Biomedical subjects

Joanne I Yeh

Publications and source records attributed to Joanne I Yeh.

9 recordsLinked to original sources

PubMed2006

Comparison of the abilities of ambient and manufactured nanoparticles to induce cellular toxicity according to an oxidative stress paradigm.

Nanomaterial properties differ from those bulk materials of the same composition, allowing them to execute novel activities. A possible downside of these capabilities is harmful interactions with biological systems, with the potential to generate toxicity. An approach to assess the safety of nanomaterials is urgently required. We compared the cellular effects of ambient ultrafine particles with manufactured titanium dioxide (TiO2), carbon black, fullerol, and polystyrene (PS) nanoparticles (NPs). The study was conducted in a phagocytic cell line (RAW 264.7) that is representative of a lung target for NPs. Physicochemical characterization of the NPs showed a dramatic change in their state of aggregation, dispersibility, and charge during transfer from a buffered aqueous solution to cell culture medium. Particles differed with respect to cellular uptake, subcellular localization, and ability to catalyze the production of reactive oxygen species (ROS) under biotic and abiotic conditions. Spontaneous ROS production was compared by using an ROS quencher (furfuryl alcohol) as well as an NADPH peroxidase bioelectrode platform. Among the particles tested, ambient ultrafine particles (UFPs) and cationic PS nanospheres were capable of inducing cellular ROS production, GSH depletion, and toxic oxidative stress. This toxicity involves mitochondrial injury through increased calcium uptake and structural organellar damage. Although active under abiotic conditions, TiO2 and fullerol did not induce toxic oxidative stress. While increased TNF-alpha production could be seen to accompany UFP-induced oxidant injury, cationic PS nanospheres induced mitochondrial damage and cell death without inflammation. In summary, we demonstrate that ROS generation and oxidative stress are a valid test paradigm to compare NP toxicity. Although not all materials have electronic configurations or surface properties to allow spontaneous ROS generation, particle interactions with cellular components are capable of generating oxidative stress.

Animals↗

PubMed2005

Peptergents: peptide detergents that improve stability and functionality of a membrane protein, glycerol-3-phosphate dehydrogenase.

Toward enhancing in vitro membrane protein studies, we have utilized small self-assembling peptides with detergent properties ("peptergents") to extract and stabilize the integral membrane flavoenzyme, glycerol-3-phosphate dehydrogenase (GlpD), and the soluble redox flavoenzyme, NADH peroxidase (Npx). GlpD is a six transmembrane spanning redox enzyme that catalyzes the oxidation of glycerol-3-phosphate to dihydroxyacetone phosphate. Although detergents such as n-octyl-beta-D-glucpyranoside can efficiently solubilize the enzyme, GlpD is inactivated within days once reconstituted into detergent micelles. In contrast, peptergents can efficiently extract and solubilize GlpD from native Escherichia coli membrane and maintain its enzymatic activity up to 10 times longer than in traditional detergents. Intriguingly, peptergents also extended the activity of a soluble flavoenzyme, Npx, when used as an additive. Npx is a flavoenzyme that catalyzes the two-electron reduction of hydrogen peroxide to water using a cysteine-sulfenic acid as a secondary redox center. The lability of the peroxidase results from oxidation of the sulfenic acid to the sulfinic or sulfonic acid forms. Oxidation of the sulfenic acid, the secondary redox center, results in inactivation, and this reaction proceeds in vitro even in the presence of reducing agents. Although the exact mechanism by which peptergents influence solution stability of Npx remains to be determined, the positive effects may be due to antioxidant properties of the peptides. Peptide-based detergents can be beneficial for many applications and may be particularly useful for structural and functional studies of membrane proteins due to their propensity to enhance the formation of ordered supramolecular assemblies.

Catalysis↗

PubMed2005

The effects of flash-annealing on glycerol kinase crystals.

Reflection profiles from glycerol kinase crystals were analyzed to determine the effect of flash-cooling on mosaicity (eta) and peak intensity in order to reveal changes in mosaic domain structure and composition. The results showed that repeated flash-annealing causes a significant decrease in the averaged mosaicity along with an increase in the overall peak counts of reflections and an enhanced signal-to-noise ratio. Individual reflection-profile analysis revealed a mostly dual domain structure, showing the minimization of one domain as a result of flash-annealing.

Crystallization↗

PubMed2005

Nanowiring of a redox enzyme by metallized peptides.

A molecular assembly consisting of a redox enzyme, NADH peroxidase, a metallized double-helical peptide, and a gold nanoparticle immobilized onto a gold wire derivatized with a benzenedithiol compound, initiated and conducted redox signals in the presence of H(2)O(2) and NADH. The current generated by the binding of NADH, the electron donor, was transduced through the molecular assembly with apparently little loss of signal to the solution. The currents measured correlate to an electron transfer rate constant on the order of 3,000 s(-1) within each assembly. This electron transfer rate is two orders of magnitude higher than the endogenous electron transfer rate from NADH to the native enzyme, 27 s(-1). This rate indicates that the metallized peptide is in a conformation conducive for electron transfer and, in conjunction with the redox enzyme, can form effective conduits of electrical signals. This work demonstrates the feasibility of utilizing designed and highly efficient biomolecular assemblies for the production of ultra-sensitive, in-situ biosensors.

Biosensing Techniques↗

PubMed2004

Structures of enterococcal glycerol kinase in the absence and presence of glycerol: correlation of conformation to substrate binding and a mechanism of activation by phosphorylation.

The first structure of a glycerol kinase from a Gram-positive organism, Enterococcus casseliflavus, has been determined to 2.8 A resolution in the presence of glycerol and to 2.5 A resolution in the absence of substrate. The substrate-induced closure of 7 degrees is significantly smaller than that reported for hexokinase, a model for substrate-mediated domain closure that has been proposed for glycerol kinase. Despite the 78% level of sequence identity and conformational similarity in the catalytic cleft regions of the En. casseliflavus and Escherichia coli glycerol kinases, remarkable structural differences have now been identified. These differences correlate well with their divergent regulatory schemes of activation by phosphorylation in En. casseliflavus and allosteric inhibition in E. coli. On the basis of our structural results, we propose a mechanism by which the phosphorylation of a histidyl residue located 25 A from the active site results in a 10-15-fold increase in the activity of the enterococcal glycerol kinase.

Amino Acid Sequence↗

PubMed2003

A manual nanoscale method for protein crystallization.

To overcome one of the major hurdles in three-dimensional crystal structure determination - the requirement for large quantities of purified material to grow crystals - crystallization methodologies have been developed that require only a total of 2-5 microl of a concentrated macromolecular solution to screen more than 100 conditions. These procedures employ a circular slide containing an array of 25 wells designed for crystallization setups in the nanolitre volume range. These 'crystallization slides' fit into the wells of standard crystallization trays. These nanoscale crystallization approaches have been used to reproducibly obtain well diffracting crystals of three proteins, two that are being actively studied (glycerol kinase and NADH peroxidase) and one test protein (lysozyme), using only 40-350 microg (0.04-0.35 mg) of proteins to screen 100 conditions. These nanolitre crystallization methods are easily adapted for the typical laboratory, without the requirement of robotics or expensive equipment.

Crystallization↗

PubMed2002

Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate.

We report the 1.96 A crystal structure of pyridoxine 5'-phosphate synthase (PdxJ) in complex with 1-deoxy-D-xylulose phosphate (dXP). The octameric enzyme possesses eight distinct binding sites, and three different binding states are observed. The observation of these three states supports a mechanism in which precise conformational changes of a peptide loop and groups of active site residues modulate binding and specificity. The differences in protein conformation when one or two substrates are bound can be correlated with a condensation mechanism that leads productively to the formation of pyridoxine 5'-phosphate (PNP). "Snapshots" of the progression from the apo form to a singly occupied "transitional binding" state and, subsequently, to a fully occupied, reactive state are revealed and indicate how the enzyme structure can be related to a plausible catalytic mechanism and, moreover, to favorable energetics of reaction.

Bacterial Proteins↗

PubMed2002

Crystal structures of oxidized and reduced forms of NADH peroxidase.

X-ray structural characterization of cysteine-sulfenic acid-containing proteins is one of the most defining approaches to characterizing this rapidly growing class of protein functional groups. Although outside the scope of this chapter, these structural analyses can lead to kinetic measurements in the crystal that allow intermediate states to be trapped, visualized, and studied. An understanding of the biochemistry of these reactive groups can be more fully gained by studying the localized protein environment in which these groups function. Increased perception of how elements of a protein can stabilize and contribute to modulation of function in these systems will allow novel means of enhancing or inhibiting function in important classes of protein molecules, including transcription factors and redox-regulated enzymes.

Crystallography, X-Ray↗

PubMedDate not supplied

Prediction of membrane proteins in Mycobacterium tuberculosis using a support vector machine algorithm.

We report our finding of linear clustering of signal sequences at the N-terminus of M.tb membrane proteins, directing membrane localization. Although it is widely accepted that membrane proteins have signal peptides at the N-terminus, statistical ensemble analysis of Support Vector Machine prediction results indicate that M.tb membrane proteins have embedded N-terminal sequence patterns beyond the signal peptides previously identified in E. coli. The additional patterns at the N-terminus of M.tb membrane proteins may have correlations to their unique enzymatic functions and unusual characteristics such as membrane interaction in pathogenes.

Algorithms↗