The reaction mechanism of the Ideonella sakaiensis PETase enzyme

Burgin, Tucker; Pollard, Benjamin C.; Knott, Brandon C.; Mayes, Heather B.; Crowley, Michael F.; McGeehan, John E.; Beckham, Gregg T.; Woodcock, H. Lee

doi:10.1038/s42004-024-01154-x

The reaction mechanism of the Ideonella sakaiensis PETase enzyme

Journal Article · Wed Mar 27 00:00:00 EDT 2024 · Communications Chemistry

DOI:https://doi.org/10.1038/s42004-024-01154-x· OSTI ID:2329368

Burgin, Tucker; Pollard, Benjamin C.; ; ; ; McGeehan, John E.; ;

Abstract

Polyethylene terephthalate (PET), the most abundantly produced polyester plastic, can be depolymerized by the Ideonella sakaiensis PETase enzyme. Based on multiple PETase crystal structures, the reaction has been proposed to proceed via a two-step serine hydrolase mechanism mediated by a serine-histidine-aspartate catalytic triad. To elucidate the multi-step PETase catalytic mechanism, we use transition path sampling and likelihood maximization to identify optimal reaction coordinates for the PETase enzyme. We predict that deacylation is likely rate-limiting, and the reaction coordinates for both steps include elements describing nucleophilic attack, ester bond cleavage, and the “moving-histidine” mechanism. We find that the flexibility of Trp185 promotes the reaction, providing an explanation for decreased activity observed in mutations that restrict Trp185 motion. Overall, this study uses unbiased computational approaches to reveal the detailed reaction mechanism necessary for further engineering of an important class of enzymes for plastics bioconversion.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: NONE; SC0014664; AC36-08GO28308

OSTI ID:: 2329368

Alternate ID(s):: OSTI ID: 2335357

Journal Information:: Communications Chemistry, Journal Name: Communications Chemistry Journal Issue: 1 Vol. 7; ISSN 2399-3669

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (109)

Theoretical studies on the possible reaction pathway for the deacylation of the AChE-catalyzed reaction Wang, Qin Mi; Jiang, Hua Liang; Chen, Kai Xian International Journal of Quantum Chemistry, Vol. 74, Issue 3 https://doi.org/10.1002/(SICI)1097-461X(1999)74:3<315::AID-QUA4>3.0.CO;2-Y	journal	January 1999
Biocatalytic Degradation Efficiency of Postconsumer Polyethylene Terephthalate Packaging Determined by Their Polymer Microstructures Wei, Ren; Breite, Daniel; Song, Chen Advanced Science, Vol. 6, Issue 14 https://doi.org/10.1002/advs.201900491	journal	May 2019
Protein Crystallography and Site‐Direct Mutagenesis Analysis of the Poly(ethylene terephthalate) Hydrolase PETase from Ideonella sakaiensis Liu, Bing; He, Lihui; Wang, Liping ChemBioChem, Vol. 19, Issue 14 https://doi.org/10.1002/cbic.201800097	journal	May 2018
Reaction Pathways for the Enzymatic Degradation of Poly(Ethylene Terephthalate): What Characterizes an Efficient PET‐Hydrolase? Schubert, Sune; Schaller, Kay; Bååth, Jenny Arnling ChemBioChem, Vol. 24, Issue 3 https://doi.org/10.1002/cbic.202200516	journal	December 2022
Computational Insights into the Catalytic Mechanism of Is‐PETase: An Enzyme Capable of Degrading Poly(ethylene) Terephthalate Shrimpton‐Phoenix, Eugene; Mitchell, John B. O.; Bühl, Michael Chemistry – A European Journal, Vol. 28, Issue 70 https://doi.org/10.1002/chem.202201728	journal	October 2022
Comparative Performance of PETase as a Function of Reaction Conditions, Substrate Properties, and Product Accumulation Erickson, Erika; Shakespeare, Thomas J.; Bratti, Felicia ChemSusChem, Vol. 15, Issue 1 https://doi.org/10.1002/cssc.202101932	journal	November 2021
Theoretical insights into the mechanism of acetylcholinesterase‐catalyzed acylation of acetylcholine Manojkumar, T. K.; Cui, Chunzhi; Kim, Kwang S. Journal of Computational Chemistry, Vol. 26, Issue 6 https://doi.org/10.1002/jcc.20199	journal	February 2005
The Amber biomolecular simulation programs Case, David A.; Cheatham, Thomas E.; Darden, Tom Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20290	journal	January 2005
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields Vanommeslaeghe, K.; Hatcher, E.; Acharya, C. Journal of Computational Chemistry https://doi.org/10.1002/jcc.21367	journal	January 2009
MATCH: An atom-typing toolset for molecular mechanics force fields Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L. Journal of Computational Chemistry, Vol. 33, Issue 2 https://doi.org/10.1002/jcc.21963	journal	November 2011
Enzymatic Degradation of Poly(ethylene terephthalate): Rapid Hydrolyse using a Hydrolase fromT. fusca Müller, Rolf-Joachim; Schrader, Hedwig; Profe, Jörn Macromolecular Rapid Communications, Vol. 26, Issue 17 https://doi.org/10.1002/marc.200500410	journal	September 2005
Review: Contributions of NMR spectroscopy to the study of hydrogen bonds in serine protease active sites Bachovchin, William W. Magnetic Resonance in Chemistry, Vol. 39, Issue S1 https://doi.org/10.1002/mrc.951	journal	January 2001
CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software Crowley, Michael F.; Williamson, Mark J.; Walker, Ross C. International Journal of Quantum Chemistry, Vol. 109, Issue 15 https://doi.org/10.1002/qua.22372	journal	December 2009
Enzymes for the Biofunctionalization of Poly(Ethylene Terephthalate) Zimmermann, Wolfgang; Billig, Susan Biofunctionalization of Polymers and their Applications https://doi.org/10.1007/10_2010_87	book	November 2010
Structural and functional studies on a thermostable polyethylene terephthalate degrading hydrolase from Thermobifida fusca Roth, Christian; Wei, Ren; Oeser, Thorsten Applied Microbiology and Biotechnology, Vol. 98, Issue 18 https://doi.org/10.1007/s00253-014-5672-0	journal	April 2014
Structural basis for the Ca2+-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190 Miyakawa, Takuya; Mizushima, Hiroki; Ohtsuka, Jun Applied Microbiology and Biotechnology, Vol. 99, Issue 10 https://doi.org/10.1007/s00253-014-6272-8	journal	December 2014
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C. Journal of Computational Physics, Vol. 23, Issue 3 https://doi.org/10.1016/0021-9991(77)90098-5	journal	March 1977
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme Warshel, A.; Levitt, M. Journal of Molecular Biology, Vol. 103, Issue 2 https://doi.org/10.1016/0022-2836(76)90311-9	journal	May 1976
Synthetic Polyester-Hydrolyzing Enzymes From Thermophilic Actinomycetes Wei, Ren; Oeser, Thorsten; Zimmermann, Wolfgang Advances in Applied Microbiology https://doi.org/10.1016/B978-0-12-800259-9.00007-X	book	August 2014
Chapter 1 - Introduction Baron, Peters Reaction Rate Theory and Rare Events Simulations https://doi.org/10.1016/B978-0-44-456349-1.00001-5	book	May 2017
Structure of a microbial homologue of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 å resolution Wei, Yunyi; Swenson, Lora; Castro, Clementina Structure, Vol. 6, Issue 4 https://doi.org/10.1016/S0969-2126(98)00052-5	journal	April 1998
A suspension-based assay and comparative detection methods for characterization of polyethylene terephthalate hydrolases Arnling Bååth, Jenny; Borch, Kim; Westh, Peter Analytical Biochemistry, Vol. 607 https://doi.org/10.1016/j.ab.2020.113873	journal	October 2020
Structural and functional characterization of polyethylene terephthalate hydrolase from Ideonella sakaiensis Liu, Congcong; Shi, Chao; Zhu, Sujie Biochemical and Biophysical Research Communications, Vol. 508, Issue 1 https://doi.org/10.1016/j.bbrc.2018.11.148	journal	January 2019
A semiempirical study of acetylcholine hydrolysis catalyzed by Drosophila melanogaster acetylcholinesterase Sant’Anna, Carlos Mauricio R.; dos Santos Viana, Andrea; do Nascimento Junior, Nailton Monteiro Bioorganic Chemistry, Vol. 34, Issue 2 https://doi.org/10.1016/j.bioorg.2006.01.002	journal	April 2006
Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase Fecker, Tobias; Galaz-Davison, Pablo; Engelberger, Felipe Biophysical Journal, Vol. 114, Issue 6 https://doi.org/10.1016/j.bpj.2018.02.005	journal	March 2018
Inertial likelihood maximization for reaction coordinates with high transmission coefficients Peters, Baron Chemical Physics Letters, Vol. 554 https://doi.org/10.1016/j.cplett.2012.10.051	journal	December 2012
Crystal structure of cutinase Est119 from Thermobifida alba AHK119 that can degrade modified polyethylene terephthalate at 1.76Å resolution Kitadokoro, Kengo; Thumarat, Uschara; Nakamura, Ryota Polymer Degradation and Stability, Vol. 97, Issue 5 https://doi.org/10.1016/j.polymdegradstab.2012.02.003	journal	May 2012
Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca ²⁺ -Driven Catalytic Cycle Numoto, Nobutaka; Kamiya, Narutoshi; Bekker, Gert-Jan Biochemistry, Vol. 57, Issue 36 https://doi.org/10.1021/acs.biochem.8b00624	journal	August 2018
Enzymes’ Power for Plastics Degradation Tournier, Vincent; Duquesne, Sophie; Guillamot, Frédérique Chemical Reviews, Vol. 123, Issue 9 https://doi.org/10.1021/acs.chemrev.2c00644	journal	March 2023
QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate Boneta, Sergio; Arafet, Kemel; Moliner, Vicent Journal of Chemical Information and Modeling, Vol. 61, Issue 6 https://doi.org/10.1021/acs.jcim.1c00394	journal	June 2021
ATESA: An Automated Aimless Shooting Workflow Burgin, Tucker; Ellis, Samuel; Mayes, Heather B. Journal of Chemical Theory and Computation, Vol. 19, Issue 1 https://doi.org/10.1021/acs.jctc.2c00543	journal	December 2022
Easy Transition Path Sampling Methods: Flexible-Length Aimless Shooting and Permutation Shooting Mullen, Ryan Gotchy; Shea, Joan-Emma; Peters, Baron Journal of Chemical Theory and Computation, Vol. 11, Issue 6 https://doi.org/10.1021/acs.jctc.5b00032	journal	May 2015
Catalytic Reaction Mechanism for Drug Metabolism in Human Carboxylesterase-1: Cocaine Hydrolysis Pathway Yao, Jianzhuang; Chen, Xiabin; Zheng, Fang Molecular Pharmaceutics, Vol. 15, Issue 9 https://doi.org/10.1021/acs.molpharmaceut.8b00354	journal	August 2018
Computational Redesign of a PETase for Plastic Biodegradation under Ambient Condition by the GRAPE Strategy Cui, Yinglu; Chen, Yanchun; Liu, Xinyue ACS Catalysis, Vol. 11, Issue 3 https://doi.org/10.1021/acscatal.0c05126	journal	January 2021
Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations Jerves, Carola; Neves, Rui P. P.; Ramos, Maria J. ACS Catalysis, Vol. 11, Issue 18 https://doi.org/10.1021/acscatal.1c03700	journal	September 2021
Substrate-Binding Mode of a Thermophilic PET Hydrolase and Engineering the Enzyme to Enhance the Hydrolytic Efficacy Zeng, Wei; Li, Xiuqin; Yang, Yunyun ACS Catalysis, Vol. 12, Issue 5 https://doi.org/10.1021/acscatal.1c05800	journal	February 2022
Mechanism-Based Design of Efficient PET Hydrolases Wei, Ren; von Haugwitz, Gerlis; Pfaff, Lara ACS Catalysis, Vol. 12, Issue 6 https://doi.org/10.1021/acscatal.1c05856	journal	February 2022
How the Same Core Catalytic Machinery Catalyzes 17 Different Reactions: the Serine-Histidine-Aspartate Catalytic Triad of α/β-Hydrolase Fold Enzymes Rauwerdink, Alissa; Kazlauskas, Romas J. ACS Catalysis, Vol. 5, Issue 10 https://doi.org/10.1021/acscatal.5b01539	journal	September 2015
Biodegradation of PET: Current Status and Application Aspects Taniguchi, Ikuo; Yoshida, Shosuke; Hiraga, Kazumi ACS Catalysis, Vol. 9, Issue 5 https://doi.org/10.1021/acscatal.8b05171	journal	April 2019
Rational Protein Engineering of Thermo-Stable PETase from Ideonella sakaiensis for Highly Efficient PET Degradation Son, Hyeoncheol Francis; Cho, In Jin; Joo, Seongjoon ACS Catalysis, Vol. 9, Issue 4 https://doi.org/10.1021/acscatal.9b00568	journal	March 2019
Decomposition of the PET Film by MHETase Using Exo-PETase Function Sagong, Hye-Young; Seo, Hogyun; Kim, Taeho ACS Catalysis, Vol. 10, Issue 8 https://doi.org/10.1021/acscatal.9b05604	journal	February 2020
Current State and Perspectives Related to the Polyethylene Terephthalate Hydrolases Available for Biorecycling Kawai, Fusako; Kawabata, Takeshi; Oda, Masayuki ACS Sustainable Chemistry & Engineering, Vol. 8, Issue 24 https://doi.org/10.1021/acssuschemeng.0c01638	journal	May 2020
IsPETase- and IsMHETase-Catalyzed Cascade Degradation Mechanism toward Polyethylene Terephthalate Feng, Shanshan; Yue, Yue; Zheng, Mingna ACS Sustainable Chemistry & Engineering, Vol. 9, Issue 29 https://doi.org/10.1021/acssuschemeng.1c02420	journal	July 2021
QM/MM Investigation to Identify the Hallmarks of Superior PET Biodegradation Activity of PETase over Cutinase Aboelnga, Mohamed M.; Kalyaanamoorthy, Subha ACS Sustainable Chemistry & Engineering, Vol. 10, Issue 48 https://doi.org/10.1021/acssuschemeng.2c04913	journal	November 2022
A Computational Study of the Deacylation Mechanism of Human Butyrylcholinesterase Suárez, Dimas; Díaz, Natalia; Fontecilla-Camps, Juan Biochemistry, Vol. 45, Issue 24 https://doi.org/10.1021/bi052176p	journal	May 2006
The Catalytic Mechanism of Carboxylesterases: A Computational Study Aranda, J.; Cerqueira, N. M. F. S. A.; Fernandes, P. A. Biochemistry, Vol. 53, Issue 36 https://doi.org/10.1021/bi500934j	journal	September 2014
CHARMMing: A New, Flexible Web Portal for CHARMM Miller, Benjamin T.; Singh, Rishi P.; Klauda, Jeffery B. Journal of Chemical Information and Modeling, Vol. 48, Issue 9 https://doi.org/10.1021/ci800133b	journal	August 2008
Serine Protease Mechanism and Specificity Hedstrom, Lizbeth Chemical Reviews, Vol. 102, Issue 12 https://doi.org/10.1021/cr000033x	journal	December 2002
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical p K _a Predictions Olsson, Mats H. M.; Søndergaard, Chresten R.; Rostkowski, Michal Journal of Chemical Theory and Computation, Vol. 7, Issue 2 https://doi.org/10.1021/ct100578z	journal	December 2010
DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB) Gaus, Michael; Cui, Qiang; Elstner, Marcus Journal of Chemical Theory and Computation, Vol. 7, Issue 4 https://doi.org/10.1021/ct100684s	journal	March 2011
Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of p K _a Values Søndergaard, Chresten R.; Olsson, Mats H. M.; Rostkowski, Michał Journal of Chemical Theory and Computation, Vol. 7, Issue 7 https://doi.org/10.1021/ct200133y	journal	June 2011
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ ₁ and χ ₂ Dihedral Angles Best, Robert B.; Zhu, Xiao; Shim, Jihyun Journal of Chemical Theory and Computation, Vol. 8, Issue 9 https://doi.org/10.1021/ct300400x	journal	August 2012
Parametrization and Benchmark of DFTB3 for Organic Molecules Gaus, Michael; Goez, Albrecht; Elstner, Marcus Journal of Chemical Theory and Computation, Vol. 9, Issue 1 https://doi.org/10.1021/ct300849w	journal	November 2012
Role of the Catalytic Triad and Oxyanion Hole in Acetylcholinesterase Catalysis: An ab initio QM/MM Study Zhang, Yingkai; Kua, Jeremy; McCammon, J. Andrew Journal of the American Chemical Society, Vol. 124, Issue 35 https://doi.org/10.1021/ja020243m	journal	September 2002
Fundamental Reaction Mechanism for Cocaine Hydrolysis in Human Butyrylcholinesterase Zhan, Chang-Guo; Zheng, Fang; Landry, Donald W. Journal of the American Chemical Society, Vol. 125, Issue 9 https://doi.org/10.1021/ja020850+	journal	February 2003
Ab Initio QM/MM Dynamics Simulation of the Tetrahedral Intermediate of Serine Proteases: Insights into the Active Site Hydrogen-Bonding Network Topf, Maya; Várnai, Peter; Richards, W. Graham Journal of the American Chemical Society, Vol. 124, Issue 49 https://doi.org/10.1021/ja026219q	journal	December 2002
A General Acid−Base Mechanism for the Stabilization of a Tetrahedral Adduct in a Serine−Carboxyl Peptidase: A Computational Study Guo, Haobo; Wlodawer, Alexander; Guo, Hong Journal of the American Chemical Society, Vol. 127, Issue 45 https://doi.org/10.1021/ja0520565	journal	October 2005
Unexpected Deacetylation Mechanism Suggested by a Density Functional Theory QM/MM Study of Histone-Deacetylase-Like Protein Corminboeuf, Clémence; Hu, Po; Tuckerman, Mark E. Journal of the American Chemical Society, Vol. 128, Issue 14 https://doi.org/10.1021/ja0600882	journal	April 2006
The Mechanism of Cellulose Hydrolysis by a Two-Step, Retaining Cellobiohydrolase Elucidated by Structural and Transition Path Sampling Studies Knott, Brandon C.; Haddad Momeni, Majid; Crowley, Michael F. Journal of the American Chemical Society, Vol. 136, Issue 1 https://doi.org/10.1021/ja410291u	journal	December 2013
Structural Reorganization and Preorganization in Enzyme Active Sites: Comparisons of Experimental and Theoretically Ideal Active Site Geometries in the Multistep Serine Esterase Reaction Cycle Smith, Adam J. T.; Müller, Roger; Toscano, Miguel D. Journal of the American Chemical Society, Vol. 130, Issue 46 https://doi.org/10.1021/ja803213p	journal	November 2008
Fundamental Reaction Mechanism and Free Energy Profile for (−)-Cocaine Hydrolysis Catalyzed by Cocaine Esterase Liu, Junjun; Hamza, Adel; Zhan, Chang-Guo Journal of the American Chemical Society, Vol. 131, Issue 33 https://doi.org/10.1021/ja903990p	journal	August 2009
Insights into the Enhancement of the Poly(ethylene terephthalate) Degradation by FAST-PETase from Computational Modeling García-Meseguer, Rafael; Ortí, Enrique; Tuñón, Iñaki Journal of the American Chemical Society, Vol. 145, Issue 35 https://doi.org/10.1021/jacs.3c04427	journal	August 2023
Sabatier Principle for Rationalizing Enzymatic Hydrolysis of a Synthetic Polyester Arnling Bååth, Jenny; Jensen, Kenneth; Borch, Kim JACS Au, Vol. 2, Issue 5 https://doi.org/10.1021/jacsau.2c00204	journal	May 2022
Fidelity in Hapten Design: How Analogous Are Phosphonate Haptens to the Transition States for Alkaline Hydrolyses of Aryl Esters? Tantillo, Dean J.; Houk, K. N. The Journal of Organic Chemistry, Vol. 64, Issue 9 https://doi.org/10.1021/jo982335t	journal	April 1999
Theoretical Study of General Base-Catalyzed Hydrolysis of Aryl Esters and Implications for Enzymatic Reactions Xie, Daiqian; Xu, Dingguo; Zhang, Lidong The Journal of Physical Chemistry B, Vol. 109, Issue 11 https://doi.org/10.1021/jp0506181	journal	March 2005
Catalytic Reaction Mechanism of Acetylcholinesterase Determined by Born−Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations Zhou, Yanzi; Wang, Shenglong; Zhang, Yingkai The Journal of Physical Chemistry B, Vol. 114, Issue 26 https://doi.org/10.1021/jp104258d	journal	July 2010
Molecular-Level Origins of Biomass Recalcitrance: Decrystallization Free Energies for Four Common Cellulose Polymorphs Beckham, Gregg T.; Matthews, James F.; Peters, Baron The Journal of Physical Chemistry B, Vol. 115, Issue 14 https://doi.org/10.1021/jp1106394	journal	April 2011
Toward a More Complete Understanding of Noncovalent Interactions Involving Aromatic Rings Wheeler, Steven E.; Bloom, Jacob W. G. The Journal of Physical Chemistry A, Vol. 118, Issue 32 https://doi.org/10.1021/jp504415p	journal	July 2014
Kinetic Pathways of Ion Pair Dissociation in Water Geissler, Phillip L.; Dellago, Christoph; Chandler, David The Journal of Physical Chemistry B, Vol. 103, Issue 18 https://doi.org/10.1021/jp984837g	journal	May 1999
Decrystallization of Oligosaccharides from the Cellulose Iβ Surface with Molecular Simulation Payne, Christina M.; Himmel, Michael E.; Crowley, Michael F. The Journal of Physical Chemistry Letters, Vol. 2, Issue 13 https://doi.org/10.1021/jz2005122	journal	June 2011
Cutinase-Catalyzed Hydrolysis of Poly(ethylene terephthalate) Ronkvist, Åsa M.; Xie, Wenchun; Lu, Wenhua Macromolecules, Vol. 42, Issue 14 https://doi.org/10.1021/ma9005318	journal	July 2009
Structural insight into catalytic mechanism of PET hydrolase Han, Xu; Liu, Weidong; Huang, Jian-Wen Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-02255-z	journal	December 2017
Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation Joo, Seongjoon; Cho, In Jin; Seo, Hogyun Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-02881-1	journal	January 2018
Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate Palm, Gottfried J.; Reisky, Lukas; Böttcher, Dominique Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09326-3	journal	April 2019
Conformational fitting of a flexible oligomeric substrate does not explain the enzymatic PET degradation Wei, Ren; Song, Chen; Gräsing, Daniel Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13492-9	journal	December 2019
Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity Erickson, Erika; Gado, Japheth E.; Avilán, Luisana Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-35237-x	journal	December 2022
An engineered PET depolymerase to break down and recycle plastic bottles Tournier, V.; Topham, C. M.; Gilles, A. Nature, Vol. 580, Issue 7802 https://doi.org/10.1038/s41586-020-2149-4	journal	April 2020
Machine learning-aided engineering of hydrolases for PET depolymerization Lu, Hongyuan; Diaz, Daniel J.; Czarnecki, Natalie J. Nature, Vol. 604, Issue 7907 https://doi.org/10.1038/s41586-022-04599-z	journal	April 2022
An absorbance method for analysis of enzymatic degradation kinetics of poly(ethylene terephthalate) films Zhong-Johnson, En Ze Linda; Voigt, Christopher A.; Sinskey, Anthony J. Scientific Reports, Vol. 11, Issue 1 https://doi.org/10.1038/s41598-020-79031-5	journal	January 2021
Directed evolution of an efficient and thermostable PET depolymerase Bell, Elizabeth L.; Smithson, Ross; Kilbride, Siobhan Nature Catalysis, Vol. 5, Issue 8 https://doi.org/10.1038/s41929-022-00821-3	journal	August 2022
Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases Mayes, Heather B.; Knott, Brandon C.; Crowley, Michael F. Chemical Science, Vol. 7, Issue 9 https://doi.org/10.1039/C6SC00571C	journal	January 2016
The critical role of Asp206 stabilizing residues on the catalytic mechanism of the Ideonella sakaiensis PETase Magalhães, Rita P.; Fernandes, Henrique S.; Sousa, Sérgio F. Catalysis Science & Technology, Vol. 12, Issue 11 https://doi.org/10.1039/D1CY02271G	journal	January 2022
From transition paths to transition states and rate coefficients Hummer, Gerhard The Journal of Chemical Physics, Vol. 120, Issue 2 https://doi.org/10.1063/1.1630572	journal	January 2004
The Activated Complex in Chemical Reactions Eyring, Henry The Journal of Chemical Physics, Vol. 3, Issue 2 https://doi.org/10.1063/1.1749604	journal	February 1935
Obtaining reaction coordinates by likelihood maximization Peters, Baron; Trout, Bernhardt L. The Journal of Chemical Physics, Vol. 125, Issue 5 https://doi.org/10.1063/1.2234477	journal	August 2006
Using the histogram test to quantify reaction coordinate error Peters, Baron The Journal of Chemical Physics, Vol. 125, Issue 24 https://doi.org/10.1063/1.2409924	journal	December 2006
Extensions to the likelihood maximization approach for finding reaction coordinates Peters, Baron; Beckham, Gregg T.; Trout, Bernhardt L. The Journal of Chemical Physics, Vol. 127, Issue 3 https://doi.org/10.1063/1.2748396	journal	July 2007
Statistically optimal analysis of samples from multiple equilibrium states Shirts, Michael R.; Chodera, John D. The Journal of Chemical Physics, Vol. 129, Issue 12 https://doi.org/10.1063/1.2978177	journal	September 2008
Statistical mechanics of isomerization dynamics in liquids and the transition state approximation Chandler, David The Journal of Chemical Physics, Vol. 68, Issue 6 https://doi.org/10.1063/1.436049	journal	January 1978
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems Darden, Tom; York, Darrin; Pedersen, Lee The Journal of Chemical Physics, Vol. 98, Issue 12 https://doi.org/10.1063/1.464397	journal	June 1993
Characterization and engineering of a plastic-degrading aromatic polyesterase Austin, Harry P.; Allen, Mark D.; Donohoe, Bryon S. Proceedings of the National Academy of Sciences, Vol. 115, Issue 19 https://doi.org/10.1073/pnas.1718804115	journal	April 2018
Characterization and engineering of a two-enzyme system for plastics depolymerization Knott, Brandon C.; Erickson, Erika; Allen, Mark D. Proceedings of the National Academy of Sciences, Vol. 117, Issue 41 https://doi.org/10.1073/pnas.2006753117	journal	September 2020
Unusual 1H NMR chemical shifts support (His) Cepsilon 1---H{middle dot}{middle dot}{middle dot}O==C H-bond: Proposal for reaction-driven ring flip mechanism in serine protease catalysis Ash, E. L.; Sudmeier, J. L.; Day, R. M. Proceedings of the National Academy of Sciences, Vol. 97, Issue 19 https://doi.org/10.1073/pnas.97.19.10371	journal	September 2000
The hydrolysis mechanism of a GH45 cellulase and its potential relation to lytic transglycosylase and expansin function Bharadwaj, Vivek S.; Knott, Brandon C.; Ståhlberg, Jerry Journal of Biological Chemistry, Vol. 295, Issue 14 https://doi.org/10.1074/jbc.RA119.011406	journal	April 2020
Reaction-rate theory: fifty years after Kramers Hänggi, Peter; Talkner, Peter; Borkovec, Michal Reviews of Modern Physics, Vol. 62, Issue 2 https://doi.org/10.1103/RevModPhys.62.251	journal	April 1990
XSEDE: Accelerating Scientific Discovery Towns, John; Cockerill, Timothy; Dahan, Maytal Computing in Science & Engineering, Vol. 16, Issue 5 https://doi.org/10.1109/MCSE.2014.80	journal	September 2014
Breaking the low barrier hydrogen bond in a serine protease Kidd, Richard D.; Sears, Pamela; Huang, Dee‐Hua Protein Science, Vol. 8, Issue 2 https://doi.org/10.1110/ps.8.2.410	journal	January 1999
Biocatalysis as a green route for recycling the recalcitrant plastic polyethylene terephthalate Wei, Ren; Zimmermann, Wolfgang Microbial Biotechnology, Vol. 10, Issue 6 https://doi.org/10.1111/1751-7915.12714	journal	April 2017
Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions Brylinski, Michal Chemical Biology & Drug Design, Vol. 91, Issue 2 https://doi.org/10.1111/cbdd.13084	journal	August 2017
Structural studies reveal the molecular mechanism of PET ase Chen, Chun‐Chi; Han, Xu; Ko, Tzu‐Ping The FEBS Journal, Vol. 285, Issue 20 https://doi.org/10.1111/febs.14612	journal	August 2018
Structural insights into the unique polylactate‐degrading mechanism of Thermobifida alba cutinase Kitadokoro, Kengo; Kakara, Mizuki; Matsui, Shingo The FEBS Journal, Vol. 286, Issue 11 https://doi.org/10.1111/febs.14781	journal	February 2019
A bacterium that degrades and assimilates poly(ethylene terephthalate) Yoshida, Shosuke; Hiraga, Kazumi; Takehana, Toshihiko Science, Vol. 351, Issue 6278 https://doi.org/10.1126/science.aad6359	journal	March 2016
New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes Danso, Dominik; Schmeisser, Christel; Chow, Jennifer Applied and Environmental Microbiology, Vol. 84, Issue 8 https://doi.org/10.1128/AEM.02773-17	journal	February 2018
Isolation of a Novel Cutinase Homolog with Polyethylene Terephthalate-Degrading Activity from Leaf-Branch Compost by Using a Metagenomic Approach Sulaiman, Sintawee; Yamato, Saya; Kanaya, Eiko Applied and Environmental Microbiology, Vol. 78, Issue 5 https://doi.org/10.1128/AEM.06725-11	journal	December 2011
T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark Bolhuis, Peter G.; Chandler, David; Dellago, Christoph Annual Review of Physical Chemistry, Vol. 53, Issue 1 https://doi.org/10.1146/annurev.physchem.53.082301.113146	journal	October 2002
Characterization of a new cutinase from Thermobifida alba for PET-surface hydrolysis Ribitsch, Doris; Acero, Enrique Herrero; Greimel, Katrin Biocatalysis and Biotransformation, Vol. 30, Issue 1 https://doi.org/10.3109/10242422.2012.644435	journal	December 2011
A Novel Polyester Hydrolase From the Marine Bacterium Pseudomonas aestusnigri – Structural and Functional Insights Bollinger, Alexander; Thies, Stephan; Knieps-Grünhagen, Esther Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.00114	journal	February 2020
UV Pretreatment Impairs the Enzymatic Degradation of Polyethylene Terephthalate Falkenstein, Patricia; Gräsing, Daniel; Bielytskyi, Pavlo Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.00689	journal	April 2020

The reaction mechanism of the Ideonella sakaiensis PETase enzyme

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The reaction mechanism of the Ideonella sakaiensis PETase enzyme

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