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• W2777260063 endingPage "e0189270" @default.
• W2777260063 startingPage "e0189270" @default.
• W2777260063 abstract "GabR from Bacillus subtilis is a transcriptional regulator belonging to the MocR subfamily of the GntR regulators. The structure of the MocR regulators is characterized by the presence of two domains: i) a N-terminal domain, about 60 residue long, possessing the winged-Helix-Turn-Helix (wHTH) architecture with DNA recognition and binding capability; ii) a C-terminal domain (about 350 residue) folded as the pyridoxal 5’-phosphate (PLP) dependent aspartate aminotransferase (AAT) with dimerization and effector binding functions. The two domains are linked to each other by a peptide bridge. Although structural and functional characterization of MocRs is proceeding at a fast pace, virtually nothing is know about the molecular changes induced by the effector binding and on how these modifications influence the properties of the regulator. An extensive molecular dynamics simulation on the crystallographic structure of the homodimeric B. subtilis GabR has been undertaken with the aim to envisage the role and the importance of conformational flexibility in the action of GabR. Molecular dynamics has been calculated for the apo (without PLP) and holo (with PLP bound) forms of the GabR. A comparison between the molecular dynamics trajectories calculated for the two GabR forms suggested that one of the wHTH domain detaches from the AAT-like domain in the GabR PLP-bound form. The most evident conformational change in the holo PLP-bound form is represented by the rotation and the subsequent detachment from the subunit surface of one of the wHTH domains. The movement is mediated by a rearrangement of the linker connecting the AAT domain possibly triggered by the presence of the negative charge of the PLP cofactor. This is the second most significant conformational modification. The C-terminal section of the linker docks into the “active site” pocket and establish stabilizing contacts consisting of hydrogen-bonds, salt-bridges and hydrophobic interactions." @default.
• W2777260063 created "2018-01-05" @default.
• W2777260063 creator A5000267232 @default.
• W2777260063 creator A5057727498 @default.
• W2777260063 creator A5068344981 @default.
• W2777260063 creator A5078917080 @default.
• W2777260063 creator A5081679633 @default.
• W2777260063 date "2017-12-18" @default.
• W2777260063 modified "2023-10-17" @default.
• W2777260063 title "Molecular dynamics simulation unveils the conformational flexibility of the interdomain linker in the bacterial transcriptional regulator GabR from Bacillus subtilis bound to pyridoxal 5’-phosphate" @default.
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• W2777260063 doi "https://doi.org/10.1371/journal.pone.0189270" @default.
• W2777260063 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/5734734" @default.
• W2777260063 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/29253008" @default.
• W2777260063 hasPublicationYear "2017" @default.
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