Matching Items (13)

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Secondary Structure Adopted by the Gly-Gly-X Repetitive Regions of Dragline Spider Silk

Description

Solid-state NMR and molecular dynamics (MD) simulations are presented to help elucidate the molecular secondary structure of poly(Gly-Gly-X), which is one of the most common structural repetitive motifs found in

Solid-state NMR and molecular dynamics (MD) simulations are presented to help elucidate the molecular secondary structure of poly(Gly-Gly-X), which is one of the most common structural repetitive motifs found in orb-weaving dragline spider silk proteins. The combination of NMR and computational experiments provides insight into the molecular secondary structure of poly(Gly-Gly-X) segments and provides further support that these regions are disordered and primarily non-β-sheet. Furthermore, the combination of NMR and MD simulations illustrate the possibility for several secondary structural elements in the poly(Gly-Gly-X) regions of dragline silks, including β-turns, 3[subscript 10]-helicies, and coil structures with a negligible population of α-helix observed.

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Date Created
  • 2016-12-02

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Modifying and Optimizing 1H NMR for Amino Acid Analysis

Description

The parameters of microwave-assisted acid hydrolysis (MAAH) and 1H NMR highly affect the quantitative analysis of protein hydrolysates. Microwave-induction source, NMR spectral resolution, and data analysis are key parameters in

The parameters of microwave-assisted acid hydrolysis (MAAH) and 1H NMR highly affect the quantitative analysis of protein hydrolysates. Microwave-induction source, NMR spectral resolution, and data analysis are key parameters in the nuclear magnetic resonance – amino acid analysis (NMR-AAA) workflow where errors accrue due to lack of an optimized protocol. Hen egg white lysozyme was hydrolyzed using an 800W domestic microwave oven for varying time points between 10-25 minutes, showing minimal protein hydrolysis after extended time periods. Studies on paramagnetic doping with varying amounts of gadolinium chloride for increased NMR resolution resulted in little T1 reduction in a majority of amino acids and resulted in significant line broadening in concentrations above 1µM. The use of the BAYESIL analysis tool with HOD suppressed 1H-NMR spectra resulted in misplaced template peaks and errors greater than 1% for 10 of 13 profiled amino acids with the highest error being 7.6% (Thr). Comparatively, Chenomx NMR Suite (v7.1) analysis resulted in errors of less than 1% for 9 of 13 profiled amino acids with a highest error value of 3.6% (Lys). Using the optimized protocol, hen egg white lysozyme C was identified at rank 1 with a score of 64 in a Gallus gallus species wide AACompIdent search. This technique reduces error associated with sample handling relative to previously used amino acid analysis (AAA) protocols and requires no derivatization or additional processing of the sample prior to analysis.

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Date Created
  • 2017-05

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A Hydrogen (1H) Nuclear Magnetic Resonance (NMR) Method for Amino Acid Analysis

Description

Amino acid analysis (AAA) of egg white lysozyme and bovine Achilles tendon collagen was performed using 1H solution-state nuclear magnetic resonance (NMR) spectroscopy. The proteins were hydrolyzed in 6M HCL

Amino acid analysis (AAA) of egg white lysozyme and bovine Achilles tendon collagen was performed using 1H solution-state nuclear magnetic resonance (NMR) spectroscopy. The proteins were hydrolyzed in 6M HCL with and without 0.02% phenol at 110\u00B0C for 24, 48, and 72 hours. For both proteins, 18 of 20 amino acids were characterized including hydroxyproline and hydroxylysine in collagen, using 1-dimensional (1D) and 2-dimensional (2D) NMR spectroscopy experiments. Errors ranging from <1% to 8% were seen in treatments with and without phenol. Both proteins could be correctly identified within their own species using the online database search AACompIdent. The proposed approach is a simple analytical technique that does not require the use of column separation or amino acid derivatization prior to compositional analysis.

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Created

Date Created
  • 2014-05

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Characterization of a Lipid Coating on the Surface of Silk Produced by the Embiid Antipaluria urichi

Description

Insects of the order Embiidina spin sheets of very thin silk fibers from their forelimbs to build silken shelters on bark and in leaf litter in tropical climates. Their shelters

Insects of the order Embiidina spin sheets of very thin silk fibers from their forelimbs to build silken shelters on bark and in leaf litter in tropical climates. Their shelters are very stiff and hydrophobic to keep out predators and rain. In this study, the existence of an outer lipid coating on silk produced by the embiid Antipaluria urichi is shown using scanning and transmission electron microscopy, FT-IR, and water drop contact angle analysis. Subsequently, the composition of the lipid layer is then characterized by 1H NMR and GC-MS.

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Date Created
  • 2014-05

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Functional and Structural Studies on Interactions of the Leukocyte Integrin αMβ2 with Cationic Ligands

Description

Integrins are a family of αβ heterodimeric transmembrane receptors. As an important class of adhesion receptors, integrins mediate cell adhesion, migration, and transformation through bidirectional signaling across the plasma membrane.

Integrins are a family of αβ heterodimeric transmembrane receptors. As an important class of adhesion receptors, integrins mediate cell adhesion, migration, and transformation through bidirectional signaling across the plasma membrane. Among the 24 different types of integrins, which are notorious for their capacity to recognize multiple ligands, the leukocyte integrin αMβ2 (Mac-1) is the most promiscuous member. In contrast to other integrins, Mac1 is unique with respect to its preference for cationic ligands. In this thesis, a new Mac-1 cationic ligand named pleiotrophin (PTN) is uncovered. PTN is an important cytokine and growth factor. Its activities in mitogenesis and angiogenesis have been extensively researched, but its function on immune cells was not widely explored. In this research, the cell biology and biochemical evidences show that PTN can regulate various Mac-1-expressing cells functions through the activation of the extracellular signal regulated kinases. Direct interactions between PTN and the αM I-domain, the major ligand-binding domain of Mac-1, has been shown using biolayer interferometry analyses and confirmed by solution NMR spectroscopy. The binding epitopes and the binding mechanism of PTN and αM I-domain interaction were further revealed by peptide array analysis and microscale thermophoresis. The data suggested that PTN’s thrombospondin type-1 repeat (TSR) domains and αM I-domain metal-ion-dependent adhesion site (MIDAS) are the major binding sites. In addition, this interaction followed a novel metal-ion independent binding mechanism which has not been found in other integrins. After a series of characterizations of αM I-domain using both experimental and computational methods, it showed that activated αM I-domain is significantly more dynamic than inactive αM I-domain, and the dynamics seem to modulate the effect of Mg2+ on its interactions with cationic ligands. To further explore the PTN induced Mac-1 structure rearrangement, intact Mac-1 was studied by negative stain electron microscopy. The results showed that the Mac-1 exhibited a very heterogeneous conformation distribution in detergents. In contrast, the Mac-1 adopted predominantly the bent conformation in phospholipid nanodisc condition. This Mac-1 nanodisc model provides a new platform for studying intact Mac-1 activation mechanism in a more physiologically relevant manner in the future.

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Date Created
  • 2020

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Mechanically active heterogeneous polymer matrix composites

Description

An evolving understanding of elastomeric polymer nanocomposites continues to expand commercial, defense, and industrial products and applications. This work explores the thermomechanical properties of elastomeric nanocomposites prepared from bisphenol A

An evolving understanding of elastomeric polymer nanocomposites continues to expand commercial, defense, and industrial products and applications. This work explores the thermomechanical properties of elastomeric nanocomposites prepared from bisphenol A diglycidyl ether (BADGE) and three amine-terminated poly(propylene oxides) (Jeffamines). The Jeffamines investigated include difunctional crosslinkers with molecular weights of 2,000 and 4,000 g/mol and a trifunctional crosslinker with a molecular weight of 3,000 g/mol. Additionally, carbon nanotubes (CNTs) were added, up to 1.25 wt%, to each thermoset. The findings indicate that the Tg and storage modulus of the polymer nanocomposites can be controlled independently within narrow concentration windows, and that effects observed following CNT incorporation are dependent on the crosslinker molecular weight.

Polymer matrix composites (PMCs) offer design solutions to produce smart sensing, conductive, or high performance composites for a number of critical applications. Nanoparticle additives, in particular, carbon nanotubes and metallic quantum dots, have been investigated for their ability to improve the conductivity, thermal stability, and mechanical strength of traditional composites. Herein we report the use of quantum dots (QDs) and fluorescently labeled carbon nanotubes (CNTs) to modify the thermomechanical properties of PMCs. Additionally, we find that pronounced changes in fluorescence emerge following plastic deformation, indicating that in these polymeric materials the transduction of mechanical force into the fluorescence occurs in response to mechanical activation.

Segmented ionenes are a class of thermoplastic elastomers that contain a permanent charged group within the polymer backbone and a spacer segment with a low glass transition temperature (Tg) to provide flexibility. Ionenes are of interest because of their synthetic versatility, unique morphologies, and ionic nature. Using phase changing ionene-based nanocomposites could be extended to create reversible mechanically, electrically, optically, and/or thermally responsive materials depending on constituent nanoparticles and polymers. This talk will discuss recent efforts to utilize the synthetic versatility of ionenes (e.g., spacer composition of PTMO or PEG) to prepare percolated ionic domains in microphase separated polymers that display a range of thermomechanical properties. Furthermore, by synthesizing two series of ionene copolymers with either PEG or PTMO spacers at various ratios with 1,12-dibromododecane will yield a range of ion contents (hard contents) and will impact nanoparticle dispersion.

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Date Created
  • 2019

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Structural Characterization & Glycosaminoglycan Binding of the Small Cytokine Pleiotrophin

Description

The small mitogenic cytokine Pleiotrophin (PTN) is well-known for its roles in

tissue growth, development, and repair. First isolated from neuronal tissues, much interest in this protein resides in development of

The small mitogenic cytokine Pleiotrophin (PTN) is well-known for its roles in

tissue growth, development, and repair. First isolated from neuronal tissues, much interest in this protein resides in development of the central nervous system and neuronal regeneration. Owning to its role in growth, development and its ability to promote angiogenesis and metastasis, PTN’s overexpression in cancers such as glioblastoma, has become the focal point of much research. Many of the receptors through which PTN acts contain glycosaminoglycans (GAGs), through which PTN binds. Thus, understanding the atomistic detail of PTN’s architecture and interaction with GAG chains is of significant importance in elucidating its functional role in growth and malignancy of biological tissues, as well as in neural development and progression of other diseases. Herein the first solution state structure of PTN was solved via nuclear magnetic resonance (NMR), with extensive characterization of its ability to bind GAG. Structurally, PTN consists of two -sheet domains connected by a short flexible linker, and flanked by long flexible termini. Broad distribution of positively charged amino acids in the protein’s sequence yields highly basic surfaces on the -sheet domains as well as highly cationic termini. With GAG chains themselves being linear anionic polymers, all interactions between these sugars and PTN are most exclusively driven through the electrostatic interactions between them, with no discernable specificity for GAG types. Moreover, this binding event is coordinated mostly through basic patches located in the C-Terminal domain (CTD). Although the flexible C- terminus has been shown to play a significant role in receptor binding, data here also reveal an adaptability of PTN to maintain high affinity interactions through its structured domains

when termini are removed. Additionally, analysis of binding information revealed for the first time the presence of a secondary GAG binding site within PTN. It is shown that PTN’s CTD constitutes the major binding site, while the N-terminal domain (NTD) contains the much weaker secondary site. Finally, compilation of high-resolution data containing the atomistic detail of PTN’s interaction with GAG provided the information necessary to produce the highest accuracy model to date of the PTN-GAG complex. Taken together, these findings provide means for specific targeting of this mitogenic cytokine in a wide array of biological applications.

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Date Created
  • 2020

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Investigating beta-sheet nanocrystal ordering and correlation with small-angle X-ray scattering

Description

In disordered soft matter system, amorphous and crystalline components might be coexisted. The interaction between the two distinct structures and the correlation within the crystalline components are crucial to the

In disordered soft matter system, amorphous and crystalline components might be coexisted. The interaction between the two distinct structures and the correlation within the crystalline components are crucial to the macroscopic property of the such material. The spider dragline silk biopolymer, is one of such soft matter material that exhibits exceptional mechanical strength though its mass density is considerably small compare to structural metal. Through wide-angle X-ray scattering (WAXS), the research community learned that the silk fiber is mainly composed of amorphous backbone and $\beta$-sheet nano-crystals. However, the morphology of the crystalline system within the fiber is still not clear. Therefore, a combination of small-angle X-ray scattering experiments and stochastic simulation is designed here to reveal the nano-crystalline ordering in spider silk biopolymer. In addition, several density functional theory (DFT) calculations were performed to help understanding the interaction between amorphous backbone and the crystalline $\beta$-sheets.

By taking advantage of the prior information obtained from WAXS, a rather crude nano-crystalline model was initialized for further numerical reconstruction. Using Markov-Chain stochastic method, a hundreds of nanometer size $\beta$-sheet distribution model was reconstructed from experimental SAXS data, including silk fiber sampled from \textit{Latrodectus hesperus}, \textit{Nephila clavipes}, \textit{Argiope aurantia} and \textit{Araneus gemmoides}. The reconstruction method was implemented using MATLAB and C++ programming language and can be extended to study a broad range of disordered material systems.

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Date Created
  • 2015

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Mixed Polyanion and Clathrate Materials as Novel Materials for Lithium-ion and Sodium-ion Batteries

Description

This work describes the investigation of novel cathode and anode materials. Specifically, several mixed polyanion compounds were evaluated as cathodes for Li and Na-ion batteries. Clathrate compounds composed of silicon

This work describes the investigation of novel cathode and anode materials. Specifically, several mixed polyanion compounds were evaluated as cathodes for Li and Na-ion batteries. Clathrate compounds composed of silicon or germanium arranged in cage-like structures were studied as anodes for Li-ion batteries.

Nanostructured Cu4(OH)6SO4 (brochantite) platelets were synthesized using polymer-assisted titration and microwave-assisted hydrothermal methods. These nanostructures exhibited a capacity of 474 mAh/g corresponding to the full utilization of the copper redox in an conversion reaction. X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) studies were preformed to understand the mechanism and structural changes.

A microwave hydrothermal synthesis was developed to prepare a series compounds based on jarosite, AM3(SO4)2(OH)6 (A = K, Na; M = Fe, V). Both the morphology and electrochemical properties showed a compositional dependence. At potentials >1.5 V vs. Li/Li+, an insertion-type reaction was observed in Na,Fe-jarosite but not in K,Fe-jarosite. Reversible insertion-type reactions were observed in both vanadium jarosites between 1 – 4 V with capacities around 40 - 60 mAh/g. Below 1 V vs. Li/Li+, all four jarosite compounds underwent conversion reactions with capacities ~500 mAh/g for the Fe-jarosites.

The electrochemical properties of hydrogen titanium phosphate sulfate, H0.4Ti2(PO4)2.4(SO4)0.6 (HTPS), a new mixed polyanion material with NASICON structure was reported. A capacity of 148 mAh/g corresponding to2 Li+ insertion per formula unit was observed. XRD and XPS were used to characterize the HTPS before and after cycling and to identify the lithium sites. Evaluation of the HTPS in Na-ion cell was also performed, and a discharge capacity of 93 mAh/g was observed.

A systematic investigation of the role of the processing steps, such as ball-milling and acid/base etching, on the electrochemical properties of a silicon clathrate compound with nominal composition of Ba8Al16Si30 was performed. According to the transmission electron microscope (TEM), XPS, and electrochemical analysis, very few Li atoms can be electrochemically inserted, but the introduction of disorder through ball-milling resulted in higher capacity, while the oxidation layer made by the acid/base treatment prevented the reation. The electrochemical property of germanium clathrate was also investigated, unlike the silicon clathrate, the germanium one underwent a conversion reaction.

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Date Created
  • 2017

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Identification of structural mechanisms that modulate glycosaminoglycan affinity in various strains of decorin binding protein A

Description

Glycosaminoglycans (GAGs) are a class of complex biomolecules comprised of linear, sulfated polysaccharides whose presence on cell surfaces and in the extracellular matrix involve them in many physiological phenomena as

Glycosaminoglycans (GAGs) are a class of complex biomolecules comprised of linear, sulfated polysaccharides whose presence on cell surfaces and in the extracellular matrix involve them in many physiological phenomena as well as in interactions with pathogenic microbes. Decorin binding protein A (DBPA), a Borrelia surface lipoprotein involved in the infectivity of Lyme disease, is responsible for binding GAGs found on decorin, a small proteoglycan present in the extracellular matrix. Different DBPA strains have notable sequence heterogeneity that results in varying levels of GAG-binding affinity. In this dissertation, the structures and GAG-binding mechanisms for three strains of DBPA (B31 and N40 DBPAs from B. burgdorferi and PBr DBPA from B. garinii) are studied to determine why each strain has a different affinity for GAGs. These three strains have similar topologies consisting of five α-helices held together by a hydrophobic core as well as two long flexible segments: a linker between helices one and two and a C-terminal tail. This structural arrangement facilitates the formation of a basic pocket below the flexible linker which is the primary GAG-binding epitope. However, this GAG-binding site can be occluded by the flexible linker, which makes the linker a negative regulator of GAG-binding. ITC and NMR titrations provide KD values that show PBr DBPA binds GAGs with higher affinity than B31 and N40 DBPAs, while N40 binds with the lowest affinity of the three. Work in this thesis demonstrates that much of the discrepancies seen in GAG affinities of the three DBPAs can be explained by the amino acid composition and conformation of the linker. Mutagenesis studies show that B31 DBPA overcomes the pocket obstruction with the BXBB motif in its linker while PBr DBPA has a retracted linker that exposes the basic pocket as well as a secondary GAG-binding site. N40 DBPA, however, does not have any evolutionary modifications to its structure to enhance GAG binding which explains its lower affinity for GAGs. GMSA and ELISA assays, along with NMR PRE experiments, confirm that structural changes in the linker do affect GAG-binding and, as a result, the linker is responsible for regulating GAG affinity.

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Date Created
  • 2015