The atomic basis for metal-DNA signalling in CUER

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http://eprints.org/relation/isVersionOf http://etheses.bham.ac.uk/id/document/817 http://eprints.org/relation/isVolatileVersionOf http://etheses.bham.ac.uk/id/document/817 http://eprints.org/relation/isIndexCodesVersionOf http://etheses.bham.ac.uk/id/document/817 archive 4031 disk0/00/00/03/38 2009-12-11 11:15:25 2019-01-23 09:51:57 2011-07-19 16:16:01 thesis show 0 Collins Christopher Ian Wilkie John Professor University of Birmingham The atomic basis for metal-DNA signalling in CUER unpub QD 10col_ephy There are separate MD trajectory files for this thesis which requires additional software available at http://www.ks.uiuc.edu/Research/vmd/ Instructions for the viewing of MD trajectory files are enclosed as a separate pdf The MD trajectory files themselves are winzipped here for convenience. 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for a variety of metal ions to produce new sensors and sequesters. 2009-12-16 2009-08-21 graduation eng author This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. public 205 University of Birmingham School of Chemistry d_ph na 2009-12-16 graduation