Biophysics Commons^™

Discrete Davydov's Soliton In Α-Helical Protein Molecule With Anharmonic Hydrogen Bond And Thermal Noise, Frank T. Ndjomatchoua, Clément Tchawoua, Joël D.T. Tchinang, Bruno P. Lerü, Henri E.Z. Tonnang

All Peer-Reviewed Publications

An improvement of the Davydov's model for energy transfer in α-helix protein is proposed. Using hyperbolic cosine potential type to model hydrogen bond potential, we have obtained from the adiabatic approximation, a discrete nonlinear Schrödinger equation with inverse hyperbolic sine nonlinearity. Using the two-dimensional discrete map approach, we have found a linearly stable intrinsic localized mode of the corresponding developed equation. Mobility of the intrinsic localized mode was achieved by moving the local impurity hypothesized as the anomalous band energy. The reactivity of the discrete breather under thermal noise was studied numerically with the Langevin's approach. It was shown that …

Case 62: Glycolysis, The Pentose Phosphate Pathway, And The Citric Acid Cycle In Tumorigenesis, Dr. Kathleen Cornely

Chemistry & Biochemistry Case Studies

Hypoxia-inducible factors are transcription factors that mediate the cellular response to hypoxia (low cellular oxygen concentration) by enhancing or suppressing the transcription of specific genes involved in metabolic pathways.

Feasibility Study Of Inversely-Optimized Intensity Modulated Grid-Therapy For Bulky Lung Tumors, M Macfarlane, J Lam, R Dar, E Yu, K Jordan, Jz Chen

Data and Test Instruments

Purpose/Objective(s): Grid therapy with megavoltage photon beams has been clinically shown to improve local control of bulky tumors. The purpose of this study is to develop intensity modulated grid therapy (IMGT) with multiple beams. We hypothesize that when compared to conventional single-field grid therapy, IMGT will provide lower spatially fractionated doses to the surrounding organs at risk (OAR) while increasing the minimum dose to the whole tumor volume and thus improve tumor control probability as supported by conventionalradiobiology. Materials/Methods: IMGT was developed with multiple photon beams using dynamic MLC segments and orthogonal blocks. Spatially fractionated fluence patterns for all beams …

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 …

The Energy Benefits Of The Pantograph Wing Mechanism In Flapping Flight: Case Study Of A Gull, Gene D. Sattler

Faculty Publications and Presentations

Bird wings generally contain a 4-bar pantograph mechanism in the forearm that enables the wrist joint to be actuated from the elbow joint thus reducing the number of wing muscles and hence reducing the wing inertia and inertial drag. In this paper we develop a theoretical model of inertial power for flapping flight to estimate the advantage of the 4-bar pantograph mechanism by comparing the inertial power required for the case where wrist muscles are present in the forearm with the case where wrist muscles are not present in the forearm. It is difficult to predict how wrist muscles would …

Elucidating The Role Of Hausp Ubiquitin Like Domains In The Catalytic Function Of Usp7, Anuj Patel, Nicole Davis, Andrew Mesecar

The Summer Undergraduate Research Fellowship (SURF) Symposium

Ubiquitin specific proteases (USPs) are a class of enzymes involved in myriad cellular processes. One USP of great interest due to its oncogenic properties is USP7. In normal conditions USP7 is closely regulated due to its responsibility for destabilizing the tumor suppressor, p53, through the deubiquitination of MDM2. In multiple myeloma cases, it appears the regulation of USP7 subsides, as it is largely overexpressed, leading to the inappropriate degradation of p53. Inhibition of USP7 could, therefore, prove a viable target for cancer therapy. A greater understanding of USP7’s function and structure can lead to more insight into how this enzyme …

Gating Mechanisms Of The Canonical Trp Channel Isoform Trpc4, Dhananjay P. Thakur

Dissertations and Theses (Open Access)

Non-selective cation channels formed by Transient Receptor Potential Canonical (TRPC) proteins play important roles in regulatory and pathophysiological processes. These channels are known to be activated downstream from phospholipase C (PLC) signaling. However, the mechanism by which the PLC pathway activates TRPC4/C5 remains unclear. Uniquely, TRPC4 is maximally activated only when two separate G protein pathways, G_q/11 and G_i/o, are co-stimulated, making it a coincidence detector of G_q/11- and G_i/o -coupled receptor activation. Using HEK293 cells co-expressing mouse TRPC4β and selected G protein-coupled receptors, I observed that coincident stimulation of G_i/o proteins and …

Prophylactic Cranial Irradiation Reduces The Incidence Of Brain Metastasis In A Mouse Model Of Metastatic Breast Cancer, Daniel L. Smith

Dissertations and Theses (Open Access)

Prophylactic cranial irradiation (PCI) is a preventative whole-brain irradiation technique used to reduce the incidence of brain metastasis and improve overall survival in select patients with small cell lung cancer and acute lymphoblastic leukemia. A population of breast cancer patients – stage IV, HER2+ or triple-negative – has emerged as having a high risk of developing brain metastases. Because only 10-20% of breast cancer patients diagnosed with brain metastases survive longer than one year, in this high-risk population the benefit of PCI – potential for reduced incidence of brain metastasis and improved overall survival – may outweigh the risks – …

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

Dissertations and 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 …

Removable Shoe Spike System, Alex Adams, Nutech Ventures, Inc.,

Athletic Performance Research

The present system, method and apparatus are adapted for the quick and easy exchange of spikes on athletic shoes. More specifically, the system, apparatus and methods comprise a spike having an opening, an aglet adapted for coupling to the shoe, for example by way of a shoelace, and a coupling head affixed to the aglet which is adapted to couple with the opening on the spike so as to allow a user to quickly and easily replace, remove or install spikes in the athletic shoe. The disclosure thus allows the user to have the tool attached to their shoe at …

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, 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, 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, Cu_B, 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, Avdesh Mishra

LSU 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), 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 …

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 …

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 …

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 …

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 …