• Login
    View Item 
    •   Home
    • Massey Documents by Type
    • Theses and Dissertations
    • View Item
    •   Home
    • Massey Documents by Type
    • Theses and Dissertations
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    An investigation of Rheo-NMR techniques to improve the capture of residual dipolar couplings : a thesis submitted in partial fulfillment of the requirements for the award of the degree of Master of Science in Chemistry, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand

    Icon
    View/Open Full Text
    01_front.pdf (309.3Kb)
    02_whole.pdf (14.86Mb)
    Export to EndNote
    Abstract
    Residual Dipolar Couplings (RDCs) are an increasingly important structural restraint that can be used to help generate high quality structural models of proteins by Nuclear Magnetic Resonance (NMR) methods. They are captured with the aid of an alignment medium that imposes some anisotropy to the protein’s tumbling. Current methods for the capture of multiple sets of these couplings are tedious, expensive, and do not always result in unique sets being captured. This thesis set out to investigate whether multiple RDC sets could be captured from a single sample by controllably shearing the liquid crystal alignment medium used. Initial experiments focused on the ability to controllably realign a number of different nematic phase liquid crystals. These experiments found that controlling the director angle of the liquid crystal is possible, and that a number of stable alignments can be achieved through the application of different shear stresses. The application of RDCs to small molecules is a very young field that is still developing and finding potential uses. In this thesis a small molecule system of (+)-isopinocampheol ((+)-IPC) was investigated with RDCs being collected from this molecule within a liquid crystal phase with the director at a number of different orientations relative to the external magnetic field. The fitting of these captured RDCs to a structural model of the (+)-IPC was not able to generate a high quality fit for any of the RDC sets collected, leading to some puzzling results. It is hypothesized that inhomogeneity of the alignment phase was responsible for these difficulties. As the application of RDCs is so heavily dominated by protein structure studies, a small protein was investigated. The protein of choice, ubiquitin, has been heavily investigated in the past, and is often used as a demonstrator protein for new NMR techniques. This work presents several RDC data sets measured from ubiquitin which were successfully captured at a variety of different director orientations of the alignment media. These RDC sets were all successfully fitted to a previously known X-Ray crystallographic structure of ubiquitin, and unique alignment tensors for each RDC data set were extracted. Finally, structure calculations were carried out incorporating these captured ubiquitin RDC data sets with the goal of investigating how the variation in the ensembles of structures generated was modified. The results from these calculations showed that the addition of RDC data (over and above NOE constraints) to the simulated annealing process results in ensembles of higher quality structures being obtained. However, the addition of multiple sets of RDC data (collected with different director alignments) did not appear to cause any further improvement.
    Date
    2015
    Author
    Munro, Ben
    Rights
    The Author
    Publisher
    Massey University
    URI
    http://hdl.handle.net/10179/7011
    Collections
    • Theses and Dissertations
    Metadata
    Show full item record

    Copyright © Massey University
    Contact Us | Send Feedback | Copyright Take Down Request | Massey University Privacy Statement
    DSpace software copyright © Duraspace
    v5.7-2020.1
     

     

    Tweets by @Massey_Research
    Information PagesContent PolicyDepositing content to MROCopyright and Access InformationDeposit LicenseDeposit License SummaryTheses FAQFile FormatsDoctoral Thesis Deposit

    Browse

    All of MROCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects

    My Account

    LoginRegister

    Statistics

    View Usage Statistics

    Copyright © Massey University
    Contact Us | Send Feedback | Copyright Take Down Request | Massey University Privacy Statement
    DSpace software copyright © Duraspace
    v5.7-2020.1