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.

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Next generation sequencing based methods allow us to identify active genes and potential regulatory elements rapidly across the genome, but an outstanding challenge is to unravel which regulatory elements control which genes. This is problematic because regulatory elements control genes over huge distances (over 1 million base pairs) and they have an unpredictable distribution around the genes they influence. In order to enhance transcription the protein complexes at distal regulatory elements make physical contact with the promoter. These interactions can be detected using Chromosome Conformation Capture (3C) technology and the position of regulatory elements can be deduced from these data. However, these methods are either low throughput or low resolution and they are prone to bias. In this 3C techniques were specifically developed to determine the interactions between regulatory elements and gene promoters promoter. The focus has been the development of Next Generation Capture-C, which allows many genetic loci and samples to be analysed simultaneously, with greater sensitivity and accuracy than has previously been possible. High resolution data can be produced from as few as 100,000 cells, and single-nucleotide polymorphisms can be used to generate allele-specific tracks. Nanostring technology has also been developed for analysis of 3C libraries, as this allows interaction profiles to be determined without PCR or sequencing bias. The Nanostring data show remarkable correlation with the interaction profiles generated by NG Capture-C.

The research work presented in this thesis is a consolidated report of experiments aimed at controlling the product selectivity in photochemical reactions. Water soluble hosts such as p-sulfonato calix[n]arenes (n= 6 or 8) and cyclodextrins have been used to solubilize organic molecules in water and to control the product selectivity. These host molecules control the product selectivity by their ability to encapsulate and interact with guest molecules. Furthermore, carrying out reactions in water as solvent is important from green chemistry point of view.

By using the building blocks Mo2(DAniF)3(O2CCH3) (DAniF = N,N'-di-panisylformamidinate) and [Mo2(cis-DAniF)2(NCCH3)4](BF4)2, a series of complexes with multiple dimolybdenum units, bridged by a variety of linkers and having various oxidation states, has been synthesized and studied by various physical and chemical methods. The isomeric neutral diamidate-bridged molecules, α– and β– (DAniF)3Mo2(ArN(O)CC(O)NAr)Mo2(DAniF)3 (Ar = p-anisyl), have been oxidized to give the PF6 salts of the four cations α1+, α2+, β1+, β2+; all four structures together with supporting evidence show that in α1+ and α2+ the unpaired electrons are localized while in β1+ and β2+ they are delocalized in the time scale of these experiments. It is also found that a hydroxide bridged complex having a [Mo2](µ-OH)2[Mo2] core undergoes a oxidative deprotomation, both in solution and in crystals, to a compound with a [Mo2](µ-O)2[Mo2] core. A probable key intermediate with one OH and one O bridge has also been characterized. One electron oxidation of the tetrabridged compounds [Mo2(cis-DAniF)2]2(µ-X)4, where X is a halogen atom (Cl, Br, I), produces a decrease of about 0.24 Å in the separation between the midpoints of the multiply bonded dimolybdenum units. DFT calculations suggest partial bond formation during the oxidation, which is consistent with NIR, EPR and electrochemical measurements. Additionally, a pair of isomeric cyclic triads containing three [Mo2(cis-DAniF)2]2+ units, bridged by six fluoride anions, have been synthesized and crystallographically characterized. The symmetry of the α isomer is C2v because the three [Mo2] units are oriented in two orthogonal directions while that of the other isomer is D3h because the three [Mo2] units are parallel. No direct interconversion between isomers has been detected by heating or irradiation of solutions but oxidation of the α isomer first generates an α+ species that changes to β+. Finally, reaction of [Mo2(cis-DAniF)2(NCCH3)4](BF4)2 and Bun 4NBH4 in ether gives [Mo2(cis-DAniF)2]2(µ-H)4 (14), a compound whose Mo4H4 core may be described as an elongated tetrahedron in which the four H atoms are along the four long edges and the Mo2 units along the short edges.

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The three dimensional structure of a protein is important for its function. When misfolded, a protein may be rendered inactive or adapt a conformation that could be toxic. Studying protein folding requires an understanding of protein conformation. Traditionally, protein conformation has been studied using x-ray crystallography and nuclear magnetic resonance (NMR). X-ray crystallography is limited in the analysis of crystallized proteins and is computationally intensive. NMR deals with proteins in solution but reports only an average of conformation and the technique severely suffers from spectral overlapping due to the thousands of resonances of the protein. More recently, mass spectrometry has been employed not only to elucidate primary structures but also gather information on the three-dimensional conformation of proteins. In this study, a mass spectrometric-based approach is used to study the changes in conformation of cytochrome c and the green fluorescent protein when subjected to aqueous-organic solvent systems. The technique involved trypsin digestion and generation of peptide mass maps. For cytochrome c, the experiments were done with ethanol, methanol and acetonitrile to gain insights on naturation and denaturation. An apparent solvent effect to the rate of digestion and propensity for missed cleavages attributed to weakening of hydrophobic interactions and strengthening of intramolecular hydrogen bonding was observed. For the green fluorescent protein, sulfolane, a known supercharging agent, was used to gain insights on the effect of supercharging to protein conformation. Addition of 2.0% sulfolane shifted the charge state envelope of the protein towards lower m/z while adding lower amounts of sulfolane enhanced lower charge states while broadening the charge state envelope. The time course study showed different patterns of digestion dependent on solvent conditions implying changes in conformation. Furthermore, absorbance and fluorescence measurements suggested that addition of sulfolane protects the fluorophore from quenching. The activity of trypsin is not affected by addition of low amounts of sulfolane.

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