Specific interactions by the N‐terminal arm inhibit self‐association of the AraC dimerization domain

Deletion of the regulatory N‐terminal arms of the AraC protein from its dimerization domain fragments increases the susceptibility of the dimerization domain to form a series of higher order polymers by indefinite self‐association. We investigated how the normal presence of the arm inhibits this sel...

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Bibliographic Details
Published in:Protein science 2006-12, Vol.15 (12), p.2828-2835
Main Authors: Weldon, John E., Schleif, Robert F.
Format: Article
Language:English
Subjects:
AraC
AraC Transcription Factor - chemistry
AraC Transcription Factor - metabolism
Binding Sites
Dimerization
entropic bristle
Entropy
Escherichia coli
fluorescence
Models, Biological
Mutant Proteins - chemistry
Mutant Proteins - metabolism
Mutation - physiology
Protein Binding
Protein Engineering - methods
Protein Folding
Protein Structure, Tertiary - physiology
regulation
Solubility
Trypsin - metabolism
trypsin cleavage
ubiquitin
velocity sedimentation
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Summary:Deletion of the regulatory N‐terminal arms of the AraC protein from its dimerization domain fragments increases the susceptibility of the dimerization domain to form a series of higher order polymers by indefinite self‐association. We investigated how the normal presence of the arm inhibits this self‐association. One possibility is that arms can act as an entropic bristles to interfere with the approach of other macromolecules, thereby decreasing collision frequencies. We examined the repulsive effect of flexible arms by measuring the rate of trypsin cleavage of a specially constructed ubiquitin‐arm protein. Adding an arm to ubiquitin or increasing its length produced only a modest repulsive effect. This suggests that arms such as the N‐terminal arm of AraC do not reduce self‐association by entropic exclusion. We consequently tested the hypothesis that the arm on AraC reduces self‐association by binding to the core of the dimerization domain even in the absence of arabinose. The behaviors of dimerization domain mutants containing deletions or alterations in the N‐terminal arms substantiate this hypothesis. Apparently, interactions between the N‐terminal arm and the dimerization domain core position the arm to interfere with the protein–protein contacts necessary for self‐association.
ISSN:0961-8368
1469-896X
DOI:10.1110/ps.062327506