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Reflections on apparent DNA bending by charge variants of bZIP proteins
Author(s) -
Hardwidge Philip R.,
Parkhurst Kay M.,
Parkhurst Lawrence J.,
Maher L. James
Publication year - 2003
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10321
Subject(s) - leucine zipper , förster resonance energy transfer , chemistry , bzip domain , dna , biophysics , dna binding domain , microbiology and biotechnology , biochemistry , transcription factor , fluorescence , gene , biology , physics , quantum mechanics
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. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 110–117, 2003