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Molecular dynamics of the FixJ receiver domain: movement of the ß4–4 loop correlates with the in and out flip of Phe101

¹ Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, UMR 215, CNRS-INRA, BP26, 31326 Castanet-Tolosan Cedex, France
² Laboratoire de Modélisation et d’Ingénierie des Protéines, Université Paris-Sud, 91405 Orsay Cedex, France
³ Institut de Pharmacologie et de Biologie Structurale, UMR 5089, 31077 Toulouse Cedex, France

Reprint requests to: Philippe Roche, Division of Structural Biology, University of Oxford, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK; e-mail: philippe{at}strubi.ox.ac.uk; fax: 44 1865 287547.

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 ß4–4 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 ß4–4 loop and the orientation of the residue Phe101. A model presenting the sequence of events during the activation/deactivation process is discussed.

Keywords: Molecular dynamics; response regulator; conformational change; transition pathway; path exploration with distance constraints

Abbreviations: MD, molecular dynamics • PEDC, path exploration with distance constraints • mrms, mass-weighed root-mean-square • FixJN, nonphosphorylated, N terminal domain of FixJ • FixJNP, phosphorylated, N terminal domain of FixJ • JN, FixJN structure modified to allow MD studies • JNP, FixJNP structure modified to allow MD studies • JNP[-P], in silico dephosphorylated JNP • JNI[-P] • initial structure in the PEDC dephosphorylation pathway • JNT, target structure in the PEDC dephosphorylation pathway • JN[+P], in silico phosphorylated JN • JNI[+P], initial structure in the PEDC phosphorylation pathway • JNTP, target structure in the PEDC phosphorylation pathway

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