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Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae
5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Mult...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8168862/ https://www.ncbi.nlm.nih.gov/pubmed/34061877 http://dx.doi.org/10.1371/journal.pone.0251751 |
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author | Ishak, Siti Nor Hasmah Kamarudin, Nor Hafizah Ahmad Ali, Mohd Shukuri Mohamad Leow, Adam Thean Chor Shariff, Fairolniza Mohd Rahman, Raja Noor Zaliha Raja Abd |
author_facet | Ishak, Siti Nor Hasmah Kamarudin, Nor Hafizah Ahmad Ali, Mohd Shukuri Mohamad Leow, Adam Thean Chor Shariff, Fairolniza Mohd Rahman, Raja Noor Zaliha Raja Abd |
author_sort | Ishak, Siti Nor Hasmah |
collection | PubMed |
description | 5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Multiple amino acids substitution might cause structural destabilization due to negative cooperation. Hence, the three-dimensional structure of 5M mutant lipase was elucidated to determine the evolution in structural elements caused by amino acids substitution. A suitable crystal for X-ray diffraction was obtained from an optimized formulation containing 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.4 and 0.2 M sodium chloride with 2.5 mg/mL protein concentration. The three-dimensional structure of 5M mutant lipase was solved at 2.64 Å with two molecules per asymmetric unit. The detailed analysis of the structure revealed that there was a decrease in the number of molecular interactions, including hydrogen bonds and ion interactions, which are important in maintaining the stability of lipase. This study facilitates understanding of and highlights the importance of hydrogen bonds and ion interactions towards protein stability. Substrate specificity and docking analysis on the open structure of 5M mutant lipase revealed changes in substrate preference. The molecular dynamics simulation of 5M-substrates complexes validated the substrate preference of 5M lipase towards long-chain p-nitrophenyl–esters. |
format | Online Article Text |
id | pubmed-8168862 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-81688622021-06-11 Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae Ishak, Siti Nor Hasmah Kamarudin, Nor Hafizah Ahmad Ali, Mohd Shukuri Mohamad Leow, Adam Thean Chor Shariff, Fairolniza Mohd Rahman, Raja Noor Zaliha Raja Abd PLoS One Research Article 5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Multiple amino acids substitution might cause structural destabilization due to negative cooperation. Hence, the three-dimensional structure of 5M mutant lipase was elucidated to determine the evolution in structural elements caused by amino acids substitution. A suitable crystal for X-ray diffraction was obtained from an optimized formulation containing 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.4 and 0.2 M sodium chloride with 2.5 mg/mL protein concentration. The three-dimensional structure of 5M mutant lipase was solved at 2.64 Å with two molecules per asymmetric unit. The detailed analysis of the structure revealed that there was a decrease in the number of molecular interactions, including hydrogen bonds and ion interactions, which are important in maintaining the stability of lipase. This study facilitates understanding of and highlights the importance of hydrogen bonds and ion interactions towards protein stability. Substrate specificity and docking analysis on the open structure of 5M mutant lipase revealed changes in substrate preference. The molecular dynamics simulation of 5M-substrates complexes validated the substrate preference of 5M lipase towards long-chain p-nitrophenyl–esters. Public Library of Science 2021-06-01 /pmc/articles/PMC8168862/ /pubmed/34061877 http://dx.doi.org/10.1371/journal.pone.0251751 Text en © 2021 Ishak et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Ishak, Siti Nor Hasmah Kamarudin, Nor Hafizah Ahmad Ali, Mohd Shukuri Mohamad Leow, Adam Thean Chor Shariff, Fairolniza Mohd Rahman, Raja Noor Zaliha Raja Abd Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae |
title | Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae |
title_full | Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae |
title_fullStr | Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae |
title_full_unstemmed | Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae |
title_short | Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae |
title_sort | structure elucidation and docking analysis of 5m mutant of t1 lipase geobacillus zalihae |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8168862/ https://www.ncbi.nlm.nih.gov/pubmed/34061877 http://dx.doi.org/10.1371/journal.pone.0251751 |
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