CoChat
Sign Up
Cited by 7Enzyme Catalysis and ImmobilizationEnzyme Production and Characterizationbiodegradable polymer synthesis and properties

The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.

Identification and characterization of substrate- and product-selective nylon hydrolases

Open access
Drufva, Erin E., Cahill, John F., Saint-Vincent, Patricia M.B., Williams, Alexis N., Bocharova, Vera, Capra, Nikolas, Meilleur, Flora, Carper, Dana L., Bourgery, Célestin, Miyazaki, Kaito, Yonemura, Maina, Shiraishi, Yuki, Parks, Jerry M., Zhou, Muchu, Dishner, Isaiah T., Foster, Jeffrey C., Koehler, Stephen J., Valentino, Hannah R., Sedova, Ada, Kertesz, Vilmos, Vasileva, Delyana P., Hochanadel, Leah H., Figg, C. Adrian, Negoro, Seiji, Kato, Dai-ichiro, Chen, Serena H., Michener, Joshua K.·2025·Chem Catalysis
DOI 10.1016/j.checat.2025.101418PMC PMC11601465

Published version of a preprint

Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.checat.2025.101418

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 67

  1. Nicholson, 2023, Manufacturing Energy and Greenhouse Gas Emissions Associated with United States Consumption of Organic Petrochemicals, ACS Sustainable Chem. Eng., 11, 2198, 10.1021/acssuschemeng.2c05417 · DOI
  2. Rahimi, 2017, Chemical recycling of waste plastics for new materials production, Nat. Rev. Chem, 1, 1, 10.1038/s41570-017-0046 · DOI
  3. Ragaert, 2017, Mechanical and chemical recycling of solid plastic waste, Waste Manag., 69, 24, 10.1016/j.wasman.2017.07.044 · DOI · Paper page
  4. Coates, 2020, Chemical recycling to monomer for an ideal, circular polymer economy, Nat. Rev. Mater., 5, 501, 10.1038/s41578-020-0190-4 · DOI · Paper page
  5. Alberti, 2019, Chemical recycling of end-of-life polyamide 6 via ring closing depolymerization, ChemistrySelect, 4, 12638, 10.1002/slct.201903970 · DOI
  6. Češarek, 2020, Chemical recycling of aliphatic polyamides by microwave-assisted hydrolysis for efficient monomer recovery, ACS Sustain. Chem. Eng., 8, 16274, 10.1021/acssuschemeng.0c05706 · DOI
  7. Arnal, 2023, Assessment of four engineered PET degrading enzymes considering large-scale industrial applications, ACS Catal., 13, 13156, 10.1021/acscatal.3c02922 · DOI
  8. Tournier, 2020, An engineered PET depolymerase to break down and recycle plastic bottles, Nature, 580, 216, 10.1038/s41586-020-2149-4 · DOI · Paper page
  9. Erickson, 2022, Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity, Nat. Commun., 13, 1, 10.1038/s41467-022-35237-x · DOI
  10. Bell, 2022, Directed evolution of an efficient and thermostable PET depolymerase, Nat. Catal., 5, 673, 10.1038/s41929-022-00821-3 · DOI
  11. Cui, 2021, Computational redesign of a PETase for plastic biodegradation under ambient condition by the GRAPE strategy, ACS Catal., 11, 1340, 10.1021/acscatal.0c05126 · DOI
  12. Tournier, 2023, Enzymes’ power for plastics degradation, Chem. Rev., 123, 5612, 10.1021/acs.chemrev.2c00644 · DOI
  13. Uekert, 2023, Technical, economic, and environmental comparison of closed-loop recycling technologies for common plastics, ACS Sustain. Chem. Eng., 11, 965, 10.1021/acssuschemeng.2c05497 · DOI
  14. Negoro, 2005, X-ray crystallographic analysis of 6-aminohexanoate-dimer hydrolase: molecular basis for the birth of a nylon oligomer-degrading enzyme, J. Biol. Chem., 280, 39644, 10.1074/jbc.M505946200 · DOI
  15. Negoro, 1992, A new nylon oligomer degradation gene (nylC) on plasmid pOAD2 from a Flavobacterium sp, J. Bacteriol., 174, 7948, 10.1128/jb.174.24.7948-7953.1992 · DOI
  16. Negoro, 2012, Three-dimensional structure of nylon hydrolase and mechanism of nylon-6 hydrolysis, J. Biol. Chem., 287, 5079, 10.1074/jbc.M111.321992 · DOI
  17. Ohki, 2006, Mutational analysis of 6-aminohexanoate-dimer hydrolase: relationship between nylon oligomer hydrolytic and esterolytic activities, FEBS Lett., 580, 5054, 10.1016/j.febslet.2006.08.031 · DOI
  18. Kato, 1991, Amino acid alterations essential for increasing the catalytic activity of the nylon-oligomer-degradation enzyme of Flavobacterium sp, Eur. J. Biochem., 200, 165, 10.1111/j.1432-1033.1991.tb21063.x · DOI
  19. Bell, 2024, Natural diversity screening, assay development, and characterization of nylon-6 enzymatic depolymerization, Nat. Commun., 15, 1217, 10.1038/s41467-024-45523-5 · DOI
  20. de Witt, 2024, Increasing the diversity of nylonases for poly(ester amide) degradation, Green Chem., 26, 9911, 10.1039/D4GC01662A · DOI
  21. Bayer, 2024, Structural elucidation of a metagenomic urethanase and its engineering towards enhanced hydrolysis profiles, Angew. Chem. Int. Ed. Engl., 63, 10.1002/anie.202404492 · DOI
  22. Puetz, 2023, Validated high-throughput screening system for directed evolution of nylon-depolymerizing enzymes, ACS Sustain. Chem. Eng., 11, 15513, 10.1021/acssuschemeng.3c01575 · DOI
  23. Mori, 1970, Gel permeation chromatography of the cyclic monomers and oliglmers in nylon 6 and nylon 66, J. Chromatogr. A, 49, 230, 10.1016/S0021-9673(00)93627-6 · DOI
  24. Bocharova, 2025, Factors modulating the hydrolysis of nylon-6,6 by a nylon hydrolase enzyme, Polym. Chem., 16, 1858, 10.1039/D5PY00023H · DOI
  25. Cahill, 2023, High-Throughput Characterization and Optimization of Polyamide Hydrolase Activity Using Open Port Sampling Interface Mass Spectrometry, J. Am. Soc. Mass Spectrom., 34, 1383, 10.1021/jasms.3c00097 · DOI
  26. Kinoshita, 1981, Purification and characterization of 6-aminohexanoic-acid-oligomer hydrolase of Flavobacterium sp. Ki72, Eur. J. Biochem., 116, 547, 10.1111/j.1432-1033.1981.tb05371.x · DOI
  27. Takehara, 2018, Metabolic pathway of 6-aminohexanoate in the nylon oligomer-degrading bacterium Arthrobacter sp. KI72: identification of the enzymes responsible for the conversion of 6-aminohexanoate to adipate, Appl. Microbiol. Biotechnol., 102, 801, 10.1007/s00253-017-8657-y · DOI
  28. de Witt, 2025, Upcycling of polyamides through chemical hydrolysis and engineered Pseudomonas putida, Nat. Microbiol., 10, 667, 10.1038/s41564-025-01929-5 · DOI
  29. Okada, 1983, Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers, Nature, 306, 203, 10.1038/306203a0 · DOI
  30. Shiraishi, 2025, Quantitative nylon monomerization by the combination of chemical pretreatment and enzymatic hydrolysis using nylon hydrolases, PLoS One, 20, 10.1371/journal.pone.0318641 · DOI
  31. Jurcik, 2018, CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories, Bioinformatics, 34, 3586, 10.1093/bioinformatics/bty386 · DOI
  32. Negoro, 2018, Structural basis of the correct subunit assembly, aggregation, and intracellular degradation of nylon hydrolase, Sci. Rep., 8, 9725, 10.1038/s41598-018-27860-w · DOI
  33. Krissinel, 2007, Inference of macromolecular assemblies from crystalline state, J. Mol. Biol., 372, 774, 10.1016/j.jmb.2007.05.022 · DOI
  34. Steinegger, 2017, MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets, Nat. Biotechnol., 35, 1026, 10.1038/nbt.3988 · DOI · Paper page
  35. Mirdita, 2022, ColabFold: making protein folding accessible to all, Nat. Methods, 19, 679, 10.1038/s41592-022-01488-1 · DOI · Paper page
  36. Remmert, 2011, HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment, Nat. Methods, 9, 173, 10.1038/nmeth.1818 · DOI · Paper page
  37. UniProt Consortium, 2018, UniProt: the universal protein knowledgebase, Nucleic Acids Res., 46, 2699, 10.1093/nar/gky092 · DOI
  38. Camacho, 2009, BLAST+: architecture and applications, BMC Bioinf., 10, 421, 10.1186/1471-2105-10-421 · DOI · Paper page
  39. Kakudo, 1993, Nylon oligomer degradation gene, nylC, on plasmid pOAD2 from a Flavobacterium strain encodes endo-type 6-aminohexanoate oligomer hydrolase: purification and characterization of the nylC gene product, Appl. Environ. Microbiol., 59, 3978, 10.1128/aem.59.11.3978-3980.1993 · DOI
  40. Van Berkel, 2017, Immediate drop on demand technology (I-DOT) coupled with mass spectrometry via an open port sampling interface, Bioanalysis, 9, 1667, 10.4155/bio-2017-0104 · DOI
  41. Van Berkel, 2015, An open port sampling interface for liquid introduction atmospheric pressure ionization mass spectrometry: Open port sampling interface, Rapid Commun. Mass Spectrom., 29, 1749, 10.1002/rcm.7274 · DOI
  42. Kertesz, 2024, High-throughput mass spectrometry analysis using immediate drop-on-demand technology coupled with an open port sampling interface, Rapid Commun. Mass Spectrom., 38, 10.1002/rcm.9687 · DOI
  43. Schuck, 2000, Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling, Biophys. J., 78, 1606, 10.1016/S0006-3495(00)76713-0 · DOI
  44. Evans, 2022, Protein complex prediction with AlphaFold-Multimer, bioRxiv
  45. Mirdita, 2019, MMseqs2 desktop and local web server app for fast, interactive sequence searches, Bioinformatics, 35, 2856, 10.1093/bioinformatics/bty1057 · DOI · Paper page
  46. Mirdita, 2017, Uniclust databases of clustered and deeply annotated protein sequences and alignments, Nucleic Acids Res., 45, D170, 10.1093/nar/gkw1081 · DOI
  47. Mitchell, 2020, MGnify: the microbiome analysis resource in 2020, Nucleic Acids Res., 48, D570
  48. Steinegger, 2019, HH-suite3 for fast remote homology detection and deep protein annotation, BMC Bioinf., 20, 473, 10.1186/s12859-019-3019-7 · DOI · Paper page
  49. Berman, 2003, Announcing the worldwide Protein Data Bank, Nat. Struct. Biol., 10, 980, 10.1038/nsb1203-980 · DOI · Paper page
  50. Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010 · DOI · Paper page
  51. Chen, 2020, Graphene-extracted membrane lipids facilitate the activation of integrin αvβ8, Nanoscale, 12, 7939, 10.1039/C9NR10469K · DOI
  52. Humphrey, 1996, VMD: visual molecular dynamics, J. Mol. Graph., 14, 33-8, 10.1016/0263-7855(96)00018-5 · DOI · Paper page
  53. Phillips, 2005, Scalable molecular dynamics with NAMD, J. Comput. Chem., 26, 1781, 10.1002/jcc.20289 · DOI · Paper page
  54. Huang, 2017, CHARMM36m: an improved force field for folded and intrinsically disordered proteins, Nat. Methods, 14, 71, 10.1038/nmeth.4067 · DOI
  55. Jorgensen, 1983, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys., 79, 926, 10.1063/1.445869 · DOI
  56. Darden, 1993, Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems, J. Chem. Phys., 98, 10089, 10.1063/1.464397 · DOI
  57. Jarzynski, 1997, Nonequilibrium Equality for Free Energy Differences, Phys. Rev. Lett., 78, 2690, 10.1103/PhysRevLett.78.2690 · DOI
  58. Lynch, 2023, 20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening, Acta Crystallogr. D Struct. Biol., 79, 198, 10.1107/S2059798323001274 · DOI
  59. Budziszewski, 2023, High-Throughput Screening to Obtain Crystal Hits for Protein Crystallography, J. Vis. Exp., 10.3791/65211 · DOI
  60. Evans, 2013, How good are my data and what is the resolution?, Acta Crystallogr. D Biol. Crystallogr., 69, 1204, 10.1107/S0907444913000061 · DOI
  61. Agirre, 2023, The CCP4 suite: integrative software for macromolecular crystallography, Acta Crystallogr. D Struct. Biol., 79, 449, 10.1107/S2059798323003595 · DOI
  62. Winn, 2011, Overview of the CCP4 suite and current developments, Acta Crystallogr. D Biol. Crystallogr., 67, 235, 10.1107/S0907444910045749 · DOI · Paper page
  63. Liebschner, 2019, Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix, Acta Crystallogr. D Struct. Biol., 75, 861, 10.1107/S2059798319011471 · DOI · Paper page
  64. Emsley, 2010, Features and development of Coot, Acta Crystallogr. D Biol. Crystallogr., 66, 486, 10.1107/S0907444910007493 · DOI · Paper page
  65. Murshudov, 2011, REFMAC5 for the refinement of macromolecular crystal structures, Acta Crystallogr. D Biol. Crystallogr., 67, 355, 10.1107/S0907444911001314 · DOI
  66. Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr. D Biol. Crystallogr., 60, 2126, 10.1107/S0907444904019158 · DOI · Paper page
  67. Smith, 2019, PyVOL: a PyMOL plugin for visualization, comparison, and volume calculation of drug-binding sites, bioRxiv

Metadata

Authors
Drufva, E. E., Cahill, J. F., Saint-Vincent, P. M. B., Williams, A. N., Bocharova, V., Capra, N., Meilleur, F., Carper, D. L., Bourgery, C., Miyazaki, K., Yonemura, M., Shiraishi, Y., Parks, J. M., Zhou, M., Dishner, I. T., Foster, J. C., Koehler, S. J., Valentino, H. R., Sedova, A., Kertesz, V., Vasileva, D. P., Hochanadel, L. H., Figg, C. A., Negoro, S., Kato, D.-I., Chen, S. H., & Michener, J. K.
Affiliations
  • Oak Ridge National Laboratory (US)
  • Kagoshima University (JP)
  • Virginia Tech (US)
  • University of Hyogo (JP)
Corresponding author
  • Chen, Serena H.
  • Michener, Joshua K.
ORCID
Venue
Chem Catalysis
Publisher
Elsevier BV
Published
2025-08
Volume
5
Issue
8
Pages
101418
ISSN
2667-1093 (ISSN-L)
DOI
10.1016/j.checat.2025.101418
PMC
PMC11601465
OpenAlex
W4411277758
Cited by
7
References
4
Citations by year
2026: 4 · 2025: 3
FWCI
2.10
Type
journal article
Language
en
Open access
Licence
Locations
  • Chem Catalysis (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by-nd)
Funders
  • U.S. Department of Energy
  • Battelle (DE-AC05-00OR22725)
  • Oak Ridge National Laboratory
  • National Institutes of Health (R24GM141256)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Enzyme Catalysis and Immobilization
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Enzyme Production and Characterization
  • Physical Sciences › Materials Science › Biomaterials › biodegradable polymer synthesis and properties
Keywords
polyamide 66, polyamide 6, substrate specificity, enzyme evolution, enzyme crystal structure, oligomeric state, enzyme engineering

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review