The function of a protein is defined by its three-dimensional structure, and in understanding the three-dimensional structure of a protein, we gain an understanding of its function and mechanism. Protein structures, especially at high resolution, can provide detailed insights into many elements of enzyme function and catalysis – identifying residues...
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...
Peroxiredoxin (Prx) enzymes catalyze the reduction of hydrogen peroxide, peroxynitrous acid, and organic peroxides, and are extremely efficient peroxidases, with k[subscript cat]/K[subscript M] on the order of 10⁷ - 10⁸ M⁻¹ s⁻¹. Besides their role in oxidative stress defense, evidence has accumulated that some eukaryotes, including humans, use Prxs as...
The solution structure determination of DNA molecules has been an important part of structural biology. NMR solution structures are a complement to structures solved via X-ray crystallography; the two methods are the only ways of obtaining three dimensional coordinates of macromolecules. Because of the nature of the molecule, the solution...
We explore the application of deep learning to the disparate fields of natural language processing and computational biology. Both the sentences uttered by humans as well as the RNA and protein sequences found within the cells of their bodies can be considered formal languages in computer science, as sets of...
Ascorbic acid, or vitamin C, is well known as a co-factor for proline-hydroxylase and as an anti-oxidant. However, it is also capable of forming covalent bonds, particularly in the role of a nucleophile, henceforth termed 'ascorbylation'.
The ascorbylation of electrophiles can occur under physiological conditions. Furthermore, there are a number...
Nanoparticles (NPs), defined as materials having at least one dimension (height, width, diameter) in the nanoscale, are increasingly being incorporated into a wide variety of products and are replacing traditional bulk materials in many applications. This is because they can be more efficacious, more sustainable, and can have unique characteristics...