Assessment of Kaistella jeonii esterase conformational dynamics in response to poly(ethylene terephthalate) binding
The pervasive presence of plastic in the environment has reached a concerning scale, being identified in many ecosystems. Bioremediation is the cheapest and most eco-friendly alternative to remove this polymer from affected areas. Recent work described that a novel cold-active esterase enzyme extrac...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2024-01-01
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| Series: | Current Research in Structural Biology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2665928X24000072 |
| _version_ | 1797300389028036608 |
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| author | Ederson Sales Moreira Pinto Arthur Tonietto Mangini Lorenzo Chaves Costa Novo Fernando Guimaraes Cavatao Mathias J. Krause Marcio Dorn |
| author_facet | Ederson Sales Moreira Pinto Arthur Tonietto Mangini Lorenzo Chaves Costa Novo Fernando Guimaraes Cavatao Mathias J. Krause Marcio Dorn |
| author_sort | Ederson Sales Moreira Pinto |
| collection | DOAJ |
| description | The pervasive presence of plastic in the environment has reached a concerning scale, being identified in many ecosystems. Bioremediation is the cheapest and most eco-friendly alternative to remove this polymer from affected areas. Recent work described that a novel cold-active esterase enzyme extracted from the bacteria Kaistella jeonii could promiscuously degrade PET. Compared to the well-known PETase from Ideonella sakaiensis, this novel esterase presents a low sequence identity yet has a remarkably similar folding. However, enzymatic assays demonstrated a lower catalytic efficiency. In this work, we employed a strict computational approach to investigate the binding mechanism between the esterase and PET. Understanding the underlying mechanism of binding can shed light on the evolutive mechanism of how enzymes have been evolving to degrade these artificial molecules and help develop rational engineering approaches to improve PETase-like enzymes. Our results indicate that this esterase misses a disulfide bridge, keeping the catalytic residues closer and possibly influencing its catalytic efficiency. Moreover, we describe the structural response to the interaction between enzyme and PET, indicating local and global effects. Our results aid in deepening the knowledge behind the mechanism of biological catalysis of PET degradation and as a base for the engineering of novel PETases. |
| first_indexed | 2024-03-07T23:05:29Z |
| format | Article |
| id | doaj.art-cb232ec9980642bca9f7cc468eb360c6 |
| institution | Directory Open Access Journal |
| issn | 2665-928X |
| language | English |
| last_indexed | 2024-03-07T23:05:29Z |
| publishDate | 2024-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Current Research in Structural Biology |
| spelling | doaj.art-cb232ec9980642bca9f7cc468eb360c62024-02-22T04:53:26ZengElsevierCurrent Research in Structural Biology2665-928X2024-01-017100130Assessment of Kaistella jeonii esterase conformational dynamics in response to poly(ethylene terephthalate) bindingEderson Sales Moreira Pinto0Arthur Tonietto Mangini1Lorenzo Chaves Costa Novo2Fernando Guimaraes Cavatao3Mathias J. Krause4Marcio Dorn5Center for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, BrazilCenter for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, BrazilCenter for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, BrazilCenter for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, BrazilInstitute for Applied and Numerical Mathematics, Karlsruhe Institute of Technology, Englerstraße 2, D-76131, Karlsruhe, BW, GermanyCenter for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Building 43424, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil; Corresponding author at: Center for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, Brazil.The pervasive presence of plastic in the environment has reached a concerning scale, being identified in many ecosystems. Bioremediation is the cheapest and most eco-friendly alternative to remove this polymer from affected areas. Recent work described that a novel cold-active esterase enzyme extracted from the bacteria Kaistella jeonii could promiscuously degrade PET. Compared to the well-known PETase from Ideonella sakaiensis, this novel esterase presents a low sequence identity yet has a remarkably similar folding. However, enzymatic assays demonstrated a lower catalytic efficiency. In this work, we employed a strict computational approach to investigate the binding mechanism between the esterase and PET. Understanding the underlying mechanism of binding can shed light on the evolutive mechanism of how enzymes have been evolving to degrade these artificial molecules and help develop rational engineering approaches to improve PETase-like enzymes. Our results indicate that this esterase misses a disulfide bridge, keeping the catalytic residues closer and possibly influencing its catalytic efficiency. Moreover, we describe the structural response to the interaction between enzyme and PET, indicating local and global effects. Our results aid in deepening the knowledge behind the mechanism of biological catalysis of PET degradation and as a base for the engineering of novel PETases.http://www.sciencedirect.com/science/article/pii/S2665928X24000072Molecular dynamics simulationPETaseBioremediationBiodegradationPET |
| spellingShingle | Ederson Sales Moreira Pinto Arthur Tonietto Mangini Lorenzo Chaves Costa Novo Fernando Guimaraes Cavatao Mathias J. Krause Marcio Dorn Assessment of Kaistella jeonii esterase conformational dynamics in response to poly(ethylene terephthalate) binding Current Research in Structural Biology Molecular dynamics simulation PETase Bioremediation Biodegradation PET |
| title | Assessment of Kaistella jeonii esterase conformational dynamics in response to poly(ethylene terephthalate) binding |
| title_full | Assessment of Kaistella jeonii esterase conformational dynamics in response to poly(ethylene terephthalate) binding |
| title_fullStr | Assessment of Kaistella jeonii esterase conformational dynamics in response to poly(ethylene terephthalate) binding |
| title_full_unstemmed | Assessment of Kaistella jeonii esterase conformational dynamics in response to poly(ethylene terephthalate) binding |
| title_short | Assessment of Kaistella jeonii esterase conformational dynamics in response to poly(ethylene terephthalate) binding |
| title_sort | assessment of kaistella jeonii esterase conformational dynamics in response to poly ethylene terephthalate binding |
| topic | Molecular dynamics simulation PETase Bioremediation Biodegradation PET |
| url | http://www.sciencedirect.com/science/article/pii/S2665928X24000072 |
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