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Proc Natl Acad Sci U S A. 2016 Jan 5;113(1):110-5. doi: 10.1073/pnas.1520483112. Epub 2015 Dec 23.

Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network.

Author information

1
Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, TX 77005;
2
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093.
3
Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, TX 77005; pwolynes@rice.edu.

Abstract

Genetic switches based on the [Formula: see text] system are master regulators of an array of cellular responses. Recent kinetic experiments have shown that [Formula: see text] can actively remove NF-κB bound to its genetic sites via a process called "molecular stripping." This allows the [Formula: see text] switch to function under kinetic control rather than the thermodynamic control contemplated in the traditional models of gene switches. Using molecular dynamics simulations of coarse-grained predictive energy landscape models for the constituent proteins by themselves and interacting with the DNA we explore the functional motions of the transcription factor [Formula: see text] and its various binary and ternary complexes with DNA and the inhibitor IκB. These studies show that the function of the [Formula: see text] genetic switch is realized via an allosteric mechanism. Molecular stripping occurs through the activation of a domain twist mode by the binding of [Formula: see text] that occurs through conformational selection. Free energy calculations for DNA binding show that the binding of [Formula: see text] not only results in a significant decrease of the affinity of the transcription factor for the DNA but also kinetically speeds DNA release. Projections of the free energy onto various reaction coordinates reveal the structural details of the stripping pathways.

KEYWORDS:

allostery; genetic switch; molecular dynamics; protein–DNA interaction; systems biology

PMID:
26699500
PMCID:
PMC4711861
DOI:
10.1073/pnas.1520483112
[Indexed for MEDLINE]
Free PMC Article

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