Thesis (Ph. D.)--Ohio State University, 2005. / Title from first page of PDF file. Document formatted into pages; contains xv, 99 p.; also includes graphics (some col.). Includes bibliographical references (p. 95-99). Available online via OhioLINK's ETD Center

Thesis (Ph.D.)--McMaster University, 2006. / Supervisor: Yingfy Li. Includes bibliographical references (leaves 151-167).

Thesis (Ph.D.) -- McMaster University, 1999. / [Íta] in title is a Greek letter. Includes bibliographical references (leaves 180-191). Also available via World Wide Web.

Thesis (Ph. D.)--University of Canterbury, 2009. / Typescript (photocopy). Includes bibliographical references. Also available via the World Wide Web.

Thesis (Ph.D.)--Victoria University of Wellington, 2010. / Includes bibliographical references.

Thesis (Ph.D.)--Memorial University of Newfoundland, 2004. / Bibliography: leaves 157-167.

In this thesis, an experimental and theoretical study of two and three vector correlations in the inelastic scattering of NO(X) with various rare gas atoms is presented. Vector correlations for a selection of rare gas systems were determined experimentally, and the observations were interpreted using a variety of classical and quantum mechanical models. The experiment is able to provide state-to-state resolution of the dynamics by means of an electrostatic hexapole and 1+1' resonantly enhanced multi-photon ionisation (REMPI). The simplest vector correlation of interest is the differential cross section (DCS), given by the <b>k</b>-<b>k</b>' correlation. The DCSs were determined experimentally for the NO(X)--Kr and NO(X)--Xe collision systems, both characterised by the relatively deep (&asymp;140cm^-1) attractive well and large extent of the attractive potential. The agreement between the experimental angular distributions and quantum mechanical DCS is very good for both systems. Classical calculations fail to correctly reproduce the form and magnitude of the DCS for either system, reflecting the inherently quantum mechanical nature of the collision. The classical calculations do however provide mechanistic insight into regions where the attractive part of the potential plays an important role in determining the dynamics. In order to investigate narrow angular features in the forward scattered direction, several experimental improvements to molecular beams and the detection ion-optic stack were made. Investigation into these structures revealed a strong contribution from molecular diffraction into the classical shadow of the NO(X), and the simple Fraunhofer model revealed a preference for scattering from an individual m&rarr;m' sub-state. Such measurements are in a region of the DCS where scattering is forbidden classically, and reveal the purely quantum nature of the collision interaction in the forward scattered direction. The low order <b>k</b>-<b>k</b>' correlation was then extended by using linearly or circularly polarised laser excitation. The interaction of the light with the molecular dipole allows the measurement of the <b>k</b>-<b>k</b>'-<b>j</b>' correlation. When linearly polarised light was used for the excitation laser, two of the rank two p^{2}_q(&theta;) renormalised polarisation dependent differential cross sections (PDDCSs), which describe rotational alignment, were obtained. With circularly polarised light, the rank one p^{1}_1-(&theta;) renormalised PDDCSs describing rotational orientation were determined. The collision induced alignment in NO(X)--Xe scattering was found to be well reproduced by classical and impulsive theories, highlighting the fact that the alignment is dominated by the propensity for the projection of <b>j</b> onto the kinematic apse to be conserved. The attractive part of the potential does augment the alignment renormalised PDDCSs, and this is most evident in states with strong features of the attractive part of the potential such as ℓ-type rainbows. The orientation is more strongly influenced by the attractive part of the potential and is also influenced by parity. In addition to the parity effect, there exist two limiting classical mechanisms which govern the orientation, one caused by attraction and the other repulsion. Finally, the bond axis of the NO(X) can be oriented by means of hexapole state selection combined with adiabatic orientation using a set of guiding rods. The integral steric effect, an <b>r</b>-<b>k</b> correlation, was measured for the NO(X)--Kr and NO(X)--Ar spin-orbit changing systems. There are large oscillations in the sign of the steric asymmetry which occur for scattering with the various rare gases. There are also large differences between the rare gases as the potentials become more attractive, and more isotropic. The steric asymmetry is well reproduced by quantum mechanics, however, a classical mechanism becomes dominant at high &Delta;j.

Dissertation

The overall goal of my work was to develop and apply new chemical methods for the study of epigenetic DNA and protein modifications. In Chapter 3 the development of Suzuki-Miyaura cross coupling (SMcc) for the post-synthetic modification of DNA is described. DNA modification by SMcc is efficient (4-6h) and proceeds under mild conditions (37°C, pH 8.5). The incorporation of various groups useful for biological investigations is demonstrated using this methodology. Using a photocrosslinker, introduced into the DNA by SMcc capture experiments are performed to identify potential binding partners of modified DNA. In Chapter 4 a dehydroalanine (Dha) based chemical protein modification method is described that enables the introduction of posttranslational modification (PTM) mimics into histones. The PTM mimics introduced by this method are tested using western- and dot-blot and binding and enzymatic assays, confirming they function as mimics of the natural modifications. Chapter 5 describes the use of a generated PTM mimics to elucidate the function of O-linked β-Nacetylglucosamine (GlcNAc) of histones in transcriptional regulation. It is shown that GlcNAcylation of Thr-101 on histone H2A can destabilize nucleosome by modulating the H2A/B dimer – H3/H4 tetramer interface. N- and C-terminal histone tails play an important role in transcriptional regulation. In Chapter 6, nuclear magnetic resonance is used to investigate the structure of the histone H3 N-terminal tail in a nucleosome. The H3 tail, while intrinsically disordered, gains some α-helical character and adopts a compact conformation in a nucleosome context. This H3 tail structure is shown to be modulated by Ser-10 phosphorylation. The effect of a new covalent DNA modification, 5- hydroxymethylcytosine (5hmC), on transcription factor binding is investigated in Chapter 7. 5hmC influences HIF1α/β, USF and MAX binding to their native recognition sequence, implying involvement of this modification in epigenetic regulation.

Macromolecular transitions such as conformational changes and protein-protein association underlie many biological processes. Conformational changes in the N-terminal domain of the transmembrane protein DsbD (nDsbD) were studied by NMR and molecular dynamics (MD) simulations. nDsbD supplies reductant to biosynthetic pathways in the oxidising periplasm of Gram-negative bacteria after receiving reductant from the C-terminal domain of DsbD (cDsbD). Reductant transfer in the DsbD pathway happens via protein-protein association and subsequent thiol-disulphide exchange reactions. The cap loop shields the active-site cysteines in nDsbD from non-cognate oxidation, but needs to open when nDsbD bind its interaction partners. The loop was rigid in MD simulations of reduced nDsbD. More complicated dynamics were observed for oxidised nDsbD, as the disulphide bond introduces frustration which led to loop opening in some trajectories. The simulations of oxidised and reduced nDsbD agreed well with previous NMR spin-relaxation and residual dipolar coupling measurements as well as chemical shift-based torsion angle predictions. NMR relaxation dispersion experiments revealed that the cap loop of oxidised nDsbD exchanges between a major and a minor conformation. The differences in their conformational dynamics may explain why oxidised nDsbD binds its physiological partner cDsbD much tighter than reduced nDsbD. The redox-state dependent interaction between cDsbD and nDsbD is thought to enhance turnover. NMR relaxation dispersion experiments gave insight into the kinetics of the redox-state dependent interaction. MD simulations identified dynamic encounter complexes in the association of nDsbD with cDsbD. The mechanism of the conformational changes in the transport cycle of LacY were also investigated. LacY switches between periplasmic open and cytoplasmic open conformations to transport sugars across the cell membrane. Two mechanisms have been proposed for the conformational change, a rocker-switch mechanism based on rigid body motions and an “airlock” like mechanism in which the transporter would switch conformation via a fully occluded structure. In MD simulations using the novel dynamics importance sampling approach such a fully occluded structure was found. The simulations argued against a strict “rocker-switch” mechanism.