Improving the thermostability of xylanase a from bacillus subtilis by combining bioinformatics and electrostatic interactions optimization
Autor(a) principal: | |
---|---|
Data de Publicação: | 2021 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1021/acs.jpcb.1c01253 http://hdl.handle.net/11449/207747 |
Resumo: | The rational improvement of the enzyme catalytic activity is one of the most significant challenges in biotechnology. Most conventional strategies used to engineer enzymes involve selecting mutations to increase their thermostability. Determining good criteria for choosing these substitutions continues to be a challenge. In this work, we combine bioinformatics, electrostatic analysis, and molecular dynamics to predict beneficial mutations that may improve the thermostability of XynA from Bacillus subtilis. First, the Tanford-Kirkwood surface accessibility method is used to characterize each ionizable residue contribution to the protein native state stability. Residues identified to be destabilizing were mutated with the corresponding residues determined by the consensus or ancestral sequences at the same locations. Five mutants (K99T/N151D, K99T, S31R, N151D, and K154A) were investigated and compared with 12 control mutants derived from experimental approaches from the literature. Molecular dynamics results show that the mutants exhibited folding temperatures in the order K99T > K99T/N151D > S31R > N151D > WT > K154A. The combined approaches employed provide an effective strategy for low-cost enzyme optimization needed for large-scale biotechnological and medical applications. |
id |
UNSP_5afb268213199150abbe4cdf3eefccdb |
---|---|
oai_identifier_str |
oai:repositorio.unesp.br:11449/207747 |
network_acronym_str |
UNSP |
network_name_str |
Repositório Institucional da UNESP |
repository_id_str |
2946 |
spelling |
Improving the thermostability of xylanase a from bacillus subtilis by combining bioinformatics and electrostatic interactions optimizationThe rational improvement of the enzyme catalytic activity is one of the most significant challenges in biotechnology. Most conventional strategies used to engineer enzymes involve selecting mutations to increase their thermostability. Determining good criteria for choosing these substitutions continues to be a challenge. In this work, we combine bioinformatics, electrostatic analysis, and molecular dynamics to predict beneficial mutations that may improve the thermostability of XynA from Bacillus subtilis. First, the Tanford-Kirkwood surface accessibility method is used to characterize each ionizable residue contribution to the protein native state stability. Residues identified to be destabilizing were mutated with the corresponding residues determined by the consensus or ancestral sequences at the same locations. Five mutants (K99T/N151D, K99T, S31R, N151D, and K154A) were investigated and compared with 12 control mutants derived from experimental approaches from the literature. Molecular dynamics results show that the mutants exhibited folding temperatures in the order K99T > K99T/N151D > S31R > N151D > WT > K154A. The combined approaches employed provide an effective strategy for low-cost enzyme optimization needed for large-scale biotechnological and medical applications.Center for Theoretical Biological Physics Rice UniversityDepartamento de Física Instituto de Biociências Letras e Ciencias Exatas Unesp-Univ. Estadual PaulistaDepartment of Physics and Astronomy Center for Theoretical Biological Physics Rice UniversityDepartment of Physics University of HoustonDepartamento de Física Instituto de Biociências Letras e Ciencias Exatas Unesp-Univ. Estadual PaulistaRice UniversityUniversidade Estadual Paulista (Unesp)University of HoustonNgo, KhoaDa Silva, Fernando Bruno [UNESP]Leite, Vitor B. P.Contessoto, Vinícius G.Onuchic, José N.2021-06-25T11:00:21Z2021-06-25T11:00:21Z2021-05-06info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article4359-4367http://dx.doi.org/10.1021/acs.jpcb.1c01253Journal of Physical Chemistry B, v. 125, n. 17, p. 4359-4367, 2021.1520-52071520-6106http://hdl.handle.net/11449/20774710.1021/acs.jpcb.1c012532-s2.0-85106144264Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Physical Chemistry Binfo:eu-repo/semantics/openAccess2021-10-23T17:45:57Zoai:repositorio.unesp.br:11449/207747Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T21:43:08.432934Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Improving the thermostability of xylanase a from bacillus subtilis by combining bioinformatics and electrostatic interactions optimization |
title |
Improving the thermostability of xylanase a from bacillus subtilis by combining bioinformatics and electrostatic interactions optimization |
spellingShingle |
Improving the thermostability of xylanase a from bacillus subtilis by combining bioinformatics and electrostatic interactions optimization Ngo, Khoa |
title_short |
Improving the thermostability of xylanase a from bacillus subtilis by combining bioinformatics and electrostatic interactions optimization |
title_full |
Improving the thermostability of xylanase a from bacillus subtilis by combining bioinformatics and electrostatic interactions optimization |
title_fullStr |
Improving the thermostability of xylanase a from bacillus subtilis by combining bioinformatics and electrostatic interactions optimization |
title_full_unstemmed |
Improving the thermostability of xylanase a from bacillus subtilis by combining bioinformatics and electrostatic interactions optimization |
title_sort |
Improving the thermostability of xylanase a from bacillus subtilis by combining bioinformatics and electrostatic interactions optimization |
author |
Ngo, Khoa |
author_facet |
Ngo, Khoa Da Silva, Fernando Bruno [UNESP] Leite, Vitor B. P. Contessoto, Vinícius G. Onuchic, José N. |
author_role |
author |
author2 |
Da Silva, Fernando Bruno [UNESP] Leite, Vitor B. P. Contessoto, Vinícius G. Onuchic, José N. |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Rice University Universidade Estadual Paulista (Unesp) University of Houston |
dc.contributor.author.fl_str_mv |
Ngo, Khoa Da Silva, Fernando Bruno [UNESP] Leite, Vitor B. P. Contessoto, Vinícius G. Onuchic, José N. |
description |
The rational improvement of the enzyme catalytic activity is one of the most significant challenges in biotechnology. Most conventional strategies used to engineer enzymes involve selecting mutations to increase their thermostability. Determining good criteria for choosing these substitutions continues to be a challenge. In this work, we combine bioinformatics, electrostatic analysis, and molecular dynamics to predict beneficial mutations that may improve the thermostability of XynA from Bacillus subtilis. First, the Tanford-Kirkwood surface accessibility method is used to characterize each ionizable residue contribution to the protein native state stability. Residues identified to be destabilizing were mutated with the corresponding residues determined by the consensus or ancestral sequences at the same locations. Five mutants (K99T/N151D, K99T, S31R, N151D, and K154A) were investigated and compared with 12 control mutants derived from experimental approaches from the literature. Molecular dynamics results show that the mutants exhibited folding temperatures in the order K99T > K99T/N151D > S31R > N151D > WT > K154A. The combined approaches employed provide an effective strategy for low-cost enzyme optimization needed for large-scale biotechnological and medical applications. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-06-25T11:00:21Z 2021-06-25T11:00:21Z 2021-05-06 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1021/acs.jpcb.1c01253 Journal of Physical Chemistry B, v. 125, n. 17, p. 4359-4367, 2021. 1520-5207 1520-6106 http://hdl.handle.net/11449/207747 10.1021/acs.jpcb.1c01253 2-s2.0-85106144264 |
url |
http://dx.doi.org/10.1021/acs.jpcb.1c01253 http://hdl.handle.net/11449/207747 |
identifier_str_mv |
Journal of Physical Chemistry B, v. 125, n. 17, p. 4359-4367, 2021. 1520-5207 1520-6106 10.1021/acs.jpcb.1c01253 2-s2.0-85106144264 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Journal of Physical Chemistry B |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
4359-4367 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808129350079348736 |