Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex
Abstract
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.
- Authors:
-
- University of Tennessee, Knoxville, TN (United States)
- University of Tennessee, Knoxville, TN (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); University of Tennessee, Knoxville, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
- OSTI Identifier:
- 1627629
- Grant/Contract Number:
- AC05-00OR22725; GM072285
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 8; Journal Issue: 8; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; protein structure; molecular dynamics; chemotaxis; Monte Carlo method; biochemical simulations; protein structure comparison; protein structure database; protein structure predictions
Citation Formats
Cashman, Derek J., Ortega, Davi R., Zhulin, Igor B., and Baudry, Jerome. Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex. United States: N. p., 2013.
Web. doi:10.1371/journal.pone.0070705.
Cashman, Derek J., Ortega, Davi R., Zhulin, Igor B., & Baudry, Jerome. Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex. United States. https://doi.org/10.1371/journal.pone.0070705
Cashman, Derek J., Ortega, Davi R., Zhulin, Igor B., and Baudry, Jerome. Wed .
"Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex". United States. https://doi.org/10.1371/journal.pone.0070705. https://www.osti.gov/servlets/purl/1627629.
@article{osti_1627629,
title = {Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex},
author = {Cashman, Derek J. and Ortega, Davi R. and Zhulin, Igor B. and Baudry, Jerome},
abstractNote = {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.},
doi = {10.1371/journal.pone.0070705},
journal = {PLoS ONE},
number = 8,
volume = 8,
place = {United States},
year = {Wed Aug 07 00:00:00 EDT 2013},
month = {Wed Aug 07 00:00:00 EDT 2013}
}
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