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Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants
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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157895/ https://www.ncbi.nlm.nih.gov/pubmed/30256816 http://dx.doi.org/10.1371/journal.pone.0204275 |
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author | Einav, Tal Duque, Julia Phillips, Rob |
author_facet | Einav, Tal Duque, Julia Phillips, Rob |
author_sort | Einav, Tal |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6157895 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-61578952018-10-19 Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants Einav, Tal Duque, Julia Phillips, Rob PLoS One Research Article 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. Public Library of Science 2018-09-26 /pmc/articles/PMC6157895/ /pubmed/30256816 http://dx.doi.org/10.1371/journal.pone.0204275 Text en © 2018 Einav et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Einav, Tal Duque, Julia Phillips, Rob Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants |
title | Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants |
title_full | Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants |
title_fullStr | Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants |
title_full_unstemmed | Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants |
title_short | Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants |
title_sort | theoretical analysis of inducer and operator binding for cyclic-amp receptor protein mutants |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157895/ https://www.ncbi.nlm.nih.gov/pubmed/30256816 http://dx.doi.org/10.1371/journal.pone.0204275 |
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