Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design?
Water content is an important factor in lipase-catalyzed reactions in organic media but is frequently ignored in the study of lipases by molecular dynamics (MD) simulation. In this study, Candida antarctica lipase B, Candida rugosa lipase and Rhizopus chinensis lipase were used as research models to...
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ftdoajarticles:oai:doaj.org/article:e0b1a39851884d66a67a43b8e18379f5 2023-05-15T13:59:31+02:00 Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design? Shang Wang Yan Xu Xiao-Wei Yu 2021-06-01T00:00:00Z https://doi.org/10.3390/biom11060848 https://doaj.org/article/e0b1a39851884d66a67a43b8e18379f5 EN eng MDPI AG https://www.mdpi.com/2218-273X/11/6/848 https://doaj.org/toc/2218-273X doi:10.3390/biom11060848 2218-273X https://doaj.org/article/e0b1a39851884d66a67a43b8e18379f5 Biomolecules, Vol 11, Iss 848, p 848 (2021) lipase molecular dynamic simulation non-aqueous phase catalysis Microbiology QR1-502 article 2021 ftdoajarticles https://doi.org/10.3390/biom11060848 2022-12-31T13:23:18Z Water content is an important factor in lipase-catalyzed reactions in organic media but is frequently ignored in the study of lipases by molecular dynamics (MD) simulation. In this study, Candida antarctica lipase B, Candida rugosa lipase and Rhizopus chinensis lipase were used as research models to explore the mechanisms of lipase in micro-aqueous organic solvent (MAOS) media. MD simulations indicated that lipases in MAOS systems showed unique conformations distinguished from those seen in non-aqueous organic solvent systems. The position of water molecules aggregated on the protein surface in MAOS media is the major determinant of the unique conformations of lipases and particularly impacts the distribution of hydrophilic and hydrophobic amino acids on the lipase surface. Additionally, two maxima were observed in the water-lipase radial distribution function in MAOS systems, implying the formation of two water shells around lipase in these systems. The energy landscapes of lipases along solvent accessible areas of catalytic residues and the minimum energy path indicated the dynamic open states of lipases in MAOS systems differ from those in other solvent environments. This study confirmed the necessity of considering the influence of the microenvironment on MD simulations of lipase-catalyzed reactions in organic media. Article in Journal/Newspaper Antarc* Antarctica Directory of Open Access Journals: DOAJ Articles Rugosa ENVELOPE(-61.250,-61.250,-62.633,-62.633) Biomolecules 11 6 848 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
lipase molecular dynamic simulation non-aqueous phase catalysis Microbiology QR1-502 |
spellingShingle |
lipase molecular dynamic simulation non-aqueous phase catalysis Microbiology QR1-502 Shang Wang Yan Xu Xiao-Wei Yu Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design? |
topic_facet |
lipase molecular dynamic simulation non-aqueous phase catalysis Microbiology QR1-502 |
description |
Water content is an important factor in lipase-catalyzed reactions in organic media but is frequently ignored in the study of lipases by molecular dynamics (MD) simulation. In this study, Candida antarctica lipase B, Candida rugosa lipase and Rhizopus chinensis lipase were used as research models to explore the mechanisms of lipase in micro-aqueous organic solvent (MAOS) media. MD simulations indicated that lipases in MAOS systems showed unique conformations distinguished from those seen in non-aqueous organic solvent systems. The position of water molecules aggregated on the protein surface in MAOS media is the major determinant of the unique conformations of lipases and particularly impacts the distribution of hydrophilic and hydrophobic amino acids on the lipase surface. Additionally, two maxima were observed in the water-lipase radial distribution function in MAOS systems, implying the formation of two water shells around lipase in these systems. The energy landscapes of lipases along solvent accessible areas of catalytic residues and the minimum energy path indicated the dynamic open states of lipases in MAOS systems differ from those in other solvent environments. This study confirmed the necessity of considering the influence of the microenvironment on MD simulations of lipase-catalyzed reactions in organic media. |
format |
Article in Journal/Newspaper |
author |
Shang Wang Yan Xu Xiao-Wei Yu |
author_facet |
Shang Wang Yan Xu Xiao-Wei Yu |
author_sort |
Shang Wang |
title |
Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design? |
title_short |
Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design? |
title_full |
Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design? |
title_fullStr |
Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design? |
title_full_unstemmed |
Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design? |
title_sort |
micro-aqueous organic system: a neglected model in computational lipase design? |
publisher |
MDPI AG |
publishDate |
2021 |
url |
https://doi.org/10.3390/biom11060848 https://doaj.org/article/e0b1a39851884d66a67a43b8e18379f5 |
long_lat |
ENVELOPE(-61.250,-61.250,-62.633,-62.633) |
geographic |
Rugosa |
geographic_facet |
Rugosa |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_source |
Biomolecules, Vol 11, Iss 848, p 848 (2021) |
op_relation |
https://www.mdpi.com/2218-273X/11/6/848 https://doaj.org/toc/2218-273X doi:10.3390/biom11060848 2218-273X https://doaj.org/article/e0b1a39851884d66a67a43b8e18379f5 |
op_doi |
https://doi.org/10.3390/biom11060848 |
container_title |
Biomolecules |
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11 |
container_issue |
6 |
container_start_page |
848 |
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1766268093885054976 |