Browsing by Subject "crystallography"

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    Structural Biology for Drug Design: Applications in Two Systems
    (2016-08) Maize, Kimberly
    Two projects comprise this dissertation; both are focused on using the technique of protein X-ray crystallography to understand the molecular interactions that small molecules make with proteins and the subsequent exploitation of these interactions to design better substrate or inhibitor molecules. The human Histidine Triad Nucleotide Binding Proteins (hHints) are a family of nucleotide phosphoramidases and acyl nucleotide hydrolases, coming to the forefront of research interest due to the role of hHint1 in the activation of sofosbuvir, the blockbuster Hepatitis C treatment. In the hHint project, protein-ligand complexes are examined in order to establish a structural reaction trajectory, including the first captured covalent intermediate for this enzyme, and to describe a general strategy for designing a prodrug moiety that will be activated by hHint1. The Lethal Factor (LF) component of the tripartite toxin produced by Bacillus anthracis is a zinc metalloproteinase. To date, there is no approved inhibitor of this protein for the treatment of anthrax infection partially due to difficulty in obtaining selectivity over endogenous metalloproteinases. A series of hydroxamate-containing inhibitors revealed that Domain 3 of LF is responsive to the molecule in the active site and that certain states of Domain 3 may be energetically favorable to target. Furthermore, a ligand-induced extension of the canonical binding area was discovered, paving the way for the development of more specific LF inhibitors.
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    Structural Investigation of Electron-Beam Sensitive Zeolites and Metal-Organic-Frameworks Using Analytical Transmission Electron Microscopy
    (2018-08) Kumar, Prashant
    An interesting class of materials that has become ubiquitous in our daily lives is the family of zeolites, which are porous scaffolds made of silicon, oxygen and aluminum atoms. Zeolites act like a coffee filter paper with pores of molecular dimensions that can be tailored to separate molecules of different diameters by adjusting the sizes of the pore openings from 2 Å (1 Å = 0.0000000001 m) to 10 Å. For example, over 90% of commercially available detergents contain zeolites, which act as water softeners by selectively removing calcium and magnesium ions from water, while any product that can be traced back to a petrochemical refinery (like fuels, chemicals and pharmaceutics) contains molecules that have passed through selective zeolite pores numerous times. To date, 231 unique zeolite frameworks have been synthesized while computer simulations predict over 330,000 new structures. TEM imaging and electron diffraction has contributed in the crystal structure determination of many of the known 231 synthesized zeolite frameworks. However, the recent development of few-atom-thick zeolites (2-dimensional zeolite nanosheets) and new classes of porous materials based on metal-organic-frameworks (MOFs) pose new demands and create new opportunities for electron microscopy. The objective of this dissertation work is to determine the atomic arrangement in zeolite nanosheets and metal organic frameworks using transmission electron microscopy to develop a fundamental relationship between their crystal structure and performance as catalysts and membranes. Using electron diffraction, imaging, spectroscopy and digital image processing, TEM data acquisition and analysis routines have been developed to mitigate electron beam sensitivity of these materials. Implementation of the developed routines enabled crystal structure, growth and defect analysis down to the atomic scale, leading to novel findings and implications discussed in detail here.