Biochemistry, Biophysics, and Structural Biology Commons^™

Amylin Structure, Aggregation, And Pancreatic Β Cell Toxicity, Sharadrao Patil

MCB Articles

In most type 2 diabetes patients, amyloid plaques have been found juxtaposed with membranes of pancreatic β-cells. These plaques are composed of amyloid fibrils of the 37 residue endocrine hormone amylin and cause distinct changes in cell membrane morphology associated with the destruction of β-cells. Research is still ongoing to identify the toxic species involved and the mechanisms by which mature fibrils or oligomers cause cytotoxicity. The projects undertaken were designed to study the molecular structural features of amylin, mechanism of amyloid aggregation and, to develop cytotoxicity inhibitors. We determined the structure of human amylin bound to SDS micelles using …

The Dissolution Of Cellulose In Ionic Liquids - A Molecular Dynamics Study, Barmak Mostofian

Doctoral Dissertations

The use of ionic liquids for the dissolution of cellulose promises an alternative method for the thermochemical pretreatment of biomass that may be more efficient and environmentally acceptable than conventional techniques in aqueous solution. Understanding how ionic liquids act on cellulose is essential for improving pretreatment conditions and thus detailed knowledge of the interactions between solute and solvent molecules is necessary. Here, results from the first all-atom molecular dynamics simulation of an entire cellulose microfibril in 1-butyl-3-methylimidazolium chloride (BmimCl) are presented and the interactions and orientations of solvent ions with respect to glucose units on the hydrophobic and hydrophilic surfaces …

Pore Selectivity And Gating Of Arabidopsis Nodulin 26 Intrinsic Proteins And Roles In Boric Acid Transport In Reproductive Growth, Tian Li

Doctoral Dissertations

Plant nodulin-26 intrinsic proteins (NIPs) are members of the aquaporin superfamily that serve as multifunctional channels of uncharged metabolites and water. They share the same canonical hourglass fold as the aquaporin family. The aromatic arginine (ar/R) selectivity filter controls transport selectivity based on size, hydrophobicity, and hydrogen bonding with substrates. In Arabidopsis thaliana, NIP II subclass proteins contain a conserved ar/R “pore signature” that is composed of Alanine at the helix 2 position (H2), Valine/Isoleucine at the helix 5 position (H5), and an Alanine (LE1) and an invariant Arginine (LE2) at the two loop E positions. In this study, …

Numerical Simulations Of In Vitro Nanoparticle Toxicity – The Case Of Poly(Amido Amine) Dendrimers., Marcus Maher, Pratap Naha, Sourav Prasanna Mukherjee, Hugh Byrne

Articles

A phenomenological rate equation model is constructed to numerically simulate nanoparticle uptake and subsequent cellular response. Polyamidoamine dendrimers (generations 4-6) are modelled and the temporal evolution of the intracellular cascade of; increased levels of reactive oxygen species, intracellular antioxidant species, caspase activation, mitochondrial membrane potential decay, tumour necrosis factor and interleukin generation is simulated, based on experimental observations.

The dose and generation dependence of several of these response factors are seen to well represent experimental observations at a range of time points. The model indicates that variations between responses of different cell-lines, including murine macrophages, human keratinocytes and colon cells, …

Photoelectric Characterization Of Bacteriorhodopsin Reconstituted In Lipid Bilayer Membrane, Joel Kamwa

Graduate Theses and Dissertations

The objective of this work was to conduct basic research in biologically inspired energy conversion solutions. A photosynthetic protein (Bacteriorhodopsin) was reconstituted in a bi-layer membrane. Then, when a laser beam was shined on the membrane, the photon energy was used by the protein to pump protons across the membrane. The translocation of protons across the membrane was measured as photocurrent. For this purpose, a system was built to characterize the lipid bilayer membranes and to measure the photocurrent. The lipid bilayer membrane was characterized by its capacitance and resistance. A picoampere photocurrent was observed when Bacteriorhodopsin protein was present …

Oligomerization Of The Sterile-2 G-Protein Coupled Receptor In Yeast Cells In The Presence And Absence Of Alpha-Factor Pheromone Using Fluorescence Spectroscopy And Forster Resonance Energy Transfer Analysis, Joel David Paprocki

Theses and Dissertations

G-protein-coupled receptors (GPCRs) are the largest family of receptors that respond to a wide variety of extracellular stimuli, including molecular ligands such as odorants, neurotransmitters, and hormones, as well as physical agents sigh as light and pressure. The stimulation event results in initiating conformational changes in the structure of the receptor, which further results in the release of the heterotrimeric G-protein; the latter has a variety of functions within signaling pathways in cellular biology. The GPCR explored in this investigation is the Sterile 2 α-factor receptor (Ste2), whose natural function is that of a yeast mating pheromone receptor. Its natural …

Swarna Ramaswamy_Thesis, Swarna S. Ramaswamy

Dissertations & Theses (Open Access)

STRUCTURAL INVESTIGATIONS OF LIGAND GATED ION CHANNELS

Swarna Ramaswamy, B.S

Advisor: Vasanthi Jayaraman, Ph.D.

Ion channels form an integral part of membrane proteins. In the nervous system including the central and the peripheral nervous system, ligand gated ion channels form a very important part of intercellular communications. They receive chemical signals and convert them to electrical signal, mainly by allowing ion passage across the cell membrane. Ion passage also translates into downstream signaling events. Faithful translation of these signals and transmittance is crucial for several physiological functions, implying that irregular ion channel function could lead to serious consequences.

This thesis …

Measuring The Role Of Inhibition In Auditory Discrimination In Mice, Tazima Nur

Graduate Theses and Dissertations

Understanding how inhibitory neurons affect sensory information processing in the cerebral cortex is an ongoing goal of both neuroscience and statistical physics research. In this master's thesis research project, an experimental system has been designed and built for studying how auditory dynamic range depends on inhibitory neurons, based on observations of mouse behavior. In this thesis, firstly, the topic of inhibition and information processing has been introduced. Then two papers related to inhibition and dynamic range has been reviewed in detail. One of the papers is an experimental work that analyzes the affect of inhibition on dynamic range. The other …

Atom-Based Geometrical Fingerprinting Of Conformal Two-Dimensional Materials, Mehrshad Mehboudi

Graduate Theses and Dissertations

The shape of two-dimensional materials plays a significant role on their chemical and physical properties. Two-dimensional materials are basic meshes that are formed by mesh points (vertices) given by atomic positions, and connecting lines (edges) between points given by chemical bonds. Therefore the study of local shape and geometry of two-dimensional materials is a fundamental prerequisite to investigate physical and chemical properties. Hereby the use of discrete geometry to discuss the shape of two-dimensional materials is initiated.

The local geometry of a surface embodied in 3D space is determined using four invariant numbers from the metric and curvature tensors which …

The Role Of Stem Cells In Adipose Tissue Remodeling., Candice Reshay Holden 1988-

Electronic Theses and Dissertations

The work presented in this dissertation outlines the role of stem cells in the remodeling of adipose tissue under conditions of nutrient excess. Obesity-induced variations in adipose tissue stem cell distribution were uncovered by analysis of the stromal vascular fraction isolated from mice fed a high fat diet for several weeks. Bone marrow cell transplantation was used to determine the derivation of progenitor cells found in adipose tissue; and supplementation of depleted progenitor cell populations achieved via direct cell transplantation, helped to determine the contribution of these progenitor cells to the remodeling process. The dissertation is presented in five chapters …

Acquisition And Reconstruction Techniques For Fat Quantification Using Magnetic Resonance Imaging, Abraam S. Soliman

Electronic Thesis and Dissertation Repository

Quantifying the tissue fat concentration is important for several diseases in various organs including liver, heart, skeletal muscle and kidney. Uniquely, MRI can separate the signal from water and fat in-vivo, rendering it the most suitable imaging modality for non-invasive fat quantification. Chemical-shift-encoded MRI is commonly used for quantitative fat measurement due to its unique ability to generate a separate image for water and fat. The tissue fat concentration can be consequently estimated from the two images. However, several confounding factors can hinder the water/fat separation process, leading to incorrect estimation of fat concentration.

The inhomogeneities of the main …

Guanidinium-Rich Romp Polymers Drive Phase, Charge, And Curvature-Specific Interactions With Phospholipid Membranes, Michael T W Lis

Doctoral Dissertations

Protein transduction domains (PTDs) and their and their synthetic mimics are short sequences capable of unusually high uptake in cells. Several varieties of these molecules, including the arginine-rich Tat peptide from HIV, have been extensively used as vectors for protein, DNA, and siRNA delivery into cells. Despite the wide-ranging utility of PTDs and their mimics, their uptake mechanism is still under considerable debate. How the molecules are able to cross phospholipid membranes, and what structural components are necessary for optimal activity are poorly understood. This thesis explores how PTDMs interact with phospholipid membrane phase, anionic lipid content and negative Gaussian …

Intranuclear Strain Measured By Iterative Warping In Cells Under Mechanical And Osmotic Stress, Jonathan T Henderson

Open Access Dissertations

The nucleus is a membrane bound organelle and regulation center for gene expression in the cell. Mechanical forces transfer to the nucleus directly and indirectly through specific cellular cytoskeletal structures and pathways. There is increasing evidence that the transferred forces to the nucleus orchestrate gene expression activity. Methods to characterize nuclear mechanics typically study isolated cells or cells embedded in 3D gel matrices. Often report only aspect ratio and volume changes, measures that oversimplify the inherent complexity of internal strain patterns. This presents technical challenges to simultaneously observe small scale nuclear mechanics and gene expression levels inside the nuclei of …

Quantum Mechanics In Complex Systems, Ross Douglas Hoehn

Open Access Dissertations

This document should be considered in its separation; there are three distinct topics contained within and three distinct chapters within the body of works. In a similar fashion, this abstract should be considered in three parts. Firstly, we explored the existence of multiply-charged atomic ions by having developed a new set of dimensional scaling equations as well as a series of relativistic augmentations to the standard dimensional scaling procedure and to the self-consistent field calculations. Secondly, we propose a novel method of predicting drug efficacy in hopes to facilitate the discovery of new small molecule therapeutics by modeling the agonist-protein …

Hierarchical Cell Fluid Extracellular Matrix Interaction In Cell Microenvironment, Soham Ghosh

Open Access Dissertations

Hierarchical structural interactions between components of cell microenvironment, the extracellular matrix (ECM), cytoplasm, nucleus and fluid, are important phenomena that decide cell level physiological process and tissue engineering applications. One of those tissue engineering modalities is freezing of biomaterials, important in a wide variety of biomedical applications including cryopreservation and cryosurgeries. In order to design these applications, freezing-induced changes of the cells and tissues and corresponding biophysical mechanisms need to be well understood. Although the effects of freezing on cells in suspension have been extensively studied, the intracellular mechanics of cells embedded in the extracellular matrix (ECM) during freezing are …

Theory For Diffusional Encounters In Heterogeneous Environments And Multivalent Electrolyte Screening Of Charged Interface, Ran Li

Open Access Dissertations

We develop a theory for encounter rates in a three-dimensional system of connected compartments. The model of connected compartments exhibits the length-scale dependent diffusion that is observed in many heterogeneous environments, such as porous catalysts and biological environments. We discovered a dimensionless number that is the dominant scaling variable and obtained, for the first time, an analytical expression for the encounter rate. The new theory generalizes the classic Smoluchowski diffusion limit to the case of heterogeneous environments. The new theory is tested using Brownian dynamics simulations.^ We also experimentally investigated the behavior of multivalent electrolyte near a charged solid-liquid interface. …

Structure-Functionality Relationship Of Collagen Scaffolds For Tissue Engineering, Seungman Park

Open Access Dissertations

Tissue engineering is a promising technology that enables scientists to create artificial organs or replace damaged tissues using animal cells and other components. For successful tissue regeneration, many factors should be taken into account, however, three components are most crucial: cell, scaffold, and soluble factor(s). In order to check the functionality after regeneration of desired tissues, various approaches have been attempted, depending on the physical, biological, and chemical properties of the tissues. Recently, the importance of the extracellular matrix (ECM) microstructure is being considered to be important in this regard. The ECM is closely associated with various functional properties of …

Understanding Preferred Leg Stiffness And Layered Control Strategies For Locomotion, Zhuohua H. Shen

Open Access Dissertations

Despite advancement in the field of robotics, current legged robots still cannot achieve the kind of locomotion stability animals and humans have. In order to develop legged robots with greater stability, we need to better understand general locomotion dynamics and control principles. Here we demonstrate that a mathematical modeling approach could greatly enable the discovery and understanding of general locomotion principles. ^ It is found that animal leg stiffness when scaled by its weight and leg length falls in a narrow region between 7 and 27. Rarely in biology does such a universal preference exist. It is not known completely …

New Experimental And Theoretical Tools For Studying Protein Systems With Elements Of Structural Disorder, Tairan Yuwen

Open Access Dissertations

Disordered proteins are one class of proteins which do not possess well-folded three-dimensional structures as their native conformations. Many eukaryotic proteins have been found to be fully disordered or contain certain disordered regions. Disordered proteins usually display several characteristic properties, such as increased motional freedom and the conformational heterogeneity caused by that. The elements of structural disorder are commonly involved in many important biological functions and are implicated in many diseases. Therefore, the study of disordered proteins has become one of the most important research topics in recent years. This thesis presents results from three different research projects; the common …

Design And Optimization Of A De Novo Protein Charge Separation Dyad, Andrew C. Mutter

Dissertations, Theses, and Capstone Projects

The ever-increasing demand for cheap, plentiful energy to fuel the needs of a growing population requires research into alternative clean energy. Solar irradiation has the potential to power the planet many times over; the challenge is efficient capture and conversion of this energy source. Nature has already solved this problem with photosynthesis, which harvests solar irradiation converting it to stored chemical energy and is the source of the energy for life. The goal of my dissertation is to use de novo designed protein to mimic the charge separation system in photosynthesis. A stable protein scaffold will be designed and used …

Protein Behavior Directed By Heparin Charge And Chain Length, Burcu Baykal Minsky

Doctoral Dissertations

Glycosaminoglycans (GAGs), highly charged biological polyelectrolytes, are of growing importance as biomaterials and pharmaceutical drugs due to their immense range of physiological functions. They bind to many proteins; however, the degree of structural selectivity in GAG-protein interactions is largely unknown .Our studies have focused on the importance of heparin (a model GAG) charge and chain length in protein binding in order to explore its potential applications in biofunctional tissue scaffold materials, as polysaccharide drugs in anticoagulation, and as inhibitory agents in protein aggregation. We used electrospray ionization mass spectrometry, capillary electrophoresis, size exclusion chromatography, dynamic/static light scattering and electrostatic protein …

Heterogeneous Rotational Diffusion Of A Fluorescent Probe In Lipid Monolayers, Christina M. Othon

Christina M Othon

The rotational correlation time of the lipid probe 1-palmitoyl-2-{6-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]hexanoyl}-sn-glycero-3-phosphocholine (NBD-PC) is measured using fluorescence anisotropy for two lipid species. We measure the rotational diffusion in a monolayer of 1,2-Didecanoyl-sn-glycero-3-phosphocholine (DPPC) which displays a phase transition at room temperature from the liquid expanded to the liquid-condensed phase. The constant rotational diffusion of the probe throughout the phase transition reflects the measurement of dynamics in only the liquid-expanded phase. We contrast the dynamic changes during this phase coexistence to the continuous density increase observed in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) at room temperature. We observe a non-exponential decay of the probe diffusion consistent with heterogeneity …

The Effect Of Docosahexaenoic Acid (Dha)-Containing Phosphatidylcholine (Pc) On Liquid-Ordered And Liquid-Disordered Coexistence, Yongwen Gu

Dissertations and Theses

Plasma membranes are essential to both the structure and function of mammalian cells. The first unifying paradigm of membrane structure, the Fluid Mosaic Model, is no longer considered adequate to describe the many non-homogeneous lipid structures that have been observed in both natural and model membranes over the past approximately thirty years. The field of membrane biophysics now appreciates that the complex mixture of different lipid species found in natural membranes produces a range of dynamic, laterally segregated, non-homogeneous structures which exist on time scales ranging from microseconds to minutes.

When sphingomyelin (SM), POPC and cholesterol are all present in …

Applications And Improvements In The Molecular Modeling Of Protein And Ligand Interactions, Jason Bret Harris

Doctoral Dissertations

Understanding protein and ligand interactions is fundamental to treat disease and avoid toxicity in biological organisms. Molecular modeling is a helpful but imperfect tool used in computer-aided toxicology and drug discovery. In this work, molecular docking and structural informatics have been integrated with other modeling methods and physical experiments to better understand and improve predictions for protein and ligand interactions. Results presented as part of this research include:

1.) an application of single-protein docking for an intermediate state structure, specifically, modeling an intermediate state structure of alpha-1-antitrypsin and using the resulting model to virtually screen for chemical inhibitors that can …

Calcium Transport Inhibition, Stimulation, And Light Dependent Modulation Of The Skeletal Calcium Release Channel (Ryr1) By The Prototropic Forms Of Pelargonidin, Thomas Joseph Dornan

Dissertations and Theses

The principle calcium regulator in the muscle cell is the calcium ion release channel (RyR). Improper calcium homeostasis in the muscle cell is the foundation of many pathological states and has been targeted as a contributing factor to ventricular tachycardia, which is known to precede sudden cardiac arrest.

Numerous endogenous and exogenous compounds can affect the way RyR regulates calcium. In this study the anthocyanidin Pelargonidin (Pg), an important natural colorant and dietary antioxidant, is evaluated for its effect on regulating the transport of calcium through the RyR1 of skeletal muscle sarcoplasmic reticulum. Pelargonidin undergoes time dependent structural changes in …

Mirna-21 Has Anti-Inflammatory Effects In The Macrophage Response To Peritonitis., Rebecca Elise Barnett

Electronic Theses and Dissertations

This project investigated the role of miRNA-21 in the macrophage response to peritonitis; with the goal of understanding whether the associated mechanism has potential benefits in the clinical treatment of peritonitis. A novel therapeutic intervention in the treatment of peritonitis could modulate the host immune response to decrease an exaggerated pro-inflammatory innate response and then prevent or ameliorate the development of sepsis and organ failure. We found the following: 1. MiRNA-21 expression increases in peritoneal macrophages after lipopolysaccharide (LPS) stimulation. 2. Over expression of miRNA-21 decreases TNF-a secretion from macrophages after LPS stimulation. Suppression of miRNA-21 expression results in increased …

Using The Microsoft Kinect To Assess Human Bimanual Coordination, Joshua James Liddy

Open Access Theses

Optical marker-based systems are the gold-standard for capturing three-dimensional (3D) human kinematics. However, these systems have various drawbacks including time consuming marker placement, soft tissue movement artifact, and are prohibitively expensive and non-portable. The Microsoft Kinect is an inexpensive, portable, depth camera that can be used to capture 3D human movement kinematics. Numerous investigations have assessed the Kinect's ability to capture postural control and gait, but to date, no study has evaluated it's capabilities for measuring spatiotemporal coordination. In order to investigate human coordination and coordination stability with the Kinect, a well-studied bimanual coordination paradigm (Kelso, 1984, Kelso; Scholz, & …

Developing Crosslinking Constructs Of Protein Kinase R, Prisma E. Lopez

Honors Scholar Theses

Protein Kinase R (PKR) is a key component of the innate immune antiviral response. PKR is activated upon binding to dsRNA. However, recent studies have shown that PKR can also bind to and become activated by duplex RNAs containing complex secondary structure. The mechanism of PKR binding and activation by these RNAs is currently not known. The approach taken here to determine the mechanism of PKR binding by these RNAs is through the development of PKR constructs that are capable of covalently binding to RNAs. Constructs were created by site-specific incorporation of an unnatural, photoactivatable amino acid within PKR. These …

Interactions Of Eukaryotic Translation Initiation Factors And 3' Untranslated Region Of Barley Yellow Dwarf Virus Mrna During Protein Synthesis: A Study Of Equilibrium Binding, Kinetics And Thermodynamics, Bidisha Banerjee

Dissertations, Theses, and Capstone Projects

Eukaryotic initiation factor (eIF) 4F binding to mRNA is the first committed step in cap-dependent protein synthesis. Barley Yellow Dwarf Virus (BYDV) employs a cap-independent mechanism of translation initiation which is mediated by a structural element BTE (BYDV translation element) located in the 3’ UTR of its mRNA. eIF4F bound the BTE and a translational inactive mutant with high affinity; thus questioning the role of eIF4F in translation of BYDV. To examine the effects of eIF4F in BYDV translation initiation, BTE mutants with widely different in vitro translation efficiencies ranging from 5-164% compared to WT were studied. Using fluorescence anisotropy …

Recruitment Of The Ribosomal 40s Subunit To The 3'Untranslated Region Of A Viral Mrna, Via The Eif4 Complex, Facilitates Cap-Independent Translation, Sohani Das Sharma

Dissertations, Theses, and Capstone Projects

Translation of uncapped plant viral RNAs can be facilitated by either an internal ribosomal entry site (IRES) in the 5' untranslated region (UTR) or a cap-independent translation element (CITE) in the 3' UTR. Barley yellow dwarf virus (BYDV) mRNA, which lacks both cap and poly(A) tail, has a translation element (3'BTE) in its 3' UTR that is essential for efficient translation initiation at the 5'-proximal AUG. This mechanism requires binding of the eukaryotic initiation factor 4G (eIF4G) subunit of the heterodimer eIF4F to the 3'BTE and base pairing between the 3'BTE and the 5' UTR. Here we investigate how this …