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Published on: March 30, 2018

Specificity determinants for the abscisic acid response element.

Aditya Kumar Sarkar1, Ansuman Lahiri

  • 1Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700 009, India.

FEBS Open Bio
|June 18, 2013
PubMed
Summary
This summary is machine-generated.

This study models how Arabidopsis thaliana ABRE binding factor 1 (AtABF1) binds to abscisic acid (ABA) response elements (ABREs). Findings reveal how DNA sequence variations influence the stability and specificity of this crucial plant transcription factor-DNA interaction.

Keywords:
ABA, abscisic acidABF1, ABRE binding factor 1ABRE, abscisic acid response elementAbscisic acid response elementBasic leucine zipperCREB, cAMP response element-binding protein.Comparative modelingFoldXHADDOCKProtein–DNA interactionRecognition specificitySSCRE, somatostatin cAMP response elementbZIP, basic leucine zipper

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Area of Science:

  • Plant molecular biology
  • Structural biology
  • Biochemistry

Background:

  • Abscisic acid (ABA) is a key plant hormone regulating stress responses.
  • ABA response elements (ABREs) are cis-acting DNA sequences mediating ABA-regulated gene expression.
  • ABRE binding factors (ABFs) are bZIP transcription factors that bind to ABREs.

Purpose of the Study:

  • To understand the binding specificity mechanism between ABREs and ABFs.
  • To model the homodimeric structure of AtABF1 bZIP domain.
  • To investigate the interaction between AtABF1 and ABRE sequences.

Main Methods:

  • Homodimeric structure modeling of the AtABF1 bZIP domain.
  • Analysis of AtABF1 interaction with ACGT core motif-containing ABREs.
  • Protein design algorithm (FoldX) for stability analysis of mutated ABRE sequences.
  • High throughput free energy calculations.

Main Results:

  • Successfully predicted AtABF1 binding to alternative core motifs (GCG T, AAG T).
  • Rationalized the role of flanking sequences in determining protein-DNA interaction specificity.
  • Quantified the impact of ABRE sequence mutations on complex stability.

Conclusions:

  • The study provides insights into the molecular basis of ABF1-ABRE recognition.
  • Flanking sequences significantly contribute to the specificity of ABA-regulated gene transcription.
  • Computational approaches can effectively predict and explain protein-DNA binding dynamics.