Reflections on apparent DNA bending by charge variants of bZIP proteins

Philip R. Hardwidge, Kay M. Parkhurst, Lawrence J Parkhurst, L. James Maher

Research output: Contribution to journalReview article

9 Citations (Scopus)

Abstract

Basic-leucine zipper (bZIP) proteins have been studied intensely as transcription factors. It has been proposed that the bZIP domain might modulate transcription activation through the induction of conformational changes in the DNA binding site. We have been interested in using bZIP peptides as convenient models with which to study the role of asymmetric phosphate neutralization in DNA bending. DNA bending experiments have yielded discordant results for bZIP peptides studied by electrophoretic- vs solution-based assays. We review the history of DNA bending assays involving bZIP peptides and introduce the reader to examples of discordant results. Our recent published experiments designed to clarify this field of study will then be reviewed. The engineering of protein fusions has established that electrophoretic phasing assays are relatively insensitive to precise protein structure/conformation and instead appear to report DNA bending, as influenced by protein charge. New applications of time-resolved fluorescence resonance energy transfer (FRET) have allowed for the first time corroboration of electrophoretic phasing assays with solution-based FRET measurements. We report that two conventional DNA bending assays that rely on DNA ligation cannot be applied to analysis of the bZIP peptides we studied due to ligation inhibition.

Original languageEnglish (US)
Pages (from-to)110-117
Number of pages8
JournalBiopolymers
Volume69
Issue number1
DOIs
StatePublished - May 1 2003

Fingerprint

Leucine Zippers
Fasteners
DNA
Proteins
Assays
Peptides
Fluorescence Resonance Energy Transfer
Ligation
Protein Engineering
Protein Conformation
Transcription factors
Binding sites
Transcription
Transcriptional Activation
Conformations
Phosphates
Transcription Factors
Fusion reactions
History
Experiments

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry

Cite this

Reflections on apparent DNA bending by charge variants of bZIP proteins. / Hardwidge, Philip R.; Parkhurst, Kay M.; Parkhurst, Lawrence J; Maher, L. James.

In: Biopolymers, Vol. 69, No. 1, 01.05.2003, p. 110-117.

Research output: Contribution to journalReview article

Hardwidge, Philip R. ; Parkhurst, Kay M. ; Parkhurst, Lawrence J ; Maher, L. James. / Reflections on apparent DNA bending by charge variants of bZIP proteins. In: Biopolymers. 2003 ; Vol. 69, No. 1. pp. 110-117.
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