Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
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- Creators: Barrett, The Honors College
- Creators: Kirian, Richard
Description
The structure-function relation in Biology suggests that every biological molecule has evolved its structure to carry out a specific function. However, for many of these processes (such as those with catalytic activity) the structure of the biomolecule changes during the course of a reaction. Understanding the structure-function relation thus becomes a question of understanding biomolecular dynamics that span a variety of timescales (from electronic rearrangements in the femtoseconds to side-chain alteration in the microseconds and more). This dissertation deals with the study of biomolecular dynamics in the ultrafast timescales (fs-ns) using electron and X-ray probes in both time and frequency domains.
It starts with establishing the limitations of traditional electron diffraction coupled with molecular replacement to study biomolecular structure and proceeds to suggest a pulsed electron source Hollow-Cone Transmission Electron Microscope as an alternative scheme to pursue ultrafast biomolecular imaging. In frequency domain, the use of Electron Energy Loss Spectroscopy as a tool to access ultrafast nuclear dynamics in the steady state, is detailed with the new monochromated NiON UltraSTEM and examples demonstrating this instrument’s capability are provided.
Ultrafast X-ray spectroscopy as a tool to elucidate biomolecular dynamics is presented in studying X-ray as a probe, with the study of the photolysis of Methylcobalamin using time-resolved laser pump – X-ray probe absorption spectroscopy. The analysis in comparison to prior literature as well as DFT based XAS simulations offer good agreement and understanding to the steady state spectra but are so far inadequate in explaining the time-resolved data. However, the trends in the absorption simulations for the transient intermediates show a strong anisotropic dependence on the axial ligation, which would define the direction for future studies on this material to achieve a solution.
It starts with establishing the limitations of traditional electron diffraction coupled with molecular replacement to study biomolecular structure and proceeds to suggest a pulsed electron source Hollow-Cone Transmission Electron Microscope as an alternative scheme to pursue ultrafast biomolecular imaging. In frequency domain, the use of Electron Energy Loss Spectroscopy as a tool to access ultrafast nuclear dynamics in the steady state, is detailed with the new monochromated NiON UltraSTEM and examples demonstrating this instrument’s capability are provided.
Ultrafast X-ray spectroscopy as a tool to elucidate biomolecular dynamics is presented in studying X-ray as a probe, with the study of the photolysis of Methylcobalamin using time-resolved laser pump – X-ray probe absorption spectroscopy. The analysis in comparison to prior literature as well as DFT based XAS simulations offer good agreement and understanding to the steady state spectra but are so far inadequate in explaining the time-resolved data. However, the trends in the absorption simulations for the transient intermediates show a strong anisotropic dependence on the axial ligation, which would define the direction for future studies on this material to achieve a solution.
ContributorsSubramanian, Ganesh (Author) / Spence, John (Thesis advisor) / Rez, Peter (Committee member) / Alford, Terry (Committee member) / Weierstall, Uwe (Committee member) / Kirian, Richard (Committee member) / Arizona State University (Publisher)
Created2016
Description
Protein crystallization is a technique for the formation of three-dimensional protein crystals, which is widely utilized by scientists, engineers, and researchers. Protein crystallography allows for protein structures and functions to be studied. As proteins play a central role in biological systems and life itself, a deeper understanding of their structure-function properties is crucial to elucidating fundamental behaviors, such as protein folding in addition to the role that they play in emerging fields, such as, tissue engineering with application to the emerging field of regenerative medicine. However, a significant limitation toward achieving further advancements in this field is that in order to determine detailed structure of proteins from protein crystals, high-quality and larger size protein crystals are needed. Because it is difficult to produce adequate size, high-quality crystals, it remains difficult to determine the structure of many proteins. However, a new method using a microgravity environment to crystallize proteins has proven effective through various studies conducted on the International Space Station (ISS). In the presence of microgravity, free convection is essentially absent in the bulk solution where crystallization occurs, thus allowing for purely random Brownian motion to exist which favors the nucleation and growth of high-quality protein crystals. Many studies from the ISS to date have demonstrated that growing protein crystals in a microgravity environment produces larger and higher-quality crystals. This method provides new opportunities for better structure identification and analysis of proteins. Although there remains many more limitations and challenges in the field, microgravity protein crystallization holds many opportunities for the future of biotechnology and scientific development. The objective of this thesis was to study the crystallization of hen egg white lysozyme (HEWL) and determine the effects of both unit and microgravity on growth/size and quality of HEWL. Through preliminary trials using a universal ground-based reduced-gravity system, the crystallization of HEWL in a simulated microgravity environment was successfully conducted and the results reported are promising. The utility of continuous, scalable ground-based, microgravity platforms for studies on a wide range of material systems and behavior, such as, protein crystallization, has significant implications regarding its impact on many industries, including drug development as well as regenerative medicine.
ContributorsTran, Amanda Marie (Author) / Pizziconi, Vincent (Thesis director) / Alford, Terry (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12