Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural information

Bibliographic Details
Main Author: Resende, Tiago Filipe Coelho
Publication Date: 2016
Other Authors: Rocha, Isabel, Soares, Cláudio M.
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/1822/47504
Summary: EJIBCE 2016 - IV Encontro de Jovens Investigadores de Biologia Computacional Estrutural
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network_name_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
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spelling Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural informationEJIBCE 2016 - IV Encontro de Jovens Investigadores de Biologia Computacional EstruturalIn this post-genomic era, gene homology annotations have become the foundation of systems biology. However, errors spread easily when functional annotation is not performed carefully due to overly unconstrained homology metrics [1,2]. As metabolic model reconstructions become a relevant tool for performing fundamental studies and bioprocess design, the impact of accurate enzymatic function assignments becomes evident [3]. The uncertainty of the usage of NADP(H) or NAD(H) as co-factors [4], even in well performed annotations, has a major impact in metabolic engineering applications, severely affecting Genome-scale metabolic model reconstruction due to the potential insertion of misleading reactions. In this work, we unveiled the molecular determinants for cofactor speci- ficity, using enzyme structural information. In order to do so, we created a representative dataset of all enzymes present in the PDB with NAD(P)(H) as cofactors and measured the occurrence of every aminoacid residue at a distance of 3.5 Angstrom[5] of all cofactor atoms. This allowed us to create a matrix with the total number of aminoacid residues at interacting distances from all cofactor atoms, for all structures. After analyzing the matrix, we identified the residues that had a signifi- cantly higher number of contacts with the cofactors, and in which atoms this occurred. With the intent of applying these findings in the unveiling of cofactor specificity for enzymes that are not structurally characterized experimentally we successfully replicated these findings using machine learning algorithms. In future work we will apply the results and machine learning models obtained in order to assign cofactor specificity to enzymes with uncertain cofactor specificity. These results may represent an important development in systems biology by allowing the reduction of annotation errors and the implementation of erroneous or redundant reactions in GEM models, improving the overall performance of metabolic simulations.info:eu-repo/semantics/publishedVersionUniversidade do MinhoResende, Tiago Filipe CoelhoRocha, IsabelSoares, Cláudio M.2016-122016-12-01T00:00:00Zconference objectinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/1822/47504engResende, Tiago F.; Rocha, Isabel; Soares, Cláudio M., Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural information. EJIBCE 2016 - IV Encontro de Jovens Investigadores de Biologia Computacional Estrutural. Oeiras, Portugal, Dec 21, 62, 2016.http://www.itqb.unl.pt/ejibce2016/home.htmlinfo:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2024-05-11T04:35:13Zoai:repositorium.sdum.uminho.pt:1822/47504Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-28T14:52:27.242693Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
dc.title.none.fl_str_mv Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural information
title Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural information
spellingShingle Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural information
Resende, Tiago Filipe Coelho
title_short Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural information
title_full Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural information
title_fullStr Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural information
title_full_unstemmed Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural information
title_sort Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural information
author Resende, Tiago Filipe Coelho
author_facet Resende, Tiago Filipe Coelho
Rocha, Isabel
Soares, Cláudio M.
author_role author
author2 Rocha, Isabel
Soares, Cláudio M.
author2_role author
author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Resende, Tiago Filipe Coelho
Rocha, Isabel
Soares, Cláudio M.
description EJIBCE 2016 - IV Encontro de Jovens Investigadores de Biologia Computacional Estrutural
publishDate 2016
dc.date.none.fl_str_mv 2016-12
2016-12-01T00:00:00Z
dc.type.driver.fl_str_mv conference object
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/1822/47504
url http://hdl.handle.net/1822/47504
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Resende, Tiago F.; Rocha, Isabel; Soares, Cláudio M., Unveiling the molecular determinants responsible for NAD(P)(H) cofactor specificity using enzyme structural information. EJIBCE 2016 - IV Encontro de Jovens Investigadores de Biologia Computacional Estrutural. Oeiras, Portugal, Dec 21, 62, 2016.
http://www.itqb.unl.pt/ejibce2016/home.html
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.source.none.fl_str_mv reponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
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