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Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants

Einav, Tal and Duque, Julia and Phillips, Rob (2018) Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants. PLoS ONE, 13 (9). Art. No. e0204275. ISSN 1932-6203. PMCID PMC6157895. https://resolver.caltech.edu/CaltechAUTHORS:20181009-105623284

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Abstract

Allosteric transcription factors undergo binding events at inducer binding sites as well as at distinct DNA binding domains, and it is difficult to disentangle the structural and functional consequences of these two classes of interactions. We compare the ability of two statistical mechanical models—the Monod-Wyman-Changeux (MWC) and the Koshland-Némethy-Filmer (KNF) models of protein conformational change—to characterize the multi-step activation mechanism of the broadly acting cyclic-AMP receptor protein (CRP). We first consider the allosteric transition resulting from cyclic-AMP binding to CRP, then analyze how CRP binds to its operator, and finally investigate the ability of CRP to activate gene expression. We use these models to examine a beautiful recent experiment that created a single-chain version of the CRP homodimer, creating six mutants using all possible combinations of the wild type, D53H, and S62F subunits. We demonstrate that the MWC model can explain the behavior of all six mutants using a small, self-consistent set of parameters whose complexity scales with the number of subunits, providing a significant benefit over previous models. In comparison, the KNF model not only leads to a poorer characterization of the available data but also fails to generate parameter values in line with the available structural knowledge of CRP. In addition, we discuss how the conceptual framework developed here for CRP enables us to not merely analyze data retrospectively, but has the predictive power to determine how combinations of mutations will interact, how double mutants will behave, and how each construct would regulate gene expression.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1371/journal.pone.0204275DOIArticle
https://doi.org/10.1371/journal.pone.0204275.s001DOIS1 Text
https://doi.org/10.1371/journal.pone.0204275.s002DOIS1 File
https://doi.org/10.1101/236455DOIDiscussion Paper
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157895/PubMed CentralArticle
ORCID:
AuthorORCID
Einav, Tal0000-0003-0777-1193
Phillips, Rob0000-0003-3082-2809
Additional Information:© 2018 Einav et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: July 5, 2018; Accepted: September 5, 2018; Published: September 26, 2018. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. This work was supported in the RP group by La Fondation Pierre-Gilles de Gennes, the Rosen Center at Caltech (http://rosen.caltech.edu/), and the National Institutes of Health (https://www.nih.gov/) through DP1 OD000217 (Director's Pioneer Award), R01 GM085286, and 1R35 GM118043-01 (MIRA). We are grateful to the Burroughs-Wellcome Fund (https://www.bwfund.org/) for its support of the Physiology Course at the Marine Biological Laboratory, where part of the work on this work was done, and for a post-course research grant (JD). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors have declared that no competing interests exist. We thank Lacramioara Bintu for bringing the recent developments on CRP to our attention as well as Terry Hwa, Tom Kuhlman, and Michael Manhart for helpful discussions. All plots were made entirely in Mathematica using the CustomTicks package [54] with data obtained from the authors or using WebPlotDigitizer [55]. This work was supported in the RP group by La Fondation Pierre-Gilles de Gennes, the Rosen Center at Caltech, and the National Institutes of Health through DP1 OD000217 (Director's Pioneer Award), R01 GM085286, and 1R35 GM118043-01 (MIRA). We are grateful to the Burroughs-Wellcome Fund for its support of the Physiology Course at the Marine Biological Laboratory, where part of the work on this work was done, and for a post-course research grant (JD). Author Contributions: Conceptualization: Tal Einav, Julia Duque, Rob Phillips. Formal analysis: Tal Einav, Julia Duque, Rob Phillips. Writing ± original draft: Tal Einav, Rob Phillips.
Group:Rosen Bioengineering Center
Funders:
Funding AgencyGrant Number
La Fondation Pierre-Gilles de GennesUNSPECIFIED
Donna and Benjamin M. Rosen Bioengineering CenterUNSPECIFIED
NIHDP1 OD000217
NIHR01 GM085286
NIH1R35 GM118043-01
Burroughs-Wellcome FundUNSPECIFIED
Issue or Number:9
PubMed Central ID:PMC6157895
Record Number:CaltechAUTHORS:20181009-105623284
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20181009-105623284
Official Citation:Einav T, Duque J, Phillips R (2018) Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants. PLoS ONE 13(9): e0204275. https://doi.org/10.1371/journal.pone.0204275
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:90190
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:10 Oct 2018 17:59
Last Modified:03 Oct 2019 20:22

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