Current Trainees
Kevin Oliver (Advisor: Gary Sulikowski, Department of Chemistry)
Currently working on two projects dealing with carbohydrate chemistry. The first is to prepare baumycin by semisynthesis starting from daunomycin in order to determine the stereochemistry of the former natural product. This work is a joint project with the Bachmann group, which isolatedbaumycin from a cave dwelling bacterium. The second is a venture with Dr. Tina Iverson to synthesize the 2,3 ST antigen. The ST antigen is a glycoprotein found on cell surfaces and is the minimum unit necessary to trigger an immuno-response from certain tumor cells. The project aims to study pathogenesis and how enzymes from Streptococcus bind to sialyl acid moieties.
Megan Wadington (Advisor: Richard Armstrong, Department of Biochemistry)
The glutathione transferase (GST) superfamily of proteins plays an important role in the cellular detoxication of endogenous and xenobiotic compounds. However, proteins in the GST family exhibit considerable diversification with regard to chemistry, activity and substrate specificity. Escherichia coli K-12 encodes nine glutathione transferase paralogues, but only two of the gene products (SspA and Gst) have been assigned a function based on experimental evidence. Megan Wadington is currently working on a project that aims at describing both functionally and structurally the other seven GST paralogues (YliJ, YncG, YfcG, YfcF, YghU, YibF and the membrane bound YecN). To this end, she has employed a variety of approaches with the aim of elucidating the function(s) of the proteins in this important superfamily. These approaches include analysis of each paralogues, (1) genome context, (2) functional and structural properties, (3) phenotypic response in knock out strains and (4) interaction with protein partners. Specifically, her investigation focuses on two E. coli GST paralogues, YghU and YfcG.
Dawn Mackley (Advisor: Jeff Johnston, Department of Chemistry)
Synthetic accessibility is typically the rate-limiting step in the development of small molecules as therapeutics. The development of new reactions thereby facilitates the preparation of diverse collections of small molecules for evaluation. I am developing new reactions to prepare amino polyol natural products which possess biological activity, yet are available in vanishing amounts. I am investigating diastereoselective olefin aziridinations and aminohydroxylations using alkyl azides. These reactions are promoted by Brønsted acid, and a long term goal is the use of a chiral Bronsted acid to provide single enantiomer products. An immediate goal is the diastereocontrolled preparation of contiguous amino polyol arrays, and the application of this new method to complex small molecule targets.
Kellen Harkness (Advisors: David Cliffel and John McClean, Department of Chemistry)
Kellen Harkness is working at the interface of mass spectrometry and nanomaterials. Both fields at this interface provide a benefit to the other. The nanomaterials being studied currently are bioactive monolayer protected clusters (MPCs); generally gold clusters capped with a variety of ligands, with a total diameter less than 5 nm. Mass spectrometry can be used to characterize these MPCs, yielding information on size and monolayer composition, both of which are vital to understanding the bioactivity and potential utility of these nanoparticles. In a reciprocal way, nanomaterials can also provide a wide array of benefits to mass spectrometry experiments, enhancing specificity, sensitivity, and other important parameters. Both of these areas of research are relatively new and offer exciting possibilities.
Adam Ketron (Advisor: Neil Osheroff, Department of Biochemistry)
Although the double-helical nature of DNA confers considerable physical stability to the genetic material, this characteristic also burdens the cell with numerous topological problems such as over- and underwinding, knotting, and tangling. The replication apparatus must deal with significant overwinding ahead of a growing replication fork, and the intertwined products of DNA replication must be decatenated to allow for mitotic segregation. The enzymes that resolve these and other topological problems in the genetic material are known collectively as DNA topoisomerases. Specifically, type II topoisomerases act by passing a double-stranded segment of DNA through a transient double-stranded break in a separate DNA segment, effectively rendering DNA invisible to itself. An important intermediate in this catalytic cycle, called the “cleavage complex,” is a stable complex in which the newly generated 5’-phosphate termini of the cleaved DNA segment are covalently linked to the active site tyrosyl residues of topoisomerase II. A moderate concentration of cleavage complexes is normally maintained by a cleavage/religation equilibrium and is essential for enzyme function; however, any process that generates double-stranded DNA breaks harbors an intrinsic threat to genomic stability. An elevated concentration of cleavage complexes increases the likelihood that DNA tracking systems will encounter one of these transient breaks, an occurrence that typically results in a permanent double-stranded break and subsequent mutagenic events. Many chemotherapeutic drugs currently in use target human topoisomerase II and shift this cleavage/religation equilibrium toward a higher concentration of cleavage complexes by enhancing cleavage, inhibiting religation, or both. These compounds are called topoisomerase II poisons because they convert this essential enzyme to a toxic agent. Adam’s current research is focused on the anticancer drug amsacrine, a DNA intercalator and a known poison of the enzyme. He is using a number of approaches to determine structure-function relationships in amsacrine and the mechanism by which this drug interacts with human topoisomerase IIalpha and beta and the ternary complex that includes the enzyme and its DNA substrate. The roles of key functional groups on the compound are being investigated by a series of DNA cleavage/religation assays, enzyme-drug binding, saturation transfer difference proton NMR spectroscopy, and mutagenesis studies.
Chinessa Adkins (Advisor: Eva Harth, Department of Chemistry)
Chinessa Adkins works on a project for the development of highly potent bimodal imaging tools derived from polymeric architectures. The star polymer architectures are well-defined nanoscopic materials that are 50-100 nm in size. The novelty of this approach is the fluorescent core, which can hold up to 50 linear polymer arms together that show imbedded functionalities for the complexation of lanthanides and conjugation units to targeting units. The star polymer architecture is believed to have an advantage over the NMR relaxation measurements and is designed to incorporate as multiple lanthanide moieties through the incorporation of multi-functionality sites, which allow for high loading of the particle. Such bimodal imaging probes remain unknown and only cross-linked micelles with a smaller nanoscopic diamenter have been studied, but showed restrictions in their loading capability and architecture. The novel star polymers meet the demand of high loading capacity combined with functional groups to allow for bio-conjugation, giving this approach the potential for a targeted approach to imaging.
Craig Garmendia (Advisor: Carmelo J. Rizzo, Department of Chemistry)
Craig Garmendia is currently exploring the role of nascent Hoogsteen versus Watson-Crick pairing for dNTP selection during replication of damaged DNA by Y-family DNA polymerases. The experimental approach is to synthesis oligonucleotides containing site-specifically modified bases. The modifications are derived from biologically relevant DNA damaging agents and have predictable Watson-Crick and Hoogsteen hydrogen-bonding properties. Mr. Garmendia has designed and synthesized a number of these modified purines and is currently working towards their site-specific incorporation into oligonucleotides. Once synthesized, the preference and rates for dNTP incorporation across from the damaged base by pol h , i , and k will be determined and related to the specific hydrogen-bonding preference of the modified base. The insertion preferences will guide structural studies by NMR and X-ray crystallography to be done in collaboration with the Stone and Egli labs.
Amanda Kussrow (Advisor: Darryl Bornhop, Department of Chemistry)
Amanda Kussrow is working on a project that brings together analytical chemistry, biochemistry and medicine. She has been using chemical sensing interferometry (CSI) which is a nanoscale interferometric detection method (1) for the study protein expression and binding properties. Ms. Kussrow has employed CSI to determine the free-solution binding constant of interleukin-2 (IL-2) in cell-free media (2) and to monitor the change in the expression of IL-2 from T-cells that have been stimulated by an external change. She is also investigating surface immobilization methods so that the instrument can be applied to study multimeric binding as well as adapting the instrument for use in point-of-care detection of disease.
Rachel Snider (Advisor: David Cliffel, Department of Chemistry)
Rachel Snider is working on two cellular metabolism based projects. The first centers upon the development of an electrochemical insulin sensor and its use in the metabolic profiling of isolated murine islets. The electrode is a multiwalled carbon nanotube/dihydropyran composite film on a glassy carbon electrode. This sensor was incorporated into the multianalyte microphysiometer; together with lactate and oxygen sensors it was used to measure the metabolic response of islets to both glucose and nutrient stimulation.
The other metabolic profiling project involves the response of cells to biological agents. In this project, currents at glucose lactate oxygen and acidification sensors are used to monitor cellular metabolism. I developed software to control and collect data from bipotentiostats built in the VIINSE laboratory. This instrument allows for simultaneous measurement of the current responses for up to eight chambers of cells. I am currently working to develop dose response curves for the effect of botulinum neurotoxin A on SK-N-SH neuroblastoma cells.
Thomas Tomasiak (Advisor: Tina Iverson, Department of Pharmacology)
Thomas Tomasiak is currently performing structural studies of two bioenergetic integral membrane proteins. His first project investigates the structure-activity relationships in respiratory complex II, which is required for mitochondrial aerobic respiration. Tom has determined the crystallographic structure of a site-directed mutant of the E. coli homolog of respiratory complex II. His crystallographic results strongly suggest that previously unanticipated protein motions play a key role in catalysis. He has combined his structural data with molecular dynamics simulations to provide an initial description of the motions accompanying the catalytic mechanism.
Tom is additionally working to understand nitric oxide chemistry during biological nitrogen cycling. As a first step, he has grown preliminary crystals of two integral-membrane proteins of unknown fold that utilize heme-based chemistry for nitric oxide conversions.
Andrew Morin (Advisor: Jens Meiler, Department of Chemistry)
Vancomycin is a small-molecule beta-lactam glycopeptide antibiotic which binds and sequesters the free D-Alanine-D-Alanine C-terminus of a key gram-positive bacterial cell wall component, thereby inhibiting proper cell wall biosynthesis and consequently rendering the bacteria vulnerable to osmotic lysis. Although vancomycin is often considered an "antibiotic of last resort", whose use is highly controlled, bacterial resistance to vancomycin and other beta-lactam antibiotics has already become widespread. While a small number of next-generation antibiotics capable of treating these resistant strains are either currently available or in the development pipeline, the pace of new therapeutic development over the last several decades, and into the foreseeable future, cannot not keeping pace with the rate of emergence of resistant pathogens. The most common mechanism of acquired resistance observed in pathogenic bacterial strains is through the substitution of a -D-Lactate in place of the -D-Ala at the free C-terminus of the bacterial peptide. This single replacement of the C-terminal amino linkage by an ester linkage of the lactate, destroying a single hydrogen bond between vancomycin and the peptide, is enough to destroy binding of vancomycin to its bacterial peptide ligand and render the bacteria resistant. The objective of Andrew's research is to develop and validate computational methods for designing novel protein therapeutics. Because the molecular and structural bases for both vancomycin binding and resistance have previously been well classified, the re-design of a protein-binding pocket to bind the resistant D-Ala-D-Lac peptide motif seems an ideal proof-of-concept experiment.
Jonas Perez (Advisor: David Wright, Department of Chemistry)
Ideally, viruses should be accurately and quickly diagnosed in order to begin patient treatment immediately. False negatives result from inadequate sensitivity. False positives result from poor specificity. The ideal strategy has very high sensitivity and very high specificity. Unfortunately, these properties usually occur as a product, meaning high sensitivity leads to poor specificity and high specificity leads to poor sensitivity. The goal of this project is to develop and evaluate a new paradigm in specific yet sensitive virus detection. This approach is based on a combination of procedures, including nanoparticle reaction surfaces, tag-specific DNA sequences, and DNA ligation logical AND operators. One of the most interesting features of this approach is that sensitivity and specificity are uncoupled. Sensitivity is controlled by the production of PCR product and is, therefore, relatively fixed. On the other hand, the number of antibodies that are used in combination controls specificity. A single antibody coupled with a subsequent PCR reaction would also yield high sensitivity. Unfortunately, PCR is so sensitive that without the logical operator proposed here, it is likely that many false positives would also occur.