Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive,...
Lignocellulosic biomass represents a vast supply of fermentable carbohydrates and functional aromatic compounds. Conversion of lignocellulosics to ethanol and other useful products would be of widespread economical and environmental benefit. Better understanding of the behavior of different lignicellulosic feedstocks in fermentation protocols as well as catalytic activities involved in lignocellulosic...
The primary purpose of this study was to (1) develop methods for the analysis of and (2) provide information on the chemical nature of reducing ends in typical cellulose substrates used for the study of cellulolytic enzymes. The studies were designed such that values obtained for cellulose substrates were compared...
In a relay network for full truckload (TL) transportation, facilities known as relay points (RPs) serve as exchange points where truck drivers can exchange trailers. This would help carriers to assign more regular tours to drivers when compared to the excessively long tours that exist in the traditional Point-to-Point (PtP)...
Peroxiredoxins (Prxs) are dominant peroxide-reducing enzymes with two important roles: they protect all organisms from oxidative damage induced by peroxides, and in eukaryotes, they participate in hydrogen peroxide signaling pathways. This dissertation presents studies aimed at the biophysical characterization of select Prxs and a Prx reductase to elucidate their structure-function...
Four-stranded DNA junctions (also known as Holliday junctions) are structural intermediates involved in a growing number of biological processes including DNA repair, genetic recombination, and viral integration. Although previous studies have focused on understanding the conformational variability and sequence-dependent formation of Holliday junctions in solution there have been relatively few...
A blood supply chain (BSC) deals with the collection, processing, storing, and distribution of blood collected from donors and delivered to patients at demand points (DPs) through a network of several temporary mobile blood units (MBUs) and permanent local blood centers (LBCs). In general, the strategic and tactical design of...
Tan spot of wheat is an economically significant disease caused by the fungal pathogen, Pyrenophora tritici-repentis. Certain races of the fungus secrete Ptr ToxA (ToxA), a 13.2 kDa proteinaceous host-selective toxin that is responsible and sufficient to cause disease in susceptible wheat varieties. Disease symptoms develop only when the ToxA...
Cellooligosaccharides are the reaction intermediates produced during the hydrolysis of cellulose to glucose. Hence, they have the same chemical structure as cellulose, just shorter chain lengths. Cellooligosaccharides up to DP eight are soluble in water. The soluble cellooligosaccharides can be used "as is" in the food industry as non-digestible oligosaccharides...
This thesis includes three studies involving different aspects of modeling protein structure. The first study illustrates the levels of insight available from atomic-resolution protein structures. The second study derives general trends of protein geometry from atomic-resolution structures and shows their implications for modeling. The third study creates a model of...