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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ftmdpi:oai:mdpi.com:/2218-273X/11/6/848/ 2023-08-20T03:59:59+02:00 Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design? Shang Wang Yan Xu Xiao-Wei Yu agris 2021-06-07 application/pdf https://doi.org/10.3390/biom11060848 EN eng Multidisciplinary Digital Publishing Institute Molecular Structure and Dynamics https://dx.doi.org/10.3390/biom11060848 https://creativecommons.org/licenses/by/4.0/ Biomolecules; Volume 11; Issue 6; Pages: 848 lipase molecular dynamic simulation non-aqueous phase catalysis Text 2021 ftmdpi https://doi.org/10.3390/biom11060848 2023-08-01T01:53:53Z 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. Text Antarc* Antarctica MDPI Open Access Publishing Rugosa ENVELOPE(-61.250,-61.250,-62.633,-62.633) Biomolecules 11 6 848 |
institution |
Open Polar |
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MDPI Open Access Publishing |
op_collection_id |
ftmdpi |
language |
English |
topic |
lipase molecular dynamic simulation non-aqueous phase catalysis |
spellingShingle |
lipase molecular dynamic simulation non-aqueous phase catalysis 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 |
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 |
Text |
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 |
Multidisciplinary Digital Publishing Institute |
publishDate |
2021 |
url |
https://doi.org/10.3390/biom11060848 |
op_coverage |
agris |
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; Volume 11; Issue 6; Pages: 848 |
op_relation |
Molecular Structure and Dynamics https://dx.doi.org/10.3390/biom11060848 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/biom11060848 |
container_title |
Biomolecules |
container_volume |
11 |
container_issue |
6 |
container_start_page |
848 |
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