Influenza A M2 Protein Conformation Depends On Choice Of Model Membrane,
2015
Swarthmore College
Influenza A M2 Protein Conformation Depends On Choice Of Model Membrane, Kei Saotome , '11, Krisna C. Duong-Ly , '05, Kathleen P. Howard
Chemistry & Biochemistry Faculty Works
While crystal and NMR structures exist of the influenza A M2 protein, there is disagreement between models. Depending on the requirements of the technique employed, M2 has been studied in a range of membrane mimetics including detergent micelles and membrane bilayers differing in lipid composition. The use of different model membranes complicates the integration of results from published studies necessary for an overall understanding of the M2 protein. Here we show using site-directed spin-label EPR spectroscopy (SDSL-EPR) that the conformations of M2 peptides in membrane bilayers are clearly influenced by the lipid composition of the bilayers. Altering the bilayer thickness …
Designing Fret Assays To Study Electrostatic Interactions Pertaining To The Binding Of Intrinsically Disordered Proteins,
2015
University of Arkansas, Fayetteville
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 …
Proton Pumping In Cytochrome C Oxidase,
2015
Graduate Center, City University of New York
Proton Pumping In Cytochrome C Oxidase, Jianxun Lu
Dissertations, Theses, and Capstone Projects
Cytochrome c oxidase (CcO) is a large trans-membrane protein, which is the final enzyme in the respiratory electron transport chain in mitochondria or aerobic bacteria. It implements proton pumping through the mitochondrial membrane against the electrochemical gradient, by utilizing the chemical energy released by reducing O2 to water. The active site of the chemical reaction is called the Binuclear Center (BNC) that is made up of heme a3, CuB, a Tyrosine residue and their ligands. The protein is reduced four times by electron from cytochromes c to reduce O2 and to generate four different …
Three-Dimensional Ideal Gas Reference State Based Energy Function,
2015
University of New Orleans
Three-Dimensional Ideal Gas Reference State Based Energy Function, Avdesh Mishra
University of New Orleans Theses and Dissertations
Energy functions are found to be a key of protein structure prediction. In this work, we propose a novel 3-dimensional energy function based on hydrophobic-hydrophilic properties of amino acid where we consider at least three different possible interaction of amino acid in a 3-dimensional sphere categorized as hydrophilic versus hydrophilic, hydrophobic versus hydrophobic and hydrophobic versus hydrophilic. Each of these interactions are governed by a 3-dimensional parameter alpha used to model the interaction and 3-dimensional parameter beta used to model weight of contribution. We use Genetic Algorithm (GA) to optimize the value of alpha, beta and Z-score. We obtain three …
Pharmacology Of Organic Cation Transporters: Focus On Structure-Function Relationships In Oct3 (Slc22a3),
2015
Washington University in St Louis
Pharmacology Of Organic Cation Transporters: Focus On Structure-Function Relationships In Oct3 (Slc22a3), Dan C. Li
Undergraduate Theses—Unrestricted
Organic Cation Transporters (OCTs) are polyspecific, facilitative transporters that play major roles in metabolite and drug clearance. OCTs are promising drug targets and elucidating their mechanisms of substrate recognition is crucial for rational drug design. OCT-mediated transport of polyvalent cations remains unexplored. OCT-expressing Xenopus laevis oocytes were used to assess transport of polyamines, ubiquitous polyvalent cations of broad physiological import, but for which transport mechanisms are unknown. Dose-response analysis of radiolabelled substrate uptake revealed that polyamines are relatively low affinity, but high turnover substrates for OCTs compared to model substrate methyl-4-phenylpyridinium (MPP+). Polyamine analogs of varying hydrophobic character …
Biophysical Characterization Of Naturally Occurring Titin M10 Mutations,
2015
James Madison University
Biophysical Characterization Of Naturally Occurring Titin M10 Mutations, Michael William Rudloff
Senior Honors Projects, 2010-2019
The giant human muscle proteins titin and obscurin are important for sarcomeric organization, stretch response, and sarcomerogenesis in myofibrils. The extreme C-terminus of titin (the M10 domain) binds to the N-terminus of obscurin (the Ig1 domain) in the M-line, an interaction that is critical for sarcomere stability. The high-resolution structure of human M10 has been solved, along with M10 bound to one of its two known molecular targets, the Ig1 domain of obscurin-like protein. Multiple M10 mutations are linked to limb-girdle muscular dystrophy type 2J (LGMD2J) and tibial muscular dystrophy (TMD), however the effect of the M10 mutations on protein …
Probing Buffer-Specific Effects On Nucleotide Binding To Reca Using Difference Fourier Transform Infrared Spectroscopy,
2015
James Madison University
Probing Buffer-Specific Effects On Nucleotide Binding To Reca Using Difference Fourier Transform Infrared Spectroscopy, Joshua E. Temple
Senior Honors Projects, 2010-2019
The Escherichia coli protein RecA catalyzes the strand exchange reaction used in DNA repair and genetic recombination. RecA is also a target for inhibiting microbial antibiotic resistance, understanding cancer propagation, and characterizing neurodegenerative disorders. Therefore, understanding factors that affect RecA structure and stability is broadly applicable to many fields. Previous studies in our lab have shown buffer-specific changes in RecA stability and unfolding transitions. These studies suggest only minimal buffer-dependent changes in nucleotide binding and secondary structure but do not explain the significant differences in RecA stability and unfolding profiles. Here we have employed various biochemical and spectroscopic techniques to …
Mirror Buckling Transitions In Freestanding Graphene Membranes Induced Through Scanning Tunneling Microscopy,
2015
University of Arkansas, Fayetteville
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 …
In Vitro Studies Of Gold And Gold Silica Nanoparticle Radiosensitization With Kilovoltage X-Rays,
2015
University of Nevada, Las Vegas
In Vitro Studies Of Gold And Gold Silica Nanoparticle Radiosensitization With Kilovoltage X-Rays, Gregory Colarch
UNLV Theses, Dissertations, Professional Papers, and Capstones
Technological advances in the ability to construct and manipulate nanoscale particles have opened up the possibility of using solid metallic nanoparticles and mixed metal nanoshells as a means to increase dose enhancement and treatment efficacy to tumors. In order for nanoparticles to be an effective form of treatment, they must be delivered to tumors in sufficient concentrations so that there is a dose enhancement factor due to ionizing radiation, as well as being essentially non-toxic to healthy cells. Gold nanoparticles and silica-gold nanoshells fit these requirements. Gold has a high atomic number (Z=79), which gives a larger cross section for …
Nmr Spectroscopy Reveals The Presence And Association Of Lipids And Keratin In Adhesive Gecko Setae,
2015
University of Akron Main Campus
Nmr Spectroscopy Reveals The Presence And Association Of Lipids And Keratin In Adhesive Gecko Setae, Dharamdeep Jain, Alyssa Y. Stark, Peter H. Niewiarowski, Toshikazu Miyoshi, Ali Dhinojwala
Polymer Science Faculty Research
Lipid and protein aggregates are one of the fundamental materials of biological systems. Examples include cell membranes, insect cuticle, vertebrate epidermis, feathers, hair and adhesive structures known as ‘setae’ on gecko toes. Until recently gecko setae were assumed to be composed entirely of keratin, but analysis of footprints left behind by geckos walking on surfaces revealed that setae include various kinds of lipids. However, the arrangement and molecular-level behavior of lipids and keratin in the setae is still not known. In the present study we demonstrate, for the first time, the use of Nuclear Magnetic Resonance (NMR) spectroscopy techniques to …
Novel Techniques For Investigating The Regulation Of Skeletal Muscle Hemodynamics,
2015
The University of Western Ontario
Novel Techniques For Investigating The Regulation Of Skeletal Muscle Hemodynamics, Baraa K. Al-Khazraji
Electronic Thesis and Dissertation Repository
The effect of the sympathetic nervous system (SNS) on blood flow distribution within skeletal muscle microvasculature is conditional upon regional activation of SNS receptors. Due to a lack of appropriate experimental models and techniques, no study has systematically evaluated the effect of SNS receptor activation in continuously branching skeletal muscle arteriolar trees. In line with previous work, we hypothesize that there will be a spatially-dependent distribution of sympathetic receptor activation along the arteriolar tree. Specifically, we anticipate a progressive decrease of adrenergic activation and a progressive increase of peptidergic and purinergic activation with increasing arteriolar order. We developed a novel …
The Effect Of Macromolecular Crowding On The Structure Of The Protein Complex Superoxide Dismutase,
2015
Purdue University
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 …
A Novel In Vivo Tumor Oxygen Profiling Assay: Combining Functional And Molecular Imaging With Multivariate Mathematical Modeling,
2015
Purdue University
A Novel In Vivo Tumor Oxygen Profiling Assay: Combining Functional And Molecular Imaging With Multivariate Mathematical Modeling, Chung-Wein Lee
Open Access Dissertations
Purpose: The objective of this study is to develop and test a novel high spatio-temporal in vivo assay to quantify tumor oxygenation and hypoxia. The assay implements a biophysical model of oxygen transport to fuse parameters acquired from in vivo functional and molecular imaging modalities. ^ Introduction: Tumor hypoxia plays an important role in carcinogenesis. It triggers pathological angiogenesis to supply more oxygen to the tumor cells and promotes cancer cell metastasis. Preclinical and clinical evidence show that anti-angiogenic treatment is capable of normalizing the tumor vasculature both structurally and functionally. The resulting normalized vasculature provides a more efficient and …
Quantitative Mrna Detection With Advanced Nonlinear Microscopy,
2015
Purdue University
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 …
Magnetic Manipulation And Multimodal Imaging For Single Cell Direct Mechanosensing,
2015
Purdue University
Magnetic Manipulation And Multimodal Imaging For Single Cell Direct Mechanosensing, Robert L. Wilson
Open Access Theses
The study of internal mechanics of single cells is paramount to understand mechanisms of mechanoregulation. External loading and cell-mediated force generation result in changes in cell shape, rheology, and the deformation of subcellular structures such as the nucleus. Moreover, alterations in the processes that regulate these responses have been further correlated to specific pathologies. Cellular deformation is often studied through application of forces in the environment of the cell, relying on strain and stress transfer through focal adhesions and the cytoskeletal system. However, the transfer of these external forces to internal mechanics can introduce uncertainties in the interpretation of subcellular …
Biochemical Investigation Of The Ubiquitin Carboxyl-Terminal Hydrolase Family,
2015
Purdue University
Biochemical Investigation Of The Ubiquitin Carboxyl-Terminal Hydrolase Family, Joseph Rashon Chaney
Open Access Dissertations
The proteasome is the machinery in eukaryotic cells that degrades protein and recycles the amino acids. Protein degradation is a highly regulated process which starts by the attachment of chains of ubiquitin, which serves as a tag that marks a protein for degradation. This function involves the work of several proteins at the proteasome that work either as ubiquitin chaperones, ubiquitin binders or cleave ubiquitin from the protein that is to be degraded. As this is a highly regulated process, various irregularities can have deleterious effects including the onset of disease, including cardiovascular, cancer, and neurological. ^ The focus of …
Development Of Experimental And Instrumental Systems To Study Biological Systems,
2015
Purdue University
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 …
Structural And Biophysical Analysis Of The Proteasomal Deubiquitinase, Uch37,
2015
Purdue University
Structural And Biophysical Analysis Of The Proteasomal Deubiquitinase, Uch37, Marie Elizabeth Morrow
Open Access Dissertations
Ubiquitin carboxyl-terminal hydrolase 37, or UCH37, is a deubiquitinating enzyme associated with the 26S proteasome, the primary protein degradation machinery in eukaryotic cells. UCH37 is responsible for the disassembly of polymeric ubiquitin chains, or polyubiquitin, which have been ligated onto proteins in order to target them for degradation. The 26S utilizes two associated deubiquitinating enzymes, UCH37 and USP14, and one intrinsic, Rpn11, to remove polyubiquitin chains from substrate proteins as they are unfolded and translocated into the proteolytic core of the proteasome, where proteins are cleaved into small peptides and then released for recycling by the cell. UCH37 associates with …
Evaluating Breast Cancer Stem Cell Response To Antiangiogenic Therapy,
2015
Purdue University
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 …
Towards The Development Of A Maga Reporter Gene Expression Construct For Magnetic Resonance Imaging,
2015
The University of Western Ontario
Towards The Development Of A Maga Reporter Gene Expression Construct For Magnetic Resonance Imaging, Karina Quiaoit
Electronic Thesis and Dissertation Repository
Development of methods to monitor cellular activity with magnetic resonance imaging (MRI) provides a powerful tool for studying disease progression and monitoring therapy. This thesis investigates components necessary for development of reporter gene expression for MRI, to track Nkx2.5 transcription factor activity during tumour growth and, in the future, to calibrate MR contrast against a well-known optical reporter gene, like firefly luciferase. In human MCF-7 breast cancer cells, Nkx2.5 is induced by all-trans retinoic acid (tRA) and activates a minimal promoter of the rat sodium iodide symporter (rNISmin) gene. Here, we used firefly luciferase reporter gene expression to examine a …
