Molecular dynamics of the FixJ receiver domain: movement of the beta4-alpha4 loop correlates with the in and out flip of Phe101 |
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Authors: | Roche Philippe Mouawad Liliane Perahia David Samama Jean-Pierre Kahn Daniel |
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Institution: | Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, UMR 215, CNRS-INRA, BP26, 31326 Castanet-Tolosan Cedex, France. philippe@strubi.ox.ac |
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Abstract: | FixJ is a two-domain response regulator involved in nitrogen fixation in Sinorhizobium meliloti. Recent X-ray characterization of both the native (unphosphorylated) and the active (phosphorylated) states of the protein identify conformational changes of the beta4-alpha4 loop and the conserved residue Phe101 as the key switches in activation. These structures also allowed investigation of the transition between conformations of this two-component regulatory receiver domain by molecular dynamics simulations. The path for the conformational change was studied with a distance constraint directing the system from one state to the other. The simulations provide evidence for a correlation between the conformation of the beta4-alpha4 loop and the orientation of the residue Phe101. A model presenting the sequence of events during the activation/deactivation process is discussed. |
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Keywords: | Molecular dynamics response regulator conformational change transition pathway path exploration with distance constraints |
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