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Evaluation of lipase access tunnels and analysis of substance transport in comparison with experimental data.

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Title: Evaluation of lipase access tunnels and analysis of substance transport in comparison with experimental data.
Authors: de Melo, Jéssica Jéssi C.1 (AUTHOR), Gonçalves, Jesica Ribeiro1 (AUTHOR), Brandão, Luma M. de S1 (AUTHOR), Souza, Ranyere L.1,2 (AUTHOR), Pereira, Matheus M.3 (AUTHOR), Lima, Álvaro S.1,2 (AUTHOR), Soares, Cleide M. F.1,2 (AUTHOR) cleide18@yahoo.com.br
Source: Bioprocess & Biosystems Engineering. Jul2022, Vol. 45 Issue 7, p1149-1162. 14p.
Subjects: Tunnels, Lipases, Palmitic acid, Burkholderia cepacia, Fatty acids, Bioconversion
Abstract: Lipases (E.C. 3.1.1.3) have buried active sites and used access tunnels in the transport of substrates and products for biotransformation processes. Computational methods are used to predict the trajectory and energy profile of ligands through these tunnels, and they complement the experimental methodologies because they filter data, optimizing laboratory time and experimental costs. Access tunnels of Burkholderia cepacia lipase (BCL), Candida rugosa lipase (CRL), and porcine pancreas lipase (PPL) and the transport of fatty acids, alcohols and esters through the tunnels were evaluated using the online server CaverWeb V1.0, and server calculation results were compared with experimental data (productivity). BCL showed higher productivity with palmitic acid-C16:0 (4029.95 µmol/h mg); CRL obtained productivity for oleic acid-C18:1 (380.80 µmol/h mg), and PPL achieved productivity for lauric acid-C12:0 (71.27 µmol/h mg). The highest probability of transport for BCL is through the tunnels 1 and 2, for CRL through the tunnel 1, and for PPL through the tunnels 1, 2, 3 and 4. Thus, the best in silico result was the transport of the substrates palmitic acid and ethanol and product ethyl palmitate in tunnel 1 of BCL. This result corroborates with the best result for the productivity data (higher productivity for BCL with palmitic acid-4029.95 µmol/h mg). The combination of in silico evaluation and experimental data gave similar results, demonstrating that in silico approaches are a promising alternative for reducing screening tests and minimizing laboratory time in the bio-catalysis area by identifying the lipases with the greatest reaction potential, as in the case of this proposal. [ABSTRACT FROM AUTHOR]
Copyright of Bioprocess & Biosystems Engineering is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Evaluation of lipase access tunnels and analysis of substance transport in comparison with experimental data.
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  Data: <searchLink fieldCode="JN" term="%22Bioprocess+%26+Biosystems+Engineering%22">Bioprocess & Biosystems Engineering</searchLink>. Jul2022, Vol. 45 Issue 7, p1149-1162. 14p.
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  Data: <searchLink fieldCode="DE" term="%22Tunnels%22">Tunnels</searchLink><br /><searchLink fieldCode="DE" term="%22Lipases%22">Lipases</searchLink><br /><searchLink fieldCode="DE" term="%22Palmitic+acid%22">Palmitic acid</searchLink><br /><searchLink fieldCode="DE" term="%22Burkholderia+cepacia%22">Burkholderia cepacia</searchLink><br /><searchLink fieldCode="DE" term="%22Fatty+acids%22">Fatty acids</searchLink><br /><searchLink fieldCode="DE" term="%22Bioconversion%22">Bioconversion</searchLink>
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  Data: Lipases (E.C. 3.1.1.3) have buried active sites and used access tunnels in the transport of substrates and products for biotransformation processes. Computational methods are used to predict the trajectory and energy profile of ligands through these tunnels, and they complement the experimental methodologies because they filter data, optimizing laboratory time and experimental costs. Access tunnels of Burkholderia cepacia lipase (BCL), Candida rugosa lipase (CRL), and porcine pancreas lipase (PPL) and the transport of fatty acids, alcohols and esters through the tunnels were evaluated using the online server CaverWeb V1.0, and server calculation results were compared with experimental data (productivity). BCL showed higher productivity with palmitic acid-C16:0 (4029.95 µmol/h mg); CRL obtained productivity for oleic acid-C18:1 (380.80 µmol/h mg), and PPL achieved productivity for lauric acid-C12:0 (71.27 µmol/h mg). The highest probability of transport for BCL is through the tunnels 1 and 2, for CRL through the tunnel 1, and for PPL through the tunnels 1, 2, 3 and 4. Thus, the best in silico result was the transport of the substrates palmitic acid and ethanol and product ethyl palmitate in tunnel 1 of BCL. This result corroborates with the best result for the productivity data (higher productivity for BCL with palmitic acid-4029.95 µmol/h mg). The combination of in silico evaluation and experimental data gave similar results, demonstrating that in silico approaches are a promising alternative for reducing screening tests and minimizing laboratory time in the bio-catalysis area by identifying the lipases with the greatest reaction potential, as in the case of this proposal. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Bioprocess & Biosystems Engineering is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1007/s00449-022-02731-x
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        Text: English
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      – SubjectFull: Tunnels
        Type: general
      – SubjectFull: Lipases
        Type: general
      – SubjectFull: Palmitic acid
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      – SubjectFull: Burkholderia cepacia
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      – SubjectFull: Fatty acids
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              Text: Jul2022
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