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Title: The recognition of telomeric DNA by Shelterin proteins
Author: Garton, Michael
Awarding Body: University of Nottingham
Current Institution: University of Nottingham
Date of Award: 2012
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Telomeres are solely responsible for the protection of linear chromosome ends. Each is a nucleoprotein complex that prevents chromosome end-to-end fusions and solves the end replication problem. Six different proteins types are involved and form a complex called Shelterin. Three of these specifically recognise the 5'-TTAGGG-3' tandem repeat DNA sequence: TRFl and TRF2 recognise the double-stranded region and POTl binds to the 3' single strand overhang. Characterisation of DNA recognition by these proteins and subsequent behaviour once associated is currently limited and conflicting. This is due in part to the incapability of conventional methods to capture detailed dynamic information at the atomistic level. In this thesis molecular modelling is employed to more fully explore the potential energy surface of each telomeric protein-DNA complex. An unprecedented level of recognition detail is accessed by molecular dynamics, which reconciles previous characterisations. New interactions emerge and time-dependent analysis predicts that some previously proposed contacts are not biologically significant. Hydrophobic and water-mediated interactions are measured, together with direct and indirect readout. This ensemble of contacts I I I I , is the first complete model for TRF-DNA recognition. TRFl and TRF2 are shown to differ, both in terms of recognition and DNA remodelling behaviour. TRF2 relies much less on indirect readout suggesting it is better suited to unusual DNA structures than TRF 1. Difference in sequence means that TRF2 develops a strong hydrophobic patch not seen in TRF 1 and this causes a change in binding mode resulting in DNA distortion. This distortion may contribute to the explanation for functional differences observed for TRF 1 and TRF2. Single strand binder POTl is shown by molecular dynamics to be able to disrupt the quadruplex structure adopted by single-stranded telomeric DNA to minimise nucleoside solvent exposure. An initial recognition site for quadruplex DNA on the surface of POTl is also determined using molecular fitting. The unfolding mechanism involves a protein groove flanked by lysines. Once accepted into the groove, the quadruplex is uncoiled by lysine penetrating the electron rich central channel, ejecting stabilising potassium IOns.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available