional","affiliation":[{"name":"The Hong Kong University of Science and Technology (Guangzhou) , , , ,","place":["Guangzhou, Guangdong, China, 511400"]},{"name":"The Hong Kong University of Science and Technology (Guangzhou) , , , ,","place":["Guangzhou, Guangdong, China, 511400"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3166-7070","authenticated-orcid":true,"given":"Xiakun","family":"Chu","sequence":"additional","affiliation":[{"name":"The Hong Kong University of Science and Technology (Guangzhou) , , , ,","place":["Guangzhou, Guangdong, China, 511400"]},{"name":"The Hong Kong University of Science and Technology (Guangzhou) , , , ,","place":["Guangzhou, Guangdong, China, 511400"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,4]]},"reference":[{"key":"2026083118574355300_cit1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.1700782","article-title":"Production, Use, and Fate of All\nPlastics Ever Made","volume":"3","author":"Geyer","year":"2017","journal-title":"Sci. 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Catal."},{"key":"2026083118574355300_cit7","doi-asserted-by":"publisher","first-page":"0046","DOI":"10.1038\/s41570-017-0046","article-title":"Chemical Recycling of Waste Plastics for New Materials\nProduction","volume":"1","author":"Rahimi","year":"2017","journal-title":"Nat. Rev. Chem."},{"key":"2026083118574355300_cit8","doi-asserted-by":"publisher","first-page":"15402","DOI":"10.1002\/anie.201915651","article-title":"Beyond Mechanical Recycling: Giving\nNew Life to Plastic Waste","volume":"59","author":"Vollmer","year":"2020","journal-title":"Angew. Chem., Int.\nEd."},{"key":"2026083118574355300_cit9","doi-asserted-by":"publisher","first-page":"4028","DOI":"10.1002\/cssc.202002666","article-title":"Biocatalysis in the Recycling Landscape for Synthetic\nPolymers and Plastics towards Circular Textiles","volume":"14","author":"Jo\u0308nsson","year":"2021","journal-title":"ChemSusChem"},{"key":"2026083118574355300_cit10","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1126\/science.adq7316","article-title":"Polyolefin Waste\nto Light Olefins with Ethylene and Base-Metal Heterogeneous Catalysts","volume":"385","author":"Conk","year":"2024","journal-title":"Science"},{"key":"2026083118574355300_cit11","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1126\/science.adh0993","article-title":"Chemical Upcycling of Polyethylene, Polypropylene, and Mixtures to\nHigh-Value Surfactants","volume":"381","author":"Xu","year":"2023","journal-title":"Science"},{"key":"2026083118574355300_cit12","doi-asserted-by":"publisher","first-page":"20190273","DOI":"10.1098\/rsta.2019.0273","article-title":"Biocatalytic\nRecycling of Polyethylene Terephthalate Plastic","volume":"378","author":"Zimmermann","year":"2020","journal-title":"Philos. Trans. R. Soc., A"},{"key":"2026083118574355300_cit13","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1038\/s41586-020-2149-4","article-title":"An Engineered PET Depolymerase to Break down and Recycle Plastic\nBottles","volume":"580","author":"Tournier","year":"2020","journal-title":"Nature"},{"key":"2026083118574355300_cit14","doi-asserted-by":"publisher","first-page":"2100843","DOI":"10.1002\/adma.202100843","article-title":"Upcycling to Sustainably\nReuse Plastics","volume":"34","author":"Zhao","year":"2022","journal-title":"Adv. Mater."},{"key":"2026083118574355300_cit15","doi-asserted-by":"publisher","first-page":"1196","DOI":"10.1126\/science.aad6359","article-title":"A Bacterium That Degrades and Assimilates\nPoly(Ethylene Terephthalate)","volume":"351","author":"Yoshida","year":"2016","journal-title":"Science"},{"key":"2026083118574355300_cit16","doi-asserted-by":"publisher","first-page":"25476","DOI":"10.1073\/pnas.2006753117","article-title":"Characterization and\nEngineering of a Two-Enzyme System for Plastics\nDepolymerization","volume":"117","author":"Knott","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U.\nS. A."},{"key":"2026083118574355300_cit17","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1038\/s41929-020-00521-w","article-title":"Possibilities\nand Limitations of\nBiotechnological Plastic Degradation and Recycling","volume":"3","author":"Wei","year":"2020","journal-title":"Nat. Catal."},{"key":"2026083118574355300_cit18","doi-asserted-by":"publisher","first-page":"4123","DOI":"10.1002\/cssc.202100652","article-title":"Waste to Wealth:\nChemical Recycling\nand Chemical Upcycling of Waste Plastics for a Great Future","volume":"14","author":"Chen","year":"2021","journal-title":"ChemSusChem"},{"key":"2026083118574355300_cit19","doi-asserted-by":"publisher","first-page":"3397","DOI":"10.1021\/acscatal.1c05548","article-title":"Conformational\nSelection in Biocatalytic Plastic Degradation by PETase","volume":"12","author":"Guo","year":"2022","journal-title":"ACS Catal."},{"key":"2026083118574355300_cit20","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1038\/s41929-022-00821-3","article-title":"Directed\nEvolution of an Efficient and Thermostable PET Depolymerase","volume":"5","author":"Bell","year":"2022","journal-title":"Nat. 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Commun."},{"key":"2026083118574355300_cit23","doi-asserted-by":"publisher","first-page":"3519","DOI":"10.1021\/acscatal.9b00568","article-title":"Rational\nProtein\nEngineering of Thermo-Stable PETase from Ideonella Sakaiensis for\nHighly Efficient PET Degradation","volume":"9","author":"Son","year":"2019","journal-title":"ACS Catal."},{"key":"2026083118574355300_cit24","doi-asserted-by":"publisher","first-page":"1340","DOI":"10.1021\/acscatal.0c05126","article-title":"Computational Redesign\nof a PETase for Plastic Biodegradation under\nAmbient Condition by the GRAPE Strategy","volume":"11","author":"Cui","year":"2021","journal-title":"ACS\nCatal."},{"key":"2026083118574355300_cit25","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1038\/s41586-022-04599-z","article-title":"Machine Learning-Aided\nEngineering of Hydrolases for\nPET Depolymerization","volume":"604","author":"Lu","year":"2022","journal-title":"Nature"},{"key":"2026083118574355300_cit26","doi-asserted-by":"publisher","first-page":"1223","DOI":"10.1021\/jacsau.2c00204","article-title":"Sabatier Principle for Rationalizing Enzymatic Hydrolysis of a Synthetic\nPolyester","volume":"2","author":"Arnling B\u00e5\u00e5th","year":"2022","journal-title":"JACS Au"},{"key":"2026083118574355300_cit27","doi-asserted-by":"publisher","first-page":"3041","DOI":"10.1021\/acs.jcim.1c00394","article-title":"QM\/MM Study\nof the Enzymatic Biodegradation\nMechanism of Polyethylene Terephthalate","volume":"61","author":"Boneta","year":"2021","journal-title":"J.\nChem. Inf. Model."},{"key":"2026083118574355300_cit28","doi-asserted-by":"publisher","first-page":"11626","DOI":"10.1021\/acscatal.1c03700","article-title":"Reaction\nMechanism of the PET Degrading Enzyme PETase Studied with DFT\/MM Molecular\nDynamics Simulations","volume":"11","author":"Jerves","year":"2021","journal-title":"ACS Catal."},{"key":"2026083118574355300_cit29","doi-asserted-by":"publisher","first-page":"19243","DOI":"10.1021\/jacs.3c04427","article-title":"Insights into\nthe Enhancement of the Poly(Ethylene\nTerephthalate) Degradation by FAST-PETase from Computational Modeling","volume":"145","author":"Garci\u0301a-Meseguer","year":"2023","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574355300_cit30","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1038\/s41929-021-00616-y","article-title":"General Features to Enhance Enzymatic Activity of Poly(Ethylene Terephthalate)\nHydrolysis","volume":"4","author":"Chen","year":"2021","journal-title":"Nat. Catal."},{"key":"2026083118574355300_cit31","doi-asserted-by":"publisher","first-page":"2106","DOI":"10.1038\/s41467-017-02255-z","article-title":"Structural Insight\ninto Catalytic Mechanism of PET Hydrolase","volume":"8","author":"Han","year":"2017","journal-title":"Nat.\nCommun."},{"key":"2026083118574355300_cit32","doi-asserted-by":"publisher","first-page":"E4350","DOI":"10.1073\/pnas.1718804115","article-title":"Characterization\nand engineering of a plastic-degrading\naromatic polyesterase","volume":"115","author":"Austin","year":"2018","journal-title":"Proc. Natl. Acad. Sci.\nU. S. A."},{"key":"2026083118574355300_cit33","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1038\/s41467-018-02881-1","article-title":"Structural\nInsight into Molecular Mechanism of Poly(Ethylene Terephthalate) Degradation","volume":"9","author":"Joo","year":"2018","journal-title":"Nat. Commun."},{"key":"2026083118574355300_cit34","doi-asserted-by":"publisher","first-page":"6842","DOI":"10.1080\/07391102.2023.2240893","article-title":"Computational Investigation\non the Binding Modes of PET Polymer to PETase","volume":"42","author":"Guo","year":"2024","journal-title":"J. Biomol. Struct. Dyn."},{"key":"2026083118574355300_cit35","doi-asserted-by":"publisher","first-page":"4000","DOI":"10.1021\/jacsau.4c00718","article-title":"From Bulk\nto Binding: Decoding the Entry of PET into\nHydrolase Binding Pockets","volume":"4","author":"Ja\u0308ckering","year":"2024","journal-title":"JACS Au"},{"key":"2026083118574355300_cit36","doi-asserted-by":"publisher","DOI":"10.1002\/anie.202511131","article-title":"Insight into\nHow PETase Functions\nat the Solid-Liquid Interface and an Activity-Stability Trade-Off","volume":"64","author":"Chen","year":"2025","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026083118574355300_cit37","doi-asserted-by":"publisher","first-page":"4112","DOI":"10.1021\/acs.jcim.4c00079","article-title":"Probing Enzymatic PET\nDegradation: Molecular Dynamics Analysis of Cutinase Adsorption and\nStability","volume":"64","author":"Sahihi","year":"2024","journal-title":"J. Chem. Inf. Model."},{"key":"2026083118574355300_cit38","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1021\/ct700324x","article-title":"The MARTINI\nCoarse-Grained Force Field: Extension to\nProteins","volume":"4","author":"Monticelli","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574355300_cit39","doi-asserted-by":"publisher","first-page":"2531","DOI":"10.1021\/ct9002114","article-title":"Combining an Elastic\nNetwork With a Coarse-Grained Molecular Force Field: Structure, Dynamics,\nand Intermolecular Recognition","volume":"5","author":"Periole","year":"2009","journal-title":"J. Chem. Theory\nComput."},{"key":"2026083118574355300_cit40","doi-asserted-by":"publisher","first-page":"1366","DOI":"10.1021\/acs.jctc.6b00986","article-title":"Combining\nthe MARTINI and Structure-Based\nCoarse-Grained Approaches for the Molecular Dynamics Studies of Conformational\nTransitions in Proteins","volume":"13","author":"Poma","year":"2017","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574355300_cit41","doi-asserted-by":"publisher","first-page":"3714","DOI":"10.1038\/s41467-020-17437-5","article-title":"Protein\u2013Ligand\nBinding with the Coarse-Grained\nMartini Model","volume":"11","author":"Souza","year":"2020","journal-title":"Nat. Commun."},{"key":"2026083118574355300_cit42","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1038\/s41592-021-01098-3","article-title":"Martini 3: A General Purpose Force Field for\nCoarse-Grained\nMolecular Dynamics","volume":"18","author":"Souza","year":"2021","journal-title":"Nat. Methods"},{"key":"2026083118574355300_cit43","doi-asserted-by":"publisher","first-page":"2100391","DOI":"10.1002\/adts.202100391","article-title":"Martini\n3 Coarse-Grained\nForce Field: Small Molecules","volume":"5","author":"Alessandri","year":"2022","journal-title":"Adv. Theory Simul."},{"key":"2026083118574355300_cit44","doi-asserted-by":"publisher","first-page":"4051","DOI":"10.1038\/s41467-025-58719-0","article-title":"Go\u0305Martini 3:\nFrom Large Conformational Changes\nin Proteins to Environmental Bias Corrections","volume":"16","author":"Souza","year":"2025","journal-title":"Nat. Commun."},{"key":"2026083118574355300_cit45","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/s41467-021-27627-4","article-title":"Polyply;\na Python Suite for Facilitating\nSimulations of Macromolecules and Nanomaterials","volume":"13","author":"Gru\u0308newald","year":"2022","journal-title":"Nat. Commun."},{"key":"2026083118574355300_cit46","doi-asserted-by":"publisher","first-page":"1556","DOI":"10.1021\/ma9714124","article-title":"Molecular Dynamics Simulation of\nAmorphous Poly(Ethylene Terephthalate)","volume":"31","author":"Hedenqvist","year":"1998","journal-title":"Macromolecules"},{"key":"2026083118574355300_cit47","doi-asserted-by":"publisher","first-page":"2978","DOI":"10.1021\/ma0352577","article-title":"Detailed Atomistic Simulation of\nthe Segmental Dynamics and Barrier Properties of Amorphous Poly(Ethylene\nTerephthalate) and Poly(Ethylene Isophthalate)","volume":"37","author":"Karayiannis","year":"2004","journal-title":"Macromolecules"},{"key":"2026083118574355300_cit48","doi-asserted-by":"publisher","first-page":"8241","DOI":"10.1021\/ma901780e","article-title":"Structure and Mobility of Poly(Ethylene Terephthalate):\nA Molecular Dynamics Simulation Study","volume":"42","author":"Eslami","year":"2009","journal-title":"Macromolecules"},{"key":"2026083118574355300_cit49","doi-asserted-by":"publisher","first-page":"2032","DOI":"10.1002\/cbic.202000841","article-title":"Novel PET-Degrading\nEnzymes: Structure\u2013Function\nfrom a Computational Perspective","volume":"22","author":"Berselli","year":"2021","journal-title":"ChemBioChem."},{"key":"2026083118574355300_cit50","doi-asserted-by":"publisher","DOI":"10.1063\/1.4976518","article-title":"Markov State\nModels from Short Non-Equilibrium Simulations\u2500Analysis and\nCorrection of Estimation Bias","volume":"146","author":"Nu\u0308ske","year":"2017","journal-title":"J. Chem. Phys."},{"key":"2026083118574355300_cit51","doi-asserted-by":"publisher","DOI":"10.1063\/1.5064530","article-title":"Generalized Markov Modeling of Nonreversible\nMolecular Kinetics","volume":"150","author":"Reuter","year":"2019","journal-title":"J. Chem. Phys."},{"key":"2026083118574355300_cit52","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.ymeth.2010.06.002","article-title":"Everything You Wanted to Know about\nMarkov State Models but Were Afraid to Ask","volume":"52","author":"Pande","year":"2010","journal-title":"Methods"},{"key":"2026083118574355300_cit53","doi-asserted-by":"publisher","DOI":"10.1063\/1.3565032","article-title":"Markov Models\nof Molecular Kinetics: Generation and Validation","volume":"134","author":"Prinz","year":"2011","journal-title":"J. Chem. Phys."},{"key":"2026083118574355300_cit54","doi-asserted-by":"publisher","first-page":"5525","DOI":"10.1021\/acs.jctc.5b00743","article-title":"PyEMMA 2: A Software Package for Estimation, Validation,\nand Analysis of Markov Models","volume":"11","author":"Scherer","year":"2015","journal-title":"J. Chem. Theory\nComput."},{"key":"2026083118574355300_cit55","doi-asserted-by":"publisher","first-page":"8868","DOI":"10.1073\/pnas.160259697","article-title":"Speeding Molecular Recognition by\nUsing the Folding Funnel: The Fly-Casting Mechanism","volume":"97","author":"Shoemaker","year":"2000","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026083118574355300_cit56","doi-asserted-by":"publisher","first-page":"738","DOI":"10.1021\/ja065531n","article-title":"Fly-Casting\nin Protein-DNA Binding:\nFrustration between Protein Folding and Electrostatics Facilitates\nTarget Recognition","volume":"129","author":"Levy","year":"2007","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574355300_cit57","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1038\/nchembio.232","article-title":"The Role\nof Dynamic Conformational\nEnsembles in Biomolecular Recognition","volume":"5","author":"Boehr","year":"2009","journal-title":"Nat.\nChem. Biol."},{"key":"2026083118574355300_cit58","doi-asserted-by":"crossref","unstructured":"Sculley, D.\n          \n          Web-Scale K-Means\nClustering.  Proceedings of the 19th International\nConference on World Wide Web, New York, NY, USA, 2010; pp 1177\u20131178.","DOI":"10.1145\/1772690.1772862"},{"key":"2026083118574355300_cit59","first-page":"2825","article-title":"Scikit-Learn: Machine Learning in Python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J.\nMach. Learn. 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