Molecular dynamics of the FixJ receiver domain: movement of the beta4-alpha4 loop correlates with the in and out flip of Phe101.
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.
Roche
Philippe
P
Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, UMR 215, CNRS-INRA, BP26, 31326 Castanet-Tolosan Cedex, France. philippe@strubi.ox.ac
Mouawad
Liliane
L
Perahia
David
D
Samama
Jean-Pierre
JP
Kahn
Daniel
D
D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D003198:Computer Simulation; D005798:Genes, Bacterial; D008958:Models, Molecular; D009586:Nitrogen Fixation / Q000235:genetics; D010649:Phenylalanine / Q000737:chemistry*; D010766:Phosphorylation; D011487:Protein Conformation; D016962:Sinorhizobium meliloti / Q000737:chemistry* / Q000378:metabolism
D001426:Bacterial Proteins; C069289:FixJ protein, Bacteria; D010649:Phenylalanine