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Specificity determinants for the abscisic acid response element()
Abscisic acid (ABA) response elements (ABREs) are a group of cis-acting DNA elements that have been identified from promoter analysis of many ABA-regulated genes in plants. We are interested in understanding the mechanism of binding specificity between ABREs and a class of bZIP transcription factors...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668542/ https://www.ncbi.nlm.nih.gov/pubmed/23772380 http://dx.doi.org/10.1016/j.fob.2013.01.006 |
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author | Sarkar, Aditya Kumar Lahiri, Ansuman |
author_facet | Sarkar, Aditya Kumar Lahiri, Ansuman |
author_sort | Sarkar, Aditya Kumar |
collection | PubMed |
description | Abscisic acid (ABA) response elements (ABREs) are a group of cis-acting DNA elements that have been identified from promoter analysis of many ABA-regulated genes in plants. We are interested in understanding the mechanism of binding specificity between ABREs and a class of bZIP transcription factors known as ABRE binding factors (ABFs). In this work, we have modeled the homodimeric structure of the bZIP domain of ABRE binding factor 1 from Arabidopsis thaliana (AtABF1) and studied its interaction with ACGT core motif-containing ABRE sequences. We have also examined the variation in the stability of the protein–DNA complex upon mutating ABRE sequences using the protein design algorithm FoldX. The high throughput free energy calculations successfully predicted the ability of ABF1 to bind to alternative core motifs like GCGT or AAGT and also rationalized the role of the flanking sequences in determining the specificity of the protein-DNA interaction. |
format | Online Article Text |
id | pubmed-3668542 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-36685422013-06-14 Specificity determinants for the abscisic acid response element() Sarkar, Aditya Kumar Lahiri, Ansuman FEBS Open Bio Article Abscisic acid (ABA) response elements (ABREs) are a group of cis-acting DNA elements that have been identified from promoter analysis of many ABA-regulated genes in plants. We are interested in understanding the mechanism of binding specificity between ABREs and a class of bZIP transcription factors known as ABRE binding factors (ABFs). In this work, we have modeled the homodimeric structure of the bZIP domain of ABRE binding factor 1 from Arabidopsis thaliana (AtABF1) and studied its interaction with ACGT core motif-containing ABRE sequences. We have also examined the variation in the stability of the protein–DNA complex upon mutating ABRE sequences using the protein design algorithm FoldX. The high throughput free energy calculations successfully predicted the ability of ABF1 to bind to alternative core motifs like GCGT or AAGT and also rationalized the role of the flanking sequences in determining the specificity of the protein-DNA interaction. Elsevier 2013-01-22 /pmc/articles/PMC3668542/ /pubmed/23772380 http://dx.doi.org/10.1016/j.fob.2013.01.006 Text en © 2013 The Authors http://creativecommons.org/licenses/BY-NC-ND/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-No Derivative Works License, which permits non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Article Sarkar, Aditya Kumar Lahiri, Ansuman Specificity determinants for the abscisic acid response element() |
title | Specificity determinants for the abscisic acid response element() |
title_full | Specificity determinants for the abscisic acid response element() |
title_fullStr | Specificity determinants for the abscisic acid response element() |
title_full_unstemmed | Specificity determinants for the abscisic acid response element() |
title_short | Specificity determinants for the abscisic acid response element() |
title_sort | specificity determinants for the abscisic acid response element() |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668542/ https://www.ncbi.nlm.nih.gov/pubmed/23772380 http://dx.doi.org/10.1016/j.fob.2013.01.006 |
work_keys_str_mv | AT sarkaradityakumar specificitydeterminantsfortheabscisicacidresponseelement AT lahiriansuman specificitydeterminantsfortheabscisicacidresponseelement |