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Single‐Molecule Experiments to Elucidate the Minimal Requirement for DNA Recognition by Transcription Factor Epitopes
Author(s) -
Wollschläger Katrin,
Gaus Katharina,
Körnig André,
Eckel Rainer,
Wilking SvenDavid,
McIntosh Matthew,
Majer Zsuzsanna,
Becker Anke,
Ros Robert,
Anselmetti Dario,
Sewald Norbert
Publication year - 2009
Publication title -
small
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.785
H-Index - 236
eISSN - 1613-6829
pISSN - 1613-6810
DOI - 10.1002/smll.200800945
Subject(s) - dna , intein , circular dichroism , biochemistry , chemistry , force spectroscopy , dna binding site , peptide , biophysics , dna binding domain , transcription factor , binding site , dna binding protein , molecular recognition , escherichia coli , protein–protein interaction , binding selectivity , transcription (linguistics) , biology , molecule , promoter , gene , rna , gene expression , linguistics , philosophy , organic chemistry , rna splicing
Interactions between proteins and DNA are essential for the regulation of cellular processes in all living organisms. In this context, it is of special interest to investigate the sequence‐specific molecular recognition between transcription factors and their cognate DNA sequences. As a model system, peptide and protein epitopes of the DNA‐binding domain (DBD) of the transcription factor PhoB from Escherichia coli are analyzed with respect to DNA binding at the single‐molecule level. Peptides representing the amphiphilic recognition helix of the PhoB DBD (amino acids 190–209) are chemically synthesized and C‐terminally modified with a linker for atomic force microscopy–dynamic force spectroscopy experiments (AFM–DFS). For comparison, the entire PhoB DBD is overexpressed in E. coli and purified using an intein‐mediated protein purification method. To facilitate immobilization for AFM–DFS experiments, an additional cysteine residue is ligated to the protein. Quantitative AFM–DFS analysis proves the specificity of the interaction and yields force‐related properties and kinetic data, such as thermal dissociation rate constants. An alanine scan for strategic residues in both peptide and protein sequences is performed to reveal the contributions of single amino acid residues to the molecular‐recognition process. Additionally, DNA binding is substantiated by electrophoretic mobility‐shift experiments. Structural differences of the peptides, proteins, and DNA upon complex formation are analyzed by circular dichroism spectroscopy. This combination of techniques eventually provides a concise picture of the contribution of epitopes or single amino acids in PhoB to DNA binding.