Physical Sciences and Mathematics Commons^™

Time-Resolved, Near Atomic Resolution Structural Studies At The Free Electron Laser, Jason James Tenboer

Theses and Dissertations

Time-resolved serial femtosecond crystallography (TR-SFX) employs X-ray free electron lasers (XFELs) to provide X-ray pulses of femtosecond (fs) duration with 1012 photons per pulse. These XFELs are more than a billion times more brilliant than 3rd generation synchrotron X-ray sources. For structure determination, protein crystals on the micrometer length scale (microcrystals) are injected into the X-ray beam and the resulting diffraction patterns are recorded on fast-readout pixel detectors. Although these intense pulses deposit enough energy to ultimately destroy the protein, the processes that lead to diffraction occur before the crystal is destroyed. This so-called diffraction-before-destruction principle overcomes radiation damage, which …

Porphyrin As A Spectroscopic Probe Of Net Electric Fields In Heme Proteins, Hannah Elizabeth Wagie

Theses and Dissertations

Heme proteins have diverse functions as well as varied structures but share the same organic, conjugated cofactor. Similarly varied approaches have been taken to deduce how heme can take on different roles based on its protein environment. A unique approach is to view the protein matrix as a constellation of point charges that generates a defined, reproducible, net internal electric field that has influence over the electronic properties of the heme cofactor. This work considers how porphyrins, the basic chromophore building block of heme, can be used as a native spectroscopic sensor of internal electric field at the active site …

Theoretical Investigation Of Interactions And Relaxation In Biological Macromolecules, Koki Yokoi

Theses and Dissertations

One of the major challenges posed to our quantitative understanding of structure, dynamics, and function of biological macromolecules has been the high level of complexity of biological structures. In the present work, we studied interactions between G protein-coupled receptors (GPCRs), and also introduced a theoretical model of relaxation in complex systems, in order to help understand interactions and relaxation in biological macromolecules.

GPCRs are the largest and most diverse family of membrane receptors that play key roles in mediating signal transduction between outside and inside of a cell. Oligomerization of GPCRs and its possible role in function and signaling currently …

Hyperpolarized 129xe Magnetic Resonance Imaging Of Radiation-Induced Lung Injury, Ozkan Doganay

Electronic Thesis and Dissertation Repository

Lung cancer is the largest contributor to cancer-related mortality worldwide. Only 20% of stage III non-small cell lung cancer patients survive after 5-years post radiation therapy (RT). Although RT is an important treatment modality for lung cancer, it is limited by Radiation-Induced Lung Injury (RILI). RILI develops in two phases: (i) the early phase (days-weeks) referred to radiation pneumonitis (RP), and (ii) the late phase (months). There is a strong interest in early detection of RP using imaging to improve outcomes of RT for lung cancer. This thesis describes a promising approach based on ¹²⁹Xe gas as a contrast …

Biophysical Characterization Of A De Novo Elastin, Kelly Nicole Greenland

Dissertations, Theses, and Capstone Projects

Natural human elastin is found in tissue such as the lungs, arteries, and skin. This protein is formed at birth with no mechanism present to repair or supplement the initial quantity formed. As a result, the functionality and durability of elastin's elasticity is critically important. To date, the mechanics of this ability to stretch and recoil is not fully understood. This study utilizes de novo protein design to create a small library of simplistic versions of elastin-like proteins, demonstrate the elastin-like proteins, maintain elastin's functionality, and inquire into its structure using solution nuclear magnetic resonance (NMR).

Elastin is formed from …

Photoacoustic Calorimetry Studies Of The Earliest Events In Horse Heart Cytochrome-C Folding, Tarah A. Word

USF Tampa Graduate Theses and Dissertations

The protein folding problem involves understanding how the tertiary structure of a protein is related to its primary structure. Hence, understanding the thermodynamics associated with the rate-limiting steps for the formation of the earliest events in folding is most crucial to understanding how proteins adopt native secondary and tertiary structures. In order to elucidate the mechanism and pattern of protein folding, an extensively studied protein, Cytochrome-c (Cc), was chosen as a folding system to obtain detailed time-resolved thermodynamic profiles for the earliest events in the protein folding process. Cytochrome-c is an ideal system for understanding the folding process for several …

Engineering Photosystem I Complexes For Use In Bio-Hybrid Dye-Sensitized Solar Cells, Richard Franklin Simmerman

Doctoral Dissertations

Increasing global population, growing per capita energy needs, diminishing fossil fuels, and climate change collectively will require new, innovative, and sustainable alternatives to meet the world’s growing energy needs. One of the most promising yet simple approaches are dye-sensitized solar cells (DSSCs). However, conventional DSSCs use semi-conductor anodes sensitized with complex synthetic organometallic dyes. Most dyes utilize ruthenium complexes to absorb photons, which upon excitation, inject electrons into the anode, while holes migrate to the cathode via liquid electrolyte. However, these dyes are expensive, difficult to make, and resource-limited. This dissertation focuses on replacing synthetic dyes with the naturally occurring, …

Computational Modeling Of Rna-Small Molecule And Rna-Protein Interactions, Lu Chen

Dissertations & Theses (Open Access)

The past decade has witnessed an era of RNA biology; despite the considerable discoveries nowadays, challenges still remain when one aims to screen RNA-interacting small molecule or RNA-interacting protein. These challenges imply an immediate need for cost-efficient while predictive computational tools capable of generating insightful hypotheses to discover novel RNA-interacting small molecule or RNA-interacting protein. Thus, we implemented novel computational models in this dissertation to predict RNA-ligand interactions (Chapter 1) and RNA-protein interactions (Chapter 2).

Targeting RNA has not garnered comparable interest as protein, and is restricted by lack of computational tools for structure-based drug design. To test the potential …

Designing Fret Assays To Study Electrostatic Interactions Pertaining To The Binding Of Intrinsically Disordered Proteins, Ashley Ann Howard

Graduate Theses and Dissertations

Fibroblast growth factor receptor plays a major role in several biological processes. Without FGFR, a human cannot live. FGFR is involved in cell differentiation and wound healing. Of course, if FGFR signaling becomes unregulated, it causes severe distress in the body. Several cancers are contributed to high signaling levels, as well as developmental conditions like rickets and Kallmann’s syndrome. FGFR is thought to undergo an auto-inhibition (or self-regulatory) process in order to try to facilitate regulation. The exact method of this inhibition is currently unknown, but is proposed to involve the unstructured acid box region of FGFR. We developed a …

Mirror Buckling Transitions In Freestanding Graphene Membranes Induced Through Scanning Tunneling Microscopy, James Kevin Schoelz

Graduate Theses and Dissertations

Graphene has the ability to provide for a technological revolution. First isolated and characterized in 2004, this material shows promise in the field of flexible electronics. The electronic properties of graphene can be tuned by controlling the shape of the membrane. Of particular interest in this endeavor are the thermal ripples in graphene membranes. Years of theoretical work by such luminaries as Lev Landau, Rudolf Peierls, David Mermin and Herbert Wagner have established that 2D crystals should not be thermodynamically stable. Experimental research on thin films has supported this finding. Yet graphene exists, and freestanding graphene films have been grown …

The Effect Of Macromolecular Crowding On The Structure Of The Protein Complex Superoxide Dismutase, Ajith Rathnaweera Rajapaksha Mudalige

Open Access Dissertations

Biological environments contain between 7 - 40% macromolecules by volume. This reduces the available volume for macromolecules and elevates the osmotic pressure relative to pure water. Consequently, biological macromolecules in their native environments tend to adopt more compact and dehydrated conformations than those in vitro. This effect is referred to as macromolecular crowding and constitutes an important physical difference between native biological environments and the simple solutions in which biomolecules are usually studied.^ We used small angle scattering (SAS) to measure the effects of macromolecular crowding on the size of a protein complex, superoxide dismutase (SOD). Crowding was induced using …

Quantitative Mrna Detection With Advanced Nonlinear Microscopy, Jing Liu

Open Access Dissertations

Cell-specific information on quantity and localization of key mRNA transcripts in single-cell level are critical to the assessment of cancer risk, therapy efficacy, and effective prevention strategies. While current techniques are not capable to visualize single mRNA transcript beyond the diffraction limit. In this thesis, two nonlinear technologies, second harmonic super-resolution microscopy (SHaSM) and transient absorption microscopy (TAM), are developed to detect and quantify single Human edimer receptor 2 (Her2) mRNA transcripts. The SHaSM is used to detect single mRNA transcript beyond the diffraction limit, while the TAM is employed to detect mRNA without the interference of fluorescence background. The …

Development Of Experimental And Instrumental Systems To Study Biological Systems, Amanda J Hemphill

Open Access Dissertations

Chapters 1-4 of this thesis describes the development of an experimental system to measure diffusion-limited reaction kinetics in a biological environment. About 100 years ago, the relationship between reaction rate and diffusion in homogenous solution, ie water or buffer, was described as a linear relationship by Smoluchowski. Applying this theory naively would suggest that since the diffusion coefficients drop by factors of 4-100 then the rates of reaction would drop by the same amount. However, recent theory and simulations suggest that this does not hold. Even though biological diffusion coefficients drop to 0.1-20% of that in buffer, these recent studies …

Evaluating Breast Cancer Stem Cell Response To Antiangiogenic Therapy, Connor J. Holloway

Open Access Theses

Angiogenic inhibitors function by blocking tumor cell signals used to recruit host tissue vasculature to the tumor site, thereby depriving the cancer of the nutriment needed for further expansion. The development and implementation of angiogenic inhibitors in conjunction with standard chemotherapy agents has increased progression-free survival but not overall patient survival. It is hypothesized that chronic exposure to large doses of AAT drugs worsens hypoxic conditions within the tumor mass, selectively stimulating aggressive cancer stem cell populations to grow and proliferate. ^ In this study, the expression of the CSC biomarkers ALDH1, DLL1, and EpCAM were evaluated in breast cancer …

De Novo Design And Engineering Of Functional Metal And Porphyrin-Binding Protein Domains, Bernard Howard Everson

Dissertations, Theses, and Capstone Projects

In this work, I describe an approach to the rational, iterative design and characterization of two functional cofactor-binding protein domains. First, a hybrid computational/experimental method was developed with the aim of algorithmically generating a suite of porphyrin-binding protein sequences with minimal mutual sequence information. This method was explored by generating libraries of sequences, which were then expressed and evaluated for function. One successful sequence is shown to bind a variety of porphyrin-like cofactors, and exhibits light- activated electron transfer in mixed hemin:chlorin e6 and hemin:Zn(II)-protoporphyrin IX complexes. These results imply that many sophisticated functions such as cofactor binding and electron …

Interaction Forces And Reaction Kinetics Of Ligand-Cell Receptor Systems Using Atomic Force Microscopy, Anwesha Sarkar

Wayne State University Dissertations

Atomic Force Microscopy (AFM) provides superior imaging resolution and the ability to measure forces at the nanoscale. It is an important tool for studying a wide range of bio-molecular samples from proteins, DNA to living cells. We developed AFM measurement procedures to measure protein interactions on live cells at the single molecular level. These measurements can be interpreted by using proper statistical approaches and can yield important parameters about ligand-receptor interactions on live cells. However, the standard theory for analyzing rupture force data does not fit the experimental rupture force histograms. Most of the experimental measurements of rupture force data …

Dynamics Of Biopolymers On Nanomaterials Studied By Quasielastic Neutron Scattering And Mdsimulations, Gurpreet Dhindsa

Wayne State University Dissertations

Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, β-Casein and Inorganic Pyrophosphatase (IPPase).

RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and …

Studying Cellular And Molecular Interaction With Two-Photon Fluorescence Microscopy, Arifur Rahaman

Open Access Theses & Dissertations

Advances in microscopy and fluorescent probes provide new insight into studying cellular and molecular interactions. Two-photon fluorescence microscopy is one of the most important recent inventions in cellular and molecular study. This technology enables noninvasive study at cellular and molecular levels in three dimensions with submicrometer resolution. Two-photon excitation of fluorophores results from the simultaneous absorption of two photons. This excitation process has a number of unique advantages, such as reduced specimen photodamage and enhanced penetration depth. In this study, we used our two-photon microscope to observe predatorial behavior of fast moving bacterivorous marine organism Cafeteria roenbergensis and quantify Mycobacterium …

Spread And Interaction Of Epidemics And Information On Adaptive Social Networks, Yunhan Long

Dissertations, Theses, and Masters Projects

The spread of diseases and opinions has profoundly affected the development of human societies. The structure of the underlying social network may change as a result of individuals changing their social connections in response to an ongoing epidemic or opinion spreading, either for self protection or as an expression of personal values. The interaction of spreading processes and the underlying network structure has been a focus of many recent studies. In this dissertation, we construct models to better incorporate heterogeneous responses to disease spread and attempted opinion spread.;We first model the simultaneous spread of an epidemic and awareness about the …

Structure And Stability Of Amyloid Fibrils Studied By Advanced Vibrational Spectroscopy, Marudachalam Shanmugasundaram

Legacy Theses & Dissertations (2009 - 2024)

Protein misfolding often leads to the formation of refractory protein aggregates like amyloid fibrils. These fibrils possess a highly ordered structure and are implicated in over 25 severe diseases including Alzheimer’s, Parkinson’s and prion diseases. This work was focused on understanding the morphology and conformation of amyloid fibrils and their stability after formation. The deconstruction of fibrils as well as other aggregates like inclusion bodies under mild conditions was also investigated using Archaeal chaperones.