QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate

Boneta S. (Universidad de Zaragoza) ; Arafet K. ; Moliner V.

Resumen: The environmental problems derived from the generalized plastic consumption and disposal could find a friendly solution in enzymatic biodegradation. Recently, two hydrolases from Ideonella sakaiensis 201-F6 and the metagenome-derived leaf-branch compost cutinase (LCC), more specially the improved ICCG variant, have revealed degradation activity toward poly ethylene terephthalate (PET). In the present study, the reaction mechanism of this polymer breakage is studied at an atomic level by multiscale QM/MM molecular dynamics simulations, using semiempirical and DFT Hamiltonians to describe the QM region. The obtained free energy surfaces confirmed a characteristic four-step path for both systems, with activation energies in agreement with the experimental observations. Structural analysis of the evolution of the active site along the reaction progress and the study of electrostatic effects generated by the proteins reveal the similarity in the behavior of the active site of these two enzymes. The origin of the apparent better performance of the LCC-ICCG protein over PETase must be due to its capabilities of working at higher temperature and its intrinsic relationship with the crystallinity grade of the polymer. Our results may be useful for the development of more efficient enzymes in the biodegradation of PET.

Idioma: Inglés

DOI: 10.1021/acs.jcim.1c00394

Año: 2021

Publicado en: Journal of Chemical Information and Modeling 61, 6 (2021), 3041-3051
ISSN: 1549-9596

Factor impacto JCR: 6.162 (2021)

Categ. JCR: CHEMISTRY, MEDICINAL rank: 9 / 63 = 0.143 (2021) - Q1 - T1
Categ. JCR: COMPUTER SCIENCE, INFORMATION SYSTEMS rank: 29 / 163 = 0.178 (2021) - Q1 - T1
Categ. JCR: COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS rank: 26 / 112 = 0.232 (2021) - Q1 - T1
Categ. JCR: CHEMISTRY, MULTIDISCIPLINARY rank: 51 / 179 = 0.285 (2021) - Q2 - T1

Factor impacto CITESCORE: 7.7 - Social Sciences (Q1) - Chemical Engineering (Q1) - Computer Science (Q1)

Factor impacto SCIMAGO: 1.223 - Chemical Engineering (miscellaneous) (Q1) - Library and Information Sciences (Q1) - Chemistry (miscellaneous) (Q1)

Financiación: info:eu-repo/grantAgreement/ES/MICIU/PGC2018-094852-B-C21

Tipo y forma: Artículo (Versión definitiva)

Área (Departamento): Área Bioquímica y Biolog.Mole. (Dpto. Bioq.Biolog.Mol. Celular)