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Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex

Homology models of the E. coli and T. maritima chemotaxis protein CheW were constructed to assess the quality of structural predictions and their applicability in chemotaxis research: i) a model of E. coli CheW was constructed using the T. maritima CheW NMR structure as a template, and ii) a model o...

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Autores principales: Cashman, Derek J., Ortega, Davi R., Zhulin, Igor B., Baudry, Jerome
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737408/
https://www.ncbi.nlm.nih.gov/pubmed/23950985
http://dx.doi.org/10.1371/journal.pone.0070705
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author Cashman, Derek J.
Ortega, Davi R.
Zhulin, Igor B.
Baudry, Jerome
author_facet Cashman, Derek J.
Ortega, Davi R.
Zhulin, Igor B.
Baudry, Jerome
author_sort Cashman, Derek J.
collection PubMed
description Homology models of the E. coli and T. maritima chemotaxis protein CheW were constructed to assess the quality of structural predictions and their applicability in chemotaxis research: i) a model of E. coli CheW was constructed using the T. maritima CheW NMR structure as a template, and ii) a model of T. maritima CheW was constructed using the E. coli CheW NMR structure as a template. The conformational space accessible to the homology models and to the NMR structures was investigated using molecular dynamics and Monte Carlo simulations. The results show that even though static homology models of CheW may be partially structurally different from their corresponding experimentally determined structures, the conformational space they can access through their dynamic variations can be similar, for specific regions of the protein, to that of the experimental NMR structures. When CheW homology models are allowed to explore their local accessible conformational space, modeling can provide a rational path to predicting CheW interactions with the MCP and CheA proteins of the chemotaxis complex. Homology models of CheW (and potentially, of other chemotaxis proteins) should be seen as snapshots of an otherwise larger ensemble of accessible conformational space.
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spelling pubmed-37374082013-08-15 Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex Cashman, Derek J. Ortega, Davi R. Zhulin, Igor B. Baudry, Jerome PLoS One Research Article Homology models of the E. coli and T. maritima chemotaxis protein CheW were constructed to assess the quality of structural predictions and their applicability in chemotaxis research: i) a model of E. coli CheW was constructed using the T. maritima CheW NMR structure as a template, and ii) a model of T. maritima CheW was constructed using the E. coli CheW NMR structure as a template. The conformational space accessible to the homology models and to the NMR structures was investigated using molecular dynamics and Monte Carlo simulations. The results show that even though static homology models of CheW may be partially structurally different from their corresponding experimentally determined structures, the conformational space they can access through their dynamic variations can be similar, for specific regions of the protein, to that of the experimental NMR structures. When CheW homology models are allowed to explore their local accessible conformational space, modeling can provide a rational path to predicting CheW interactions with the MCP and CheA proteins of the chemotaxis complex. Homology models of CheW (and potentially, of other chemotaxis proteins) should be seen as snapshots of an otherwise larger ensemble of accessible conformational space. Public Library of Science 2013-08-07 /pmc/articles/PMC3737408/ /pubmed/23950985 http://dx.doi.org/10.1371/journal.pone.0070705 Text en © 2013 Cashman 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, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Cashman, Derek J.
Ortega, Davi R.
Zhulin, Igor B.
Baudry, Jerome
Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex
title Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex
title_full Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex
title_fullStr Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex
title_full_unstemmed Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex
title_short Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex
title_sort homology modeling of the chew coupling protein of the chemotaxis signaling complex
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737408/
https://www.ncbi.nlm.nih.gov/pubmed/23950985
http://dx.doi.org/10.1371/journal.pone.0070705
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