Biochemistry Commons^™

Identification And Quantification Of Gaseous Organic Compounds Emitted From Biomass Burning Using Two-Dimensional Gas Chromatography–Time-Of-Flight Mass Spectrometry, L. E. Hatch, W. Luo, J. F. Pankow, Robert Yokelson, C. Stockwell, K. C. Barsanti

Chemistry and Biochemistry Faculty Publications

The current understanding of secondary organic aerosol (SOA) formation within biomass burning (BB) plumes is limited by the incomplete identification and quantification of the non-methane organic compounds (NMOCs) emitted from such fires. Gaseous organic compounds were collected on sorbent cartridges during laboratory burns as part of the fourth Fire Lab at Missoula Experiment (FLAME-4) and analyzed by two-dimensional gas chromatography-time-of-flight mass spectrometry (GC x GC-ToFMS). The sensitivity and resolving power of GC x GC-ToFMS allowed the acquisition of the most extensive data set of BB NMOCs to date, with measurements from 708 positively or tentatively identified compounds. Estimated emission factors …

The Exchanged Ef-Hands In Calmodulin And Troponin C Chimeras Impair The Ca2+-Induced Hydrophobicity And Alter The Interaction With Orai1: A Spectroscopic, Thermodynamic And Kinetic Study, Drake Jensen, Nicole Reynolds, Ya-Ping Yang, Shubha Shakya, Zhi-Qiang Wang, Dennis J. Stuehr, Chin-Chuan Wei

Chemistry Faculty Research, Scholarship, and Creative Activity

Background

Calmodulin (CaM) plays an important role in Ca²⁺-dependent signal transduction. Ca²⁺ binding to CaM triggers a conformational change, forming a hydrophobic patch that is important for target protein recognition. CaM regulates a Ca²⁺-dependent inactivation process in store-operated Ca²⁺entry, by interacting Orai1. To understand the relationship between Ca²⁺-induced hydrophobicity and CaM/Orai interaction, chimera proteins constructed by exchanging EF-hands of CaM with those of Troponin C (TnC) are used as an informative probe to better understand the functionality of each EF-hand.

Results

ANS was used to assess the context of the induced …

Gamma-Aapeptides As A New Class Of Peptidomimetics: Synthesis, Structures, And Functions, Haifan Wu

USF Tampa Graduate Theses and Dissertations

Peptidomimetics are synthetic oligomers that resemble the activities of peptides. Their advantages over peptides include high stability towards proteolysis and enormous chemical diversity. Over the past two decades, there have been extensive efforts to develop peptide mimics, such as beta-peptides, peptoids, D-peptides, etc. The research on peptidomimetics have led to many important applications in both medicinal and material science. In order to explore new functions, the discovery of peptidomimetics with novel frameworks is essential. We reported the synthesis and evaluation of a new class of peptidomimetics, termed as gamma-AApeptides. Previous studies of gamma-AApeptides have revealed that gamma-AApeptides are highly resistant …

Functional Expression And Characterization Of A Truncated Candida Antarctica Lipase B In Yeast, Samantha Robinson

Theses and Dissertations

Candida antarctica lipase B is an enzyme capable of hydrolyzing ester bonds in a lipid-water interface with potential to become a useful biocatalyst for production of biodiesel fuel. Enzymatically catalyzing the transesterification of triacylglycerides to produce fatty acid alkyl esters (biodiesel) is an environmentally cleaner alternative to the current process which utilizes chemical reagents as catalysts. Optimization and development of strains to express highly active, stable, large quantities of these biocatalysts is essential for inexpensive production of biodiesel. Additionally, lipase enzymes can be immobilized onto a resin, eliminating the need to recover the catalyst from the product and allowing multiple …

Characterization Of Ranbpm Molecular Determinants That Control Its Subcellular Localization, Louisa M Salemi, Sandra O Loureiro, Caroline Schild-Poulter

Biochemistry Publications

RanBPM/RanBP9 is a ubiquitous, nucleocytoplasmic protein that is part of an evolutionary conserved E3 ubiquitin ligase complex whose function and targets in mammals are still unknown. RanBPM itself has been implicated in various cellular processes that involve both nuclear and cytoplasmic functions. However, to date, little is known about how RanBPM subcellular localization is regulated. We have conducted a systematic analysis of RanBPM regions that control its subcellular localization using RanBPM shRNA cells to examine ectopic RanBPM mutant subcellular localization without interference from the endogenously expressed protein. We show that several domains and motifs regulate RanBPM nuclear and cytoplasmic localization. …

The Artificial Divide Between Biomedical Sciences And Clinical Medicine In Undergraduate Medical Education, Abdul Rehman, Noor Ul-Ain Baloch, Muhammad Awais

Department of Biological & Biomedical Sciences

No abstract provided.

Proline Metabolism Increases Katg Expression And Oxidative Stress Resistance In Escherichia Coli, Lu Zhang, James R. Alfano, Donald F. Becker

Department of Biochemistry: Faculty Publications

The oxidation of L-proline to glutamate in Gram-negative bacteria is catalyzed by the proline utilization A (PutA) flavoenzyme, which contains proline dehydrogenase (PRODH) and _1-pyrroline-5-carboxylate (P5C) dehydrogenase domains in a single polypeptide. Previous studies have suggested that aside from providing energy, proline metabolism influences oxidative stress resistance in different organisms. To explore this potential role and the mechanism, we characterized the oxidative stress resistance of wild-type and putA mutant strains of Escherichia coli. Initial stress assays revealed that the putA mutant strain was significantly more sensitive to oxidative stress than the parental wild-type strain. Expression of PutA in the …

Intramolecular S···O Chalcogen Bond As Stabilizing Factor In Geometry Of Substituted Phenyl-Sf3 Molecules, Vincent De Paul Nziko, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Density functional methods are used to examine the geometries and energetics of molecules containing a phenyl ring joined to the trigonal bipyramidal SF3 framework. The phenyl ring has a strong preference for an equatorial position. This preference remains when one or two ether -CH2OCH3 groups are added to the phenyl ring, ortho to SF3, wherein an apical structure lies nearly 30 kcal/mol higher in energy. Whether equatorial or apical, the molecule is stabilized by a S···O chalcogen bond, sometimes augmented by CH···F or CH···O H-bonds. The strength of the intramolecular S···O bond is estimated to lie in the range between …

Synthesis Of Bioinspired Carbohydrate Amphiphiles That Promote And Inhibit Biofilms, Eric L. Dane, Alicia E. Ballok, George A. O'Toole, Mark W. Grinstaff

Dartmouth Scholarship

The synthesis and characterization of a new class of bioinspired carbohydrate amphiphiles that modulate Pseudomonas aeruginosa biofilm formation are reported. The carbohydrate head is an enantiopure poly-amido-saccharide (PAS) prepared by a controlled anionic polymerization of β-lactam monomers derived from either glucose or galactose. The supramolecular assemblies formed by PAS amphiphiles are investigated in solution using fluorescence assays and dynamic light scattering. Dried samples are investigated using X-ray, infrared spectroscopy, and transmission electron microscopy. Additionally, the amphiphiles are evaluated for their ability to modulate biofilm formation by the Gram-negative bacterium Pseudomonas aeruginosa. Remarkably, from a library of eight amphiphiles, we identify …

Conformational Heterogeneity And Exchange Within The Junction Of The Human U2-U6 Snrna Complex Measured By 19f Nmr Spectroscopy, Caijie Zhao

Dissertations, Theses, and Capstone Projects

Pre-mRNA splicing, the process by which non-coding sequences are removed and coding sequences are ligated, plays an important role in the maturation of precursor messenger RNA molecules prior to their translation into proteins. In eukaryotes, splicing is catalyzed by the spliceosome, a large and dynamic nuclear macromolecular "machine" that comprises five small nuclear (sn)RNA molecules and more than one hundred proteins. Among the RNA components, the complex formed between the U2 and U6 snRNA molecules is implicated in catalytic activity. In this dissertation, I have used ¹⁹F NMR techniques to characterize the conformation ("fold") and dynamics of a protein-free …

Protein Motions Control Activity In Biologically Important Phosphatases, Ryan Hirschi, Gwen Moise

Research on Capitol Hill

No abstract provided.

Characterization Of Biomass Burning Emissions From Cooking Fires, Peat, Crop Residue, And Other Fuels With High-Resolution Proton-Transfer-Reaction Time-Of-Flight Mass Spectrometry, C. Stockwell, P. Veres, J. Williams

Chemistry and Biochemistry Faculty Publications

We deployed a high-resolution proton-transferreaction time-of-flight mass spectrometer (PTR-TOF-MS) to measure biomass-burning emissions from peat, crop residue, cooking fires, and many other fire types during the fourth Fire Lab at Missoula Experiment (FLAME-4) laboratory campaign. A combination of gas standard calibrations and composition sensitive, mass-dependent calibration curves was applied to quantify gas-phase non-methane organic compounds (NMOCs) observed in the complex mixture of fire emissions. We used several approaches to assign the best identities to most major “exact masses”, including many high molecular mass species. Using these methods, approximately 80–96% of the total NMOC mass detected by the PTR-TOFMS and Fourier …

Observations And Analysis Of Organic Aerosol Evolution In Some Prescribed Fire Smoke Plumes, A. A. May, T. Lee, G. R. Mcmeeking, Sheryl Kashi Akagi, A. P. Sullivan, S. P. Urbanski, Robert Yokelson, S. M. Kreidenweis

Chemistry and Biochemistry Faculty Publications

Open biomass burning is a significant source of primary air pollutants such as particulate matter and non-methane organic gases. However, the physical and chemical atmospheric processing of these emissions during transport is poorly understood. Atmospheric 5 transformations of biomass burning emissions have been investigated in environmental chambers, but there have been limited opportunities to investigate these transformations in the atmosphere. In this study, we deployed a suite of real-time instrumentation on a Twin Otter aircraft to sample smoke from prescribed fires in South Carolina, conducting measurements at both the source and downwind to character10 ize smoke evolution with atmospheric aging. …

Accidental Poison: Analysis Of 1,4-Butanediol In A Popular Children's Arts And Crafts Toy, Christopher R. Dockery, John H. Shugart, Jonathan D. Parker, William J. Lawson

Faculty Articles

A popular children's arts and crafts toy made international headlines when it was discovered that 1,4-butanediol had been substituted into some of its formulations. The chemical 1,4-butanediol rapidly converts to the date-rape drug g-hydroxybutyric acid (GHB) upon ingestion and resulted in the accidental poisoning of some children. In this experiment, students extract 1,4-butanediol from commercially available toy beads (or prepared simulations) using their knowledge of pharmaceutical chemistry, solubility, etc. Using case studies available in the literature, students develop a quantitative analysis experiment for 1,4-butanediol extracted from the toy beads and, through approximation, relate the extractable amount of 1,4-butanediol to dose-response …

Identification And Characterization Of N-Acyltransferase Enzymes That Are Involved In The Biosynthesis Of Fatty Acid Amides, Daniel Robert Dempsey

USF Tampa Graduate Theses and Dissertations

Fatty acid amides are an emerging family of bioactive lipids that consists of N-acylethanolamines, N-acylarylalkylamides, N-acylglycines, N-acyl amino acids, N-monoacylpolyamides, and primary fatty acid amides. Short chain fatty acid amides are products of inactivated biogenic amines such as dopamine, histamine, octopamine, and serotonin, whereas long chain fatty acid amides have been implicated in a number of physiological process such as the perception and inhibition of chronic pain through binding to their specific receptors. The most famous; therefore, the most studied long chain fatty acid amide is anandamide or also known as N-arachidonylethanolamine. The biosynthesis …

An Investigation Of The Effect Of Mn2+ On The Fth1 Ire-Irp Complex, Eric Thomas Mendenhall

Theses, Dissertations and Capstones

Iron is a widely distributed metal found in almost every physiological system in nature, thus being an essential part of life. Iron homeostasis in the human body must be tightly regulated as iron is both beneficial and harmful to different cellular processes. Ferritin is a protein that has a prominent role in maintaining iron homeostasis via iron sequestration. Additionally, this protein itself is regulated by the Iron Responsive Element (IRE) and its interaction with an apoaconitase protein or the Iron Regulatory Protein (IRP). The binding of the IRP to this IRE, located on the 5’ untranslated stem loop region of …

Glycation Of Lysozyme, Wisam Talib Joudah

Theses, Dissertations and Capstones

For this research project, I propose a method for the analysis of glycated lysozyme using Matrix Associated Laser Desorption / Ionization-Time of Flight Mass spectrometry (MALDI-TOF MS). Glycation or "Maillard reaction" is a non-enzymatic reaction that occurs between amino acid residues, usually primary and secondary amines, of proteins and the carbonyl group of reducing sugars to yield Schiff bases. The glycation mechanism occurs between the carbonyl group of the reducing sugars and a primary amine by nucleophilic addition, resulting in the formation of a Schiff base. The Schiff base can then rearrange into the more stable Amadori product which is …

Investigation Into The Biological Importance And Function Of Proinsulin C-Peptide, Christina L. Newsome

Theses, Dissertations and Capstones

The C-peptide of insulin was thought to be biologically inactive, but recent studies have shown that the C-peptide causes multiple molecular and physiological effects. Evidence has shown that C-peptide binds to a cell surface receptor, probably a G-protein coupled receptor, and that the COOH-terminal pentapeptide is essential for binding and constitutes an active site. For a further understanding of the detailed nature of the physiological effects of C-peptide, the receptor structure needs to be determined. We designed an affinity column using C-peptide to try and gain a better understanding of the biological effects by examining what proteins the affinity column …

Atrial Fibrillation: Biophysics, Molecular Mechanisms, And Novel Therapies., Alexey V. Glukhov, Leonid V. Rosenshtraukh, Anamika Bhargava, Michele Miragoli, Bas J. D. Boukens

Anatomy and Regenerative Biology Faculty Publications

No abstract provided.

Bacterial Expression Of Plant Pyruvate Kinase, Kristina Fuller

STAR Program Research Presentations

Pyruvate kinases serve an important role in regulating glycolysis pathways. Different pyruvate kinase isozymes can dictate which of several different products will be formed during the final step of glycolysis. Being able to reliably copy active pyruvate kinases (PK) would allow study of the different isozymes, with the goal of eventually creating plants that are more nutritionally beneficial for humans. This study focused on improving the protocol for replicating each of two isolated PK isozymes from the model plant Arabidopsis thaliana. Previous attempts had resulted in the PK denaturing and consequently precipitating out of solution and so we manipulated the …