ASU Electronic Theses and Dissertations
This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.
In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.
Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.
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- All Subjects: Biochemistry
This dissertation presents on the first time-resolved data set of Photosystem II where structural changes can actually be seen without radiation damage. In order to accomplish this, new crystallization techniques had to be developed so that enough crystals could be made for the liquid jet to deliver a fully hydrated stream of crystals to the high-powered X-ray source. These changes are still in the preliminary stages due to the slightly lower resolution data obtained, but they are still a promising show of the power of this new technique. With further optimization of crystal growth methods and quality, injection technique, and continued development of data analysis software, it is only a matter of time before the ability to make movies of molecules in motion from X-ray diffraction snapshots in time exists. The work presented here is the first step in that process.
WW domains are small modules consisting of 32-40 amino acids that recognize proline-rich peptides and are found in many signaling pathways. We use WW domain sequences to explore protein folding by simulations using Zipping and Assembly Method. We identified five crucial contacts that enabled us to predict the folding of WW domain sequences based on those contacts. We then designed a folded WW domain peptide from an unfolded WW domain sequence by introducing native contacts at those critical positions.
This dissertation presents results towards this end, including the successful implementations of the first diffusive mixing chemoactivated reactions and ultrafast dynamics in the femtosecond regime. The primary focus is on photosynthetic membrane proteins and enzymatic drug targets, in pursuit of strategies for sustainable energy and medical advancement by gaining understanding of the structure-function relationships evolved in nature. In particular, photosystem I, photosystem II, the complex of photosystem I and ferredoxin, and 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase are reported on, from purification and isolation, to crystallogenesis, to experimental design and data collection and subsequent interpretation of results and novel insights gained.
The availability of X-ray free electron lasers presents an opportunity to study micron-sized crystals that could be triggered (using light, small molecules or physical conditions) to capture macromolecules in action. This method of ‘Time-resolved serial crystallography’ answers key biological questions by capturing snapshots of conformational changes associated with multi-step reactions. This dissertation describes approaches for studying structures of large membrane protein complexes. Both macro and micro-seeding techniques have been implemented for improving crystal quality and obtaining high-resolution structures. Well-diffracting 15-20 micron crystals of active Photosystem II were used to perform time-resolved studies with fixed-target Roadrunner sample delivery system. By employing continuous diffraction obtained up to 2 A, significant progress can be made towards understanding the process of water oxidation.
Structure of Photosystem I was solved to 2.3 A by X-ray crystallography and to medium resolution of 4.8 A using Cryogenic electron microscopy. Using complimentary techniques to study macromolecules provides an insight into differences among methods in structural biology. This helps in overcoming limitations of one specific technique and contributes in greater knowledge of the molecule under study.
centers from the bacterium Rhodobacter sphaeroides. I characterized interactions
between a variety of secondary electron donors and modified reaction centers. In Chapter
1, I provide the research aims, background, and a summary of the chapters in my thesis.
In Chapter 2 and Chapter 3, I present my work with artificial four-helix bundles as
secondary electron donors to modified bacterial reaction centers. In Chapter 2, I
characterize the binding and energetics of the P1 Mn-protein, as a secondary electron
donor to modified reaction centers. In Chapter 3, I present the activity of a suite of four
helix bundles behaving as secondary electron donors to modified reaction centers. In
Chapter 4, I characterize a suite of modified reaction centers designed to bind and oxidize
manganese. I present work that characterizes bound manganese oxides as secondary
electron donors to the oxidized bacteriochlorophyll dimer in modified reaction centers. In
Chapter 5, I present my conclusions with a short description of future work in
characterizing multiple electron transfers from a multi-nuclear manganese cofactor in
modified reaction centers. To conclude, my thesis presents a characterization of a variety
of secondary electron donors to modified reaction centers that establish the feasibility to
characterize multiple turnovers from a multi-nuclear manganese cofactor.
The second part of Chapter 1 is discussed about site-specific chemical modification of peptides and proteins. Proteins have been used to generate therapeutic materials, proteins-based biomaterials. To achieve all these properties in protein there is a need for site-specific protein modification.
To be able to successfully monitor biomolecular interaction using AFM there is a need for organic linker molecule which helps one of the investigating molecules to get attached to the AFM tip. Most of the linker molecules available are capable of investigating one type of interaction at a time. Therefore, it is significant to have linker molecule which can monitor multiple interactions (same or different type) at the same time. Further, these linker molecules are modified so that biomolecular interactions can also be monitored using SPR instrument. Described in Chapter 2 are the synthesis of organic linker molecules and their use to study biomolecular interaction through AFM and SPR.
In Chapter 3, N-terminal chemical modification of peptides and proteins has been discussed. Further, modified peptides are attached to DNA thread for their translocation through the solid-state nanopore to identify them. Synthesis of various peptide-DNA conjugates and their nanopore studies have been discussed in this chapter.