The atomic basis for metal-DNA signalling in CUER

Abstract

Gram-negative bacteria can control the concentrations of metal ions through the MerR family of transcriptional activators. Several proteins in this family have been characterised, including MerR, CueR and ZntR. MerR family proteins work through an unusual route, for which there is little chemical data in the literature. Crystal structures are available for activator forms of CueR and ZntR, but repressor forms were not previously characterised. This thesis studies mechanisms of binding, information transfer and activation of transcription. CueR binds exceptionally strongly to Cu(I), and this thesis shows that this is due to the binding site being very well set up. A hydrogen bonding chain which transfers data about the metal binding event to the DNA has been characterised. ZntR works through a similar mechanism with the hydrogen bonding chain replaced by a direct ionic bond to the metal ion. Mutants are considered which disrupt the hydrogen bonding chain. CueR with and without Cu(I) is studied using Molecular Dynamics along with mutants and a resting state for CueR is proposed with a larger dihedral angle than the activator form. Alternative binding sites are proposed for a variety of metal ions to produce new sensors and sequesters.