Ricerc@Sapienza

MocR bacterial transcriptional regulators (TRs) are a subfamily of the larger GntR family. The proteins of this family possess a characteristic molecular architecture: an N-terminal DNA-binding domain containing a winged Helix-Turn-Helix (wHTH) motif and a C-terminal domain with oligomerization and/or effector binding function, interconnected through a linker of variable length. The MocR subfamily is characterised by a C-terminal domain homologous to the fold type I pyridoxal 5¿-phosphate (PLP)-dependent enzymes (such as aspartate aminotransferase), connected to the wHTH domain by a linker of variable length. The PLP cofactor is covalently bound to an active site lysine residue via a Schiff base. The project aims at studying the functional and structural properties of the MocR-TRs using in-silico techniques and it is focused on one particular regulator, namely GabR from B. subtilis for which a significant amount of structural and functional information is available. The project includes two tasks: the first consists in the delineation of the molecular mechanism underlying the function of the GabR using molecular dynamics (MD) simulations; the second one is aimed at understanding the pathway through which the MocR subfamily has emerged during evolution.
A model of the entire GabR dimer complexed with the gamma-amino butyric acid (GABA), its effector, will be built using the GabR crystallographic structures available in the PDB. A long run of MD will be applied to the model to simulate the effect of GABA binding on the conformation of GabR.
Multiple sequence alignment, cluster and phylogenetic analysis, and homology modeling will be applied on a representative set of MocRs. This study should help delineating the MocR regulator evolution path and functional diversification which may have proceeded either through a single or subsequent multiple fusion events between an ancestral gene coding for a wHTH domain and one or different fold type-I PLP enzyme-coding genes.