Intrinsically disordered proteins (IDPs) do not form stable tertiary structures like their ordered partners. They exist as heterogeneous ensembles that fluctuate over a time scale. Intrinsically disordered regions and proteins are found across different phyla and exert crucial biological functions. They exhibit transient secondary structures in their free state and become folded upon binding to their protein partners via a mechanism called coupled folding and binding. Some IDPs form alpha helices when bound to their protein partners. We observed a set of cancer associated IDPs where the helical binding segments of IDPs are flanked by prolines on both the sides. Helix-breaking prolines are frequently found in IDPs flanking the binding segment and are evolutionarily conserved across phyla. Two studies have shown that helix flanking prolines modulate the function of IDPs by regulating the levels of disorder in their free state and in turn regulating the binding affinities to their partners. We aimed to study if this is a common phenomenon in IDPs that exhibit similar pattern in the conservation of helix flanking prolines. We chose to test the hypothesis in c-Myb-KIX : IDP-target system in which the disordered protein exhibits high residual helicity levels in its free state. c-Myb is a hematopoietic regulator that plays a crucial role in cancer by binding to the KIX domain of CBP. Studying the functional regulation of c-Myb by modulating the disorder levels in c-Myb and in IDPs in general provides a better understanding of the way IDPs function and can be used in therapeutic strategies as IDPs are known to be involved in regulating various cellular processes and diseases. To study the effect of conserved helix flanking prolines on the residual helicity levels of c-Myb and its binding affinity to the KIX domain of CBP, we mutated the prolines to alanines. Mutating prolines to alanines increased the helicity levels of c-Myb in its free state. This small increase in the helicity levels of a highly helical c-Myb showed almost no effect on the binding affinity between cMyb and KIX. We hypothesized that there is a helical threshold for coupled folding and binding beyond which helicity levels of the free state IDP have no effect on its binding to their ordered protein partner. To test this hypothesis, we mutated solvent exposed amino acid residues in c-Myb that reduce its overall helicity and studied its effect on the binding affinity between c-Myb and KIX. Over a broad range of reduction in helicity levels of the free state did not show an effect on the binding affinity but beyond a certain level, decrease in helicity levels showed pronounced effects on the binding affinity between c-Myb and KIX.

Thesis (Ph. D.)--Ohio State University, 2007. / Title from first page of PDF file. Includes bibliographical references (p. 157-170).

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 143-156).

Thesis (Ph. D.)--University of Missouri-Columbia, 1999. / Typescript. Vita. Includes bibliographical references (leaves 128-134). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 1999. / Typescript. Vita. Includes bibliographical references (leaves 128-134). Also available on the Internet.

Thesis (Ph. D.)--University of California, Riverside, 2008. / Includes abstract. Available via ProQuest Digital Dissertations. Title from first page of PDF file (viewed March 10, 2010). Includes bibliographical references. Also issued in print.

Thesis (Ph. D.)--University of Washington, 2002. / Vita. Includes bibliographical references (leaves 141-161).

Thesis (Ph. D.)--University of Oregon, 2002. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 159-167). Also available for download via the World Wide Web; free to University of Oregon users.

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

This dissertation presents solid-state NMR studies that probe the dynamic and conformational properties of polymers adsorbed on solid surfaces in the dry state. The systems studied include a series of ethylene based random copolymers where the binding group is modified, and two diblock copolymer systems where the blocks have different intrinsic mobilities and surface interactions. The thesis begins by looking at the structures formed by the adsorption of poly (ethylene-co-acrylic acid) (PEA), poly (ethylene- co-vinyl alcohol) (EVOH), poly (ethylene-co-vinyl acetate) (EVA), and polyethylene (PE) on metal oxide powders (zirconia and alumina). NMR spectroscopy, FTIR-PAS, and TGA were used to characterize the surface behaviour of the systems with comparisons made between the bulk and adsorbed copolymers. 13C CPMAS, 1H and T 1 relaxation measurements were all recorded with the aim of correlating the microscopic structure of the surface with changes in NMR data. The chain conformation of adsorbed ethylene copolymers was found to strongly depend on the binding strength of the polar sticker groups with the substrates. / The chain dynamics of adsorbed diblock copolymers in the dry state are reported for the first time. Poly (styrene)-b-poly ( t-butyl acrylate) (PS-PtButA) and poly (styrene)-b-poly (acrylic acid) (PS-PAA) were selected to vary both the block size and the binding strength. Once again the primary surface characterization methods are NMR spectroscopy, FTIR-PAS, and TGA. 13C CPMAS, 1H, T1, and T1rho relaxation measurements were all recorded with the aim of correlating the surface structures with changes in NMR data. For the most part, the observed trends in the chain mobilities of the anchor (PAA) and buoy (PS) blocks with block size can be correlated with the predicted mushroom, intermediate and extended brush structures which collapse upon removal of the solvent. However, the chain mobility of the PS buoys decreases with increasing anchor block size. Although the chain mobility of the PS buoys are moderately enhanced relative to the bulk state, the mobility is sufficiently restricted to comfirm the picture of a thin glassy layer with adhesive properties similar to the surface of bulk polystyrene. / The diblock copolymers poly (2-vinylpyridine), poly (isoprene)- b-poly (2--vinylpyridine), (PI-P2VP) and poly (isoprene)- b-poly (4-vinylpyridine) (PI-P4VP) were selected to complement the PS-PAA system as both systems have been studied by surface force microscopy. The large contrast in chain mobilities of the PI and PVP blocks allowed spectral editing through variation of the 13C cross polarization parameters. The trends in mobility with block size differ from that of PS-PAA in that the segmental mobility of the buoys increases with anchor block size as expected. The chain mobility of the collapsed PI brushes is significantly enhanced as compared to the bulk state, again supporting the interpretation of surface microscopy studies which require an entropically unfavorable flattened, yet rubbery, surface structure.