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by Poon Hoi To. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1981. / Bibliography: leaves 40-41.

by Mok Hing-Yim = 蛋白質結構鬆弛之超聲測量 / 莫慶炎. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1983. / Includes bibliographical references (leaves 76-77). / by Mok Hing-Yim = Dan bai zhi jie gou song chi zhi chao sheng ce liang / Mo Qingyan.

Graduation date: 1997

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Protein-protein and ligand-protein interactions as well as the effect of temperature and applied pressure on protein conformation were investigated by Fourier transform infrared (FTIR) spectroscopy with the use of Fourier self-deconvolution, Fourier derivative, and two-dimensional correlation techniques. The effect of the binding of biotin to avidin on the conformation of the protein was examined. At a biotin concentration of 0.05% (w/v), avidin was stabilized against thermal and pressure-induced denaturation. The IR spectra of avidin recorded as a function of increasing hydrostatic pressure in the presence and the absence of biotin indicated that, in the presence of biotin, avidin adopts a very compact structure in solution. The 2D correlation analysis of the infrared spectra of avidin recorded as a function of increasing temperature over the range of 25--95°C revealed that the protein unfolded via different pathways in the presence and the absence of biotin. Furthermore, the thermally induced conformational changes observed in the absence of biotin were irreversible upon cooling of the protein solution, owing to aggregation of the thermally unfolded protein, whereas in the presence of biotin the protein unfolded and refolded via the same pathway. Variable-temperature FTIR spectroscopy and 2D correlation analysis were also employed to examine correlations between absorptions in the amide I and amide III regions in the spectra of four proteins. The results suggested that the band at 1284 cm-1 in the amide III region may be tentatively assigned to the intermolecular beta-sheet structure formed upon aggregation of thermally unfolded protein. FTIR studies were also conducted to investigate the interaction between the catalytic and regulatory subunits of the enzyme ATCase. The secondary structure of the ATCase holoenzyme was stable up to 60°C. The isolated regulatory subunit denatured at approximately 47°C while the isolated catalytic subunit was thermall

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Although the native conformation of a protein is thermodynamically its most stable form, this stability is only marginal. As a consequence, globular proteins have a certain amount of flexibility in their backbones which allows for conformational changes in the course of their biological function. In the course of this thesis, we study protein models at the edge of stability in different contexts: (1) First, we use molecular dynamics to determine the force needed to rupture a chain molecule (an unfolded protein) being stretched at constant loading rate and temperature. When all energy bonds of the molecule are identical, we find that the force F depends on the pulling rate r and temperature T according to F ~ const -- T 1/3|ln(r/T)|1/3 When a single weak bond is introduced, this result is modified to F ~ const -- T2/3|ln(r/ T)|2/3 This scaling, which is model independent, can be used with force-spectroscopy experiment to quantitatively extract relevant microscopic parameters of biomolecules. (2) Second, we study the structural stability of models of proteins for which the selected folds are unusually stable to mutation, that is, designable. A two-dimensional hydrophobic-polar lattice model is used to determine designable folds and these folds were investigated under shear through Langevin dynamics. We find that the phase diagram of these proteins depends on their designability. In particular, highly designable folds are found to be weaker, i.e. easier to unfold, than low designable ones. This is argued to be related to protein flexibility. (3) Third, we study the mechanism of cold denaturation through constant-pressure simulations for a model of hydrophobic molecules in an explicit solvent. We find that the temperature dependence of the hydrophobic effect is the driving force for cold denaturation. The physical mechanism underlying this phenomenon is identified as the destabilization of hydrophobic contact in favor of solvent separated configurations, the same mechanism seen in pressure induced denaturation. A phenomenological explanation proposed for the mechanism is suggested as being responsible for cold denaturation in real proteins.