Chemistry Commons^™

Bioinformatic And Biophysical Analyses Of Proteins, Jonathan Catazaro

Department of Chemistry: Dissertations, Theses, and Student Research

The prevailing dogma in structural genomics is the existence of a strong correlation between protein sequence, structure, and biological function. Proteins with high sequence similarity typically have a similar, if not the same, structure and function. In many cases this logic can fail due to distantly related proteins having very low sequence similarity, a lack of a representative structure, structural novelty, or the absence of a characterized function. Further, the paradigm fails to account for dynamics, which have a significant effect on structural stability and enzymatic efficacy.

Nuclear magnetic resonance (NMR) spectroscopy is uniquely capable of solving the structure, assisting …

The Intersection Of Nuclear Magnetic Resonance And Quantum Chemistry, Yali Wang

Department of Chemistry: Dissertations, Theses, and Student Research

Nuclear Magnetic resonance and quantum chemistry have been recognized to be strong tools for probing the structure and dynamics of molecules to further solve chemistry and biological problems. Chemical shift measured by NMR experiment and chemical shielding, molecular energy and molecular structure calculated by quantum chemistry provide extensive information.

Exact analytic gradients, are obtained for cavitation, dispersion and repulsion energies and time-dependent density functional theory for the continuum solvation model, which could be used to probe the structure, dynamics and properties of molecules. Copper in Cu_A azurin is recognized to be coordinated by a structure water molecule by comparing …

Application Of Nuclear Magnetic Resonance Based Metabolomics To Study The Central Metabolism Of Staphylococci, Bo Zhang

Department of Chemistry: Dissertations, Theses, and Student Research

Metabolomics studies the collection of small molecules (metabolites) involved in enzymatically catalyzed reactions, cell signaling and cellular structure. Perturbations in metabolite concentrations have been used to reflect the activity of corresponding enzymes or proteins. Nuclear magnetic resonance (NMR) spectroscopy is a well-known approach for the structure determination of biological macromolecules. Alternatively, NMR has recently been established as a valuable tool of metabolomics, in which NMR spectral signals correlate small molecules with cellular activities. This has been accomplished through the chemometric analysis of high-throughput one dimensional ¹H spectra (metabolic fingerprinting) and quantitative metabolite identification based on two dimensional ¹H, …

The Development And Applications Of Nmr Metabolomics Analysis Of Bacterial Metabolomes, Steven M. Halouska

Department of Chemistry: Dissertations, Theses, and Student Research

Metabolomics is a relatively new field that involves the study of metabolic responses that are occurring within a biological system. Metabolite profiles of an organism, tissue extract, and biofluids are important indicators to determine the physiological state of a biological profile. Comparison of such profiles from different phenotypes can be used to identify specific metabolic changes leading to the understanding of metabolic pathways, disease progression, drug toxicity and efficacy, and cellular responses to different intracellular and extracellular conditions. Metabolomics investigations often use sophisticated analytical techniques such as NMR spectroscopy to provide an unbiased and comprehensive approach to evaluate metabolic perturbation …

Utilizing Nmr Spectroscopy And Molecular Docking As Tools For The Structural Determination And Functional Annotation Of Proteins, Jaime Stark

Department of Chemistry: Dissertations, Theses, and Student Research

With the completion of the Human Genome Project in 2001 and the subsequent explosion of organisms with sequenced genomes, we are now aware of nearly 28 million proteins. Determining the role of each of these proteins is essential to our understanding of biology and the development of medical advances. Unfortunately, the experimental approaches to determine protein function are too slow to investigate every protein. Bioinformatics approaches, such as sequence and structure homology, have helped to annotate the functions of many similar proteins. However, despite these computational approaches, approximately 40% of proteins still have no known function. Alleviating this deficit will …

Experimental And Theoretical Studies In Nuclear Magnetic Resonance, John D. Persons

Department of Chemistry: Dissertations, Theses, and Student Research

Nuclear Magnetic Resonance (NMR) has proven to be an excellent tool to probe the structure of molecules by gaining insight into nuclear interactions. Used in conjunction with theoretical calculations, NMR has the potential to elucidate these nuclear interactions and how they affect structure, bonding and dynamics on a molecular scale. The first two projects presented herein study the peroxide explosive hexamethylene triperoxide diamine (HMTD). In the first project, we use the characteristics of the solid-state NMR lineshape to determine the ¹⁴N quadrupole coupling constant (C_Q). The second project uses multi-dimensional solution-state NMR and chiral shift reagents …

Experimental And Theoretical Studies In Solid-State Nuclear Magnetic Resonance, Monica N. Kinde

Department of Chemistry: Dissertations, Theses, and Student Research

Solid-state nuclear magnetic resonance (SSNMR) has proven to be a powerful tool for probing molecular structure and dynamics. Deuterium SSNMR is particularly useful due to the presence of anisotropic interactions whose motional averaging contributes structural and dynamical insight. The magnitude and type of molecular motion can be determined from analysis of solid echo deuterium lineshapes and/or relaxation studies. This work uses various applications of solid-state NMR as well as ab initio and density functional computational methods to study three different areas of physical chemistry: biophysical chemistry, materials science and fundamental concepts of physical chemistry. The first project addressed the dynamics …

Nuclear Magnetic Resonance Affinity Screening Methods For Functional Annotation Of Proteins And Drug Discovery, Matthew D. Shortridge Phd

Department of Chemistry: Dissertations, Theses, and Student Research

With nearly 1,350 complete genome sequences available our understanding of biology at the molecular level has never been more complete. A consequence of these sequencing projects was the discovery of large functionally unannotated segments of each genome. The genes (and proteins they encode) found in these unannotated regions are considered “hypothetical proteins”. Current estimates suggest between 12%-50% of the known gene sequences are functionally unannotated. Incomplete functional annotation of the various genomes significantly limits our understanding of biology. Pragmatically, identifying the functions of these proteins could lead to new therapeutics; making functional annotation of paramount importance.

This dissertation describes the …