2010 Summer Research Projects
Organic Chemistry: Rearrangement of Propargyloxypyridines to N-Substituted Pyridones
Carolyn Anderson and Keun Ah Ryu
Organic synthesis is a powerful technique that allows access to a wide range of different structural motifs. In this project, we are working to develop a method for the synthesis of N-substituted pyridones; an interesting functional group found in a series of pharmacologically interesting compounds. To date, we have developed an experimental method for accessing this motif by rearranging a related system. The student working in this area is responsible for preparing and testing additional substrates in the rearrangement and for optimizing this reaction to give the desired products. The student will gain experience with synthetic organic chemistry techniques, including: running reactions, purification, organic spectroscopy, and experimental design.
Organic Chemistry: Gold-catalyzed Rearrangement of N-Propargyloxypyridines
Carolyn Anderson and Nathan Romero
Organic synthesis is a powerful technique that allows access to a wide range of different structural motifs. In this project, we are working to advance a method for the synthesis of N-substituted pyridones; an interesting functional group found in a series of pharmacologically interesting compounds. To date, we have developed a new gold-catalyzed method for accessing this motif by rearranging a related system. The student working in this area is responsible for preparing and testing additional substrates in the rearrangement and for optimizing this reaction to give the desired products. The student will gain experience with synthetic organic chemistry techniques, including: running reactions, purification, organic spectroscopy, and experimental design.
Diffusion and Transport of Galectin-3
Eric Arnoys and Cheri Ackerman
Characterization of Novel Proteins from Zebrafish
Eric Arnoys and Eric Prins
We have cloned, sequenced, and expressed three distinct zebrafish proteins that arise from alternative splicing of RNA from the same gene. Next we would like to determine 1) whether the mRNA variants differ in their expression in different tissues and in different stages of development 2) whether the protein products interact with each other 3) if the three variants bind to different sugars.
Watching Membrane Proteins in Real Time
Eric Arnoys and Jacob Artz
We are characterizing the behavior of several membrane-bound proteins in living cells with state-of-the-art techniques to examine their cellular localization, mobility, and interactions with other proteins. Protein targets are tagged with fluorescent proteins so that they can be viewed in living systems. We are also examining what effect extracellular signals have on the proteins' behavior.
Fluorescence of protein-attached quantum dots
Dave Benson, Stacey De Haan, Anand Divakaran, and Elizabeth Porter
The students involved on this project are producing fluorophore-modified proteins that will be attached to semiconductor nanoparticles (quantum dots). They are also analyzing the fluorescence properties of these products, especially how the properties change when the molecule that binds to the protein (ligand, maltose) is introduced at various concentrations. These fluorescent proteins will be examined using conventional fluorimetry instrumentation and examined at the single molecule level using a fluorescence micorscope.
Relating Biological Function to Potential Tyrosine-Cysteine Cofactors
Dave Benson, Ryan Martinie and Matt Borr
Covalent bond formation between tyrosine and cystiene sidechains provides the enzymatic function(s) of a variety of proteins. The most relevant to human health is cysteine dioxygenase. The students on this project are examining how this bond formation occurs and the function(s) actually provided by bond formation. This project makes extensive use of the new MALDI mass spectrometer doing proteomic experiments. There is also significant computational evaluation of these experiments.
Rhodium-Catalyzed, Allylic Substitution Reactions
Ron Blankespoor and Timothy Atallah
This project is a mechanistic study in which a series of aryl-substituted, allyl carbonates, previously prepared in our laboratory, are reacted with benzylamine in the presence of a rhodium catalyst. In earlier work, these carbonates, which contain a phenyl group substituted with a variety of different groups at the para position, were reacted under identical conditions to determine how the substituents impacted the rate and enantioselectivity of the reaction. This summer, the chiral amine products are reacted with HBr to form salts. From the crystal structures of these salts we should be able to determine the absolute configurations of these chiral amines. This project is being done in collaboration with a Pfizer laboratory in Ann Arbor, which has provided some of the funding for this work. The goal of this work is to provide another synthetic tool for making drugs that are composed of a single substance, thereby making them safer and more effective in their applications.
Sites of Protonation and Ligand Migration in Bimetallic Organometallic Complexes
Roger DeKock and Brandon Burkhart
We are examining sites of protonation and ligand migration in bimetallic organometallic complexes by means of computational chemistry. The systems we are studying include the metals Ru, Rh, Os, and Ir. We are interested in, among other things, migration of a bridging hydride ligand to react with a bridging methylene ligand. The result of this reaction is to form an agostically bonded methyl group. We want to know if this migration takes place by a transition between the two metals, or by some other means. We are employing electronic structure methods to examine the different possibilities.
Cooperativity in Hydrogen Bonding: Nudged Elastic Band
Roger DeKock and Ryan Martinie
For several years we have been completing theoretical studies that relate to cooperativity in hydrogen bonding. For example, we examine molecular cubes with the formula NH3(H2O)7. In our unpublished work on thirty nine of these cubes, we have found that fourteen of them transition from a "neutral" structure to an "ion-pair" structure, NH4+ and OH–, after going through a low energy transition state. We believe that these small cubes can serve as prototypes for cooperativity in hydrogen bonded networks in real chemical systems, such as ammonia, NH3, in water. Of the fourteen cubes that form ion pairs, nine of them form "face" ion pairs, four form "contact" ion pairs, and one forms a "zwitter" ion pair. Thirteen of the fourteen ion pairs that are formed involve "shuffling" of hydrogen atoms in the hydrogen bonded network. Heretofore, our preferred method of locating the transition state between the neutral structure and the ion pair structure has been to scan the potential energy surface along the N–H–O coordinate. But this method does not guarantee finding the minimum energy pathway between reactants and products. Hence, we intend to go beyond scanning the potential energy surface to employ the more modern "nudged elastic band" method. We believe that our prototypical studies on hydrogen bonded networks to be of interest in chemical biology, as evidenced by a number of studies that have employed the nudged elastic band procedure in the past five years, e.g. Journal of Molecular Biology, 2006, Vol. 357, pp. 1683-93.
Detecting and classifying barriers to two-way faculty/student feedback in science, math, and engineering
Herb Fynewever, Monica Turner and Katherine Vander Heide
Usually when students are learning science, math, and engineering they reveal their thinking to the instructor and the instructor uses this information to give feedback to the students. Often, however, this two-way communication is limited to formal assessments such as quizzes and exams, which happen after most of the learning has happened. Research has shown that there are many effective ways to better integrate this communication into the learning process (e.g. interactive classroom delivery and activity) realizing significant gains in student learning. Further research is needed to determine what the barriers are to two-way communication and to devise strategies to remedy these barriers.
In this research, students are analyzing data from classroom observations and interviews with faculty and students to detect and classify these barriers. Research students are also conducting further observations and interviews with science, math, and engineering students and faculty during the summer research period at Calvin. This aspect of the research will address the largely unexplored research question: how does student/faculty communication in the research laboratory differ from communication in the classroom and what techniques can be transferred from one environment to the other?
Effects of membrane cholesterol on the transport activity of GluT1
Larry Louters and Matt Salie
We are both increasing and decreasing the content of cholesterol in the cell membrane to see if that alters either basal level glucose uptake or the ability to activate glucose uptake by cell stress. The content of cholesterol will be altered using cholesterol binding drugs.
Activation of glucose uptake by cell stress in muscle and fat cells
Larry Louters and Daniel Oram
A family of membrane imbedded proteins, known as GluT, transport glucose into cells. It has been shown that one member of this family, GluT1, can increase its transport activity very quickly when cells are stressed. However, it is not known if this transporter is activated by stress in cells, such as muscle and fat, which also contain GluT4. This project measures glucose uptake in muscle and fat tissue culture cells when the cells are stimulated by both insulin and cell stress to see which fraction of uptake in each case can be attributed to transport via GluT1.
Selective activation of glucose transporters in fat and muscle cells
Larry Louters and Alexandra Cok
Fishing for Cytochrome P450s in Mycobacterium chlorophenolicum
Darla McCarthy, Alvin Aquino and Tu Danh
Pentachlorophenol (PCP) is a potent toxin that was formerly used extensively as a wood preservative and currently contaminates soil at many sites. It is considered a "priority pollutant" for regulation by the US EPA. Soil bacteria capable of degrading PCP have been isolated from several PCP-contaminated sites; we are interested in understanding the metabolic pathways used to degrade PCP in these microbes. Recent research in our laboratory confirms that the first enzyme in the metabolic pathway for mineralization of pentachlorophenol by Mycobacterium chlorophenolicum is a member of the Cytochrome P450 superfamily of enzymes. This summer we are using degenerate PCR to identify and clone members of this superfamily from M. chlorophenolicum. We are also characterizing the cloned enzymes to identify which one is able to dechlorinate PCP.
Modeling photochemical reactions
Mark Muyskens and Nate Gifford
This project is using computational tools to model the kinetic and molecular structure details of a photochemical reaction. My research group has experimental results from the ultraviolet photoelimination of hydrogen fluoride from fluorine containing acetylacetone in the gas phase. This work will be greatly assisted by modeling the data. Some experimental work to complement the calculations may be included in the summer project.
Characterizing the Binding Interaction of Topoisomerase I with G-Quadruplex DNA: From Single Molecule to Bulk Measurements
Kumar Sinniah, Christine Timmer, and Anna Plantinga
The goal of the summer project is to investigate the biophysical and biochemical interactions between G-quadruplex DNA and topoisomerase I, a DNA-binding enzyme that modulates DNA topology. The project is a collaboration between Dr. Amy Wilstermann (Biology) and Dr. Kumar Sinniah (Chemistry & Biochemistry) and involves single molecule studies of DNA-enzyme interactions using an atomic force microscope (AFM) and calorimetric studies utilizing an isothermal titration calorimeter (ITC).
Studies on a Targeted Drug Delivery System for Cancer Therapeutics
Kumar Sinniah and Stephenie Graf
This project develops a general understanding of how multivalency functions in biology which is relevant to a broad array of biomedically important processes. This summer we are examining a system that can be applied to cancer therapeutics - the specific folic acid-folate receptor protein interactions using single molecule atomic force microscopy and isothermal titration calorimetry methods. This project is a collaboration with scientists from the University of Michigan-Ann Arbor.
Examining Enzyme-Inhibitor Interactions One Molecule At a Time
Kumar Sinniah and Rachel Battershell
Carbonic anhydrase (CA), an enzyme present in the eye when over-active tends to produce excess fluid that can result in damage to the optical nerve, a condition known as glaucoma. The enzyme activity can be inhibited with the use of sulfonamide inhibitors. Our group has investigated the interactions between the CA enzyme and sulfonamide inhibitors at the single molecule level using an atomic force microscope. Our summer studies involve the use of biolevers for force measurements and will improve upon past studies of this system.
Protofibrils: nucleation, structure and therapeutic binding
Chad Tatko, Ian Robertson and Gillian Morris
Students are exploring model peptides (typically 2/3 stranded beta-hairpins) for the role of oxidative damage as a means for protofibril nucleation. By taking advantage of L-Dopa type residues covalent strategies for macrocyclization are being explored. Additionally, a protofibril replica is being used to determine the role of aromatic networks in thermodynamic stability and Alzheimer's therapeutic binding.
Noncovalent Interactions: Biocatalytic desulfurization and pKa perturbation
Chad Tatko, Lauren Kelley, Alexandra Batt and Isabella Felzer-Kim
Small peptide scaffolds are being decorated with functional groups that will bind and alter chemical activity. Specifically, diagonally disposed aromatic resonances will bind dibenzothiophene to promote oxidation for desulfurization of fuel stocks. Additionally, laterally positioned residues will be explored for the electronic susceptibility of pKa modification of tyrosine.
Nanomolecular Building Projects with Spectrophotometric Characterization via Factor Analysis
Doug Vander Griend, Lauren Manck and Alex Wrobel
Understanding and controlling the synthesis of supramolecules is a key goal of nanotechnology. Our students are using UV-vis spectroscopy to investigate the solution chemistry of nickel(II) and copper(I) cations, which typically bind to four molecules. Composite data is measured and then modeled via equilibrium-restricted factor analysis, a mathematical technique for studying specific chemical species while they interact in an equilibrium mixture. A significant element of the research involves collaboration with graduate labs at Indiana University and the University of Pavia, Italy, and an industrial lab at Pleotint, LLC.