FixL,a dimeric protein of bradyrhizobia japonicum, is an oxygensensor that regulates the expression of the genes involved innitrogen fixation.  It contains an N-terminal heme-bound PAS domain(bjFixLH) that controls the activity of the C-terminal histidineKinase domain depending on heme ligation state. To investigate theligand behavior after CO dissociation as well as protein structuralchanges involved in the relaxation to the deoxy state, 10ns moleculardynamics simulations of the CO-bound and CO-unbound bjFixL hemedomain in crystal and solution environments were performed andanalyzed using PCA and NMA. Our simulations show that the diffusionof the ligand is influenced by internal motions of the boundstructure of the protein before the CO bond dissociation event.Comparison of our results to experimental data shows that differentenvironments and Arg220 affect the dynamics of the ligand, which inturn influences the structural changes within important regions ofthe protein.

Molecular dynamics simulations of deoxy and carboxy bjFixLH in crystal and solution: Intrinsic dynamics affects the behavior of the ligand after dissociation

239th National Meeting (2010)

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