Seminars begin at 3:30 pm on Friday afternoons in Merrill Lecture Room 4, except as noted, and are preceeded by refreshments at 3:15.
Discussion seminars begin at 3:30pm on Friday afternoons in Merrill Science Center Room 315.
Fri, Sep 8, 2017
Fri, Sep 15, 2017
Kaeli Mathias '18 and John Strahan '18 are both working with Professor Sheila Jaswal.
Kaeli Mathias will discuss "Investigation of Acetonitrile as a Mass-Spectrometry Compatible Denaturant." Biological function is highly reliant on the structure, folding and stability of proteins in the appropriate cellular conditions. Traditional methods to study folding and stability map a protein’s free energy landscape using harsh denaturants to perturb the equilibrium between the native and unfolded states, enabling measurement of unfolding kinetics and thermodynamics. The Jaswal lab has developed a method, hydrogen exchange mass spectrometry (HXMS,) that can map protein landscapes under much more physiological conditions, requiring little to no denaturant. This project focuses on validating the organic solvent acetonitrile as a mild denaturant. Mathias '18 is monitoring the unfolding as a function of acetonitrile concentration of protein L, a well-characterized two state protein, using tryptophan fluorescence and HXMS. These experiments will help establish the scope of Acetonitrile in enabling HXMS mapping of protein folding landscapes.
John Strahan will discuss "Modeling Hydrogen Exchange with Gillespie Algorithm Simulations and Approximate Bayesian Computation." Hydrogen exchange mass spectrometry has recently emerged as a useful tool for studying protein folding mechanisms and free energy landscapes. The underlying kinetics of the exchange process are complicated and resistant to simple analytical treatment when the protein is under native conditions. In previous work, members of the Jaswal Lab have developed a stochastic simulation using the Gillespie algorithm to calculate the mass spectrum as a function of time, and then fit this simulation to experimental data using a least squares scheme. In the present work, Strahan '18 refines and extends this analysis by using Bayesian Computation, which allows for determination of distributions of kinetic parameters which are consistent with the observed experimental data. From this information, he can estimate parameter means and variances, as well as correlations between parameters.
Fri, Sep 22, 2017
Fri, Sep 29, 2017
Lila Manstein and Bailey Plaman will be presenting. Lila is working with Professor Patricia O'Hara, and Bailey is working with Professor Anthony Bishop.
Lila Manstein will discuss “Nutraceuticals: A Study of Antioxidants in Food”. In chemistry, oxidants react with other species by removing electrons. Biologically, oxidants are generated during normal biological functioning of a cell or organ at low concentrations and at higher concentrations during a pathological or diseased state. These molecules, generically called Reactive Oxygen Species (ROS), are free radical oxygen-containing molecules and are very reactive. Fortunately, there are other species in the body known as antioxidants that can decrease the concentrations of ROS by one of several methods. In the simplest method, the antioxidant sacrifices itself by donating an electron, reducing the ROS and thereby protecting other biological molecules such as proteins, fats, and DNA. In another model, the antioxidants turn on or off signaling systems responsible for the production of ROS. Polyphenols are common class of antioxidants found in many foods such as wine and olive oil. The goal of my research project is to create a simple quantitative means for consumers to measure the polyphenol content in foods such as olive oil. One assay I have explored is a chemical reaction that results in a bathochromic shift on the absorbance peak of a reporter dye when exposed to an antioxidant. In this assay, a ferric ferricyanide dye solution that is made by mixing ferric chloride and potassium ferricyanide. In the presence of antioxidants (reducing agents), the peak absorption of the dye shifts from 440 nm to approximately 700 nm. Visibly, the solution turns from a dull brown to brilliant blue color known as Prussian Blue. The exact wavelength and the intensity depend not only on the quantity, but also upon the antioxidant tested. I hope to further characterize this reaction and to use this information to develop a reliable tool that uses visible photochemistry for non-scientists to measure the polyphenols in food.
Bailey Plaman will discuss “Biarsenical Small Molecule Activation of Engineered Kinase Interaction Motif (KIM) Family Protein Tyrosine Phosphatases (PTPs)”. Protein tyrosine phosphatases (PTPs) are a large class of enzymes that catalyze the cleavage of phosphate groups from phosphorylated tyrosine residues of proteins. Since dephosphorylation is a critical regulatory method for cell signaling, the human genome codes for a large variety of PTPs that serve distinct roles in diverse signaling pathways. Dysregulation in PTP signaling pathways often results in disease, which makes PTPs an attractive target from a pharmaceutical standpoint. Although the structure and function of PTPs vary greatly, the protein sequence of the catalytic site is highly conserved, making it difficult to create small-molecule ligands that specifically target individual PTPs. As a result, the cellular function of most PTPs remains poorly understood. We aim to develop a strategy to specifically activate PTPs to better understand their function within the cell and the consequences of their dysregulation. To do so, we genetically engineer PTPs to be susceptible for biarsenical small molecule activation. To make the method generalizable to all PTPs, we introduce three cysteine point mutations to the highly conserved WPD loop motif. Biarsenical small molecules bind specifically to the cysteine-rich region to activate only mutant PTPs. Previous experiments from the Bishop lab showed promising results for the target-specific activation of hematopoietic protein tyrosine phosphatase (HePTP) using this strategy. My project uses the same activation strategy to determine whether the success with HePTP, a member of the kinase interaction motif (KIM) family of PTPs, is common to the other two members of the family: striatal enriched protein tyrosine phosphatase (STEP) and Protein Tyrosine Phosphatase Receptor Type R (PTPRR). KIM-family PTPs are generally thought to play a role in memory and learning, so success with activation strategies could provide important tools to better understand neurodegenerative disease.
Fri, Oct 6, 2017
Alina Dao, Leonard Yoon, and Gyu-Hee Min will be presenting. Alina is working with Professor Mark Marshall, Leonard is working with Professor Helen Leung, and Gyu-Hee is working with Professor Anthony Bishop.
Alina Dao will discuss "Structure Determination of (E)-1-Chloro-3,3,3-Trifluoropropene Complexed with Hydrogen Fluoride using Microwave Spectroscopy." Microwave spectroscopy has greatly advanced the study of small molecules and their molecular complexes, allowing for a precise determination of their structures and a detailed understanding of intermolecular interactions. This deeper understanding can stand as a basis from which more complicated systems can be investigated. The focus of this research is the experimental structure of the complex formed by (E)-1-chloro-3,3,3-trifluoropropene and the protic acid hydrogen fluoride. It is an extension of prior work by the Marshall and Leung labs on complexes formed by both haloethylenes and, more recently, halopropenes with three different protic acids. To investigate the acid dimer, it is necessary to first characterize the halopropene monomer, (E)-1-chloro-3,3,3-trifluoropropene. To do this, ab initio calculations are performed using the Gaussian09 program at the MP2/6-311++G(2d,2p) level. The theoretical spectroscopic constants given by this program are then used to generate a spectrum, which can be used to assign experimental transitions recorded by a broad-band chirped pulse Fourier transform microwave spectrometer. Spectral assignments have been made for eight isotopologues of the molecule, and will be used to derive an experimental structure. From here, the structure of first the argon complex, and then the complex with hydrogen fluoride, will be characterized.
Leonard Yoon will discuss “Determining the structure of the (Z)-1-chloro-2-fluoroethylene – hydrogen fluoride complex using microwave spectroscopy." Understanding a molecule’s ability to form van der Waals interactions in different electronic environments forms a basis for more complicated (biological) systems. In the case of complexes between hydrogen fluoride and haloethylenes, as researched in the Leung and Marshall labs, a delicate balance between electrostatics and sterics dictates the geometry of the complex. Hydrogen fluoride chooses to interact with the sterically accessible cis H-atom in vinyl fluoride and vinyl chloride as opposed to the electrostatically favorable geminal hydrogen. However, in (Z)-1-chloro-2-fluoroethylene, only electrostatically-inequivalent geminal H-atoms are present. To determine the structure of the (Z)-1-chloro-2-fluoroethylene – hydrogen fluoride complex, ab initio calculations are performed at the MP2/6–311++G(2d,2p) level using GAUSSIAN 09. Holding the geometric parameters of (Z)-1-chloro-2-fluoroethylene fixed at their literature values, the structure corresponding to the minima on the ab initio potential energy surface of the (Z)-1-chloro-2-fluoroethylene – hydrogen fluoride complex suggests a bifurcated hydrogen bond with the two halogen atoms on the haloethylene, and there is no secondary interaction involving the fluorine atom on hydrogen fluoride. This unexpected structure will be corroborated experimentally using microwave spectroscopy in my thesis.
Gyu-Hee Min will discuss “Synthesis of a compound library targeting the allosteric site of Shp-2." Protein tyrosine phosphatases (PTPs) are enzymes that remove a phosphate group from phosphotyrosine from protein substrates. Their role in controlling signal transduction pathways highlights their overall importance; misregulation of PTP activity levels can lead to a variety of pathological effects, including cancer, diabetes, and obesity. Highly selective PTP inhibitors are sought after as drug candidates due to these associations between PTPs and human disease. Unfortunately, PTP-inhibitor discovery is inherently difficult due to two recurring problems observed with many active-site-directed inhibitors: lack of target specificity and poor bioavailability. However, recently a few allosteric regions have been discovered - these have more unique proteins within the group so this makes actively regulating these sites more feasible. In 2014, the Bishop Lab discovered one of these sites in the catalytic domains of Shp-2, a PTP that has been shown to cause both cancer and leukemia when hyperactive, and has been a target for pharmaceutical research. Within the Shp-2 region is an allosteric site with a non-conserved cysteine residue which allows for potential selective inhibition. My project involves the synthesis of a compound series involving vinyl sulphonamides, shown to have yielded highly selective covalent inhibition of the cysteine mutant of our target residue. Beginning with the synthesis of the main structure of the target molecule, this project looks into creating a library of various compounds to test for inhibition by utilizing different functional (R) groups.
Fri, Oct 13, 2017
Craig Nelson and Wayne Maumbe will be presenting. Craig is working with Professor David Hansen, and Wayne is working with Professor Sandra Burkett.
Craig Nelson will discuss “Can Amino-Acid-Functionalized Naphthalenediimide Nanotubes Function as Ion-Channels?” Since their discovery, self-assembling organic nanotubes have attracted considerable attention for their industrial, ecological and biological potential. Work done by the Ghadiri group at the Scripps Research Institute in La Jolla, CA, has been a major contributor to this field, and has illuminated the biocidal potential of nanotubes formed from cyclic D,L α-peptides. Biocidal activity stems from the nanotubes’ capacity to pierce the cell membrane and form ion-channels, inducing cell death through the rapid breakdown of critical concentration gradients. My research project intends to expand upon this previous work, specifically by studying amino-acid-functionalized naphthalenediimide (NDI) derivatives, which the Sanders group at Cambridge University has demonstrated form nanotubes in solution. Using synthetic unilamellar vesicles as a model, membrane insertion and ion-channel formation by NDI nanotubes will be assayed through the use of the pH-dependent dye carboxyflourescein and fluorescence spectroscopy. If membrane insertion is confirmed, successive experiments will compare the activity of the NDI system to naturally occurring channel formers, including the antibiotic gramacidin.
Wayne Maumbe will discuss “NMR Investigations of Magnesium Organosilicate Clay Layers”. Clays are inorganic solids with crystalline, layered structures. Organically functionalized derivatives of the magnesium silicate clay talc have been used in the Burkett lab to synthesize polymer–clay nanocomposites with a brush-like structure. At the macroscopic level, these materials resemble the component polymer, including being soluble in organic solvents. In order to better understand the molecular-level properties of these nanocomposites, a derivative of talc, magnesium hexadecylsilicate, is used as a model system. This organoclay has a layered brush-like structure, with hexadecyl chains end-tethered to a talc core. The clay exfoliates into individual brush-like layers in solvents such as chloroform, THF, toluene, and 1,1,2,2-tetrachloroethane, making it possible to obtain solution 1H NMR and 13C NMR spectra. 1H NMR provides evidence of restricted alkyl chain mobility, and 13C NMR provides information about chain conformation. To further study mobility, the spacing between the hexadecyl chains is increased by incorporating propyl groups into the clay. Magnesium mixed-organosilicate clays were synthesized with 75%, 50%, and 25% hexadecyl groups, and magnesium propylsilicate was also prepared. NMR studies of alkyl chain mobility and conformation include 1H peak linewidth analysis and integration, 1H T1 and T2 relaxation time measurements, and 13C chemical shift analysis. The alkyl chain distributions within the mixed clays will be studied by investigating through-bond and through-space interactions using 1H 2D COSY and NOESY NMR experiments.