Hunsicker-Wang Lab

Biochemistry & Bioinorganic Chemistry

Professor: Laura Hunsicker-Wang, Ph.D.

Overview: Research in the Hunsicker-Wang laboratory will focus on studying enzymes that utilize or bind metal ions, called metalloproteins. There are two major areas of interest:

Iron-sulfur cluster enzymes

Iron-sulfur proteins make up ~30% of all metalloproteins.  These proteins utilize iron and sulfur atoms that are organized into clusters.  These proteins are often involved in electron transfer reactions.  Specifically, the Rieske protein, which is part of Complex III in the respiratory chain, contains a [2Fe-2S] cluster, which is ligated to the protein via 2 cysteine and 2 histidine residues.  The reduction potential of this protein depends on the organism and the type of system that it was derived from.  Previous studies have shown that the number of hydrogen bonds to the cluster, the solvent accessibility, and the type of charge residues near the cluster all affect the reduction potential.  Research on this protein involves making site-specific mutations, purifying, and sometimes crystallizing and solving the structure of the mutant enzymes. The reduction potentials of these mutants are also evaluated.  This protein is also be chemically modified with reagents that alter the properties of specific amino acids.  This approach allows a greater variety of chemical properties to explore.  Chemical modification also allows study of how individual amino acids contribute to the electron transport function within the protein.  We are studying proteins from Thermus thermophilus, yeast, and spinach to compare how the proteins are similar and different.

Reactive oxygen species (ROS) are destructive and form from the reduction of molecular oxygen.  One hypothesis is that a mismatch in the potential of the Rieske protein with its partners within Complex III leads to the production of ROS and may lead to neurodegenerative diseases.  The Hunsicker-Wang lab is exploring this hypothesis.

Cytochrome oxidase proteins

Cytochrome oxidase is complex IV in the respiratory system. Within this protein, there are 4 metal sites, 2 heme-iron sites and 2 copper binding sites.  One of the copper sites is the CuA center, found in subunit II of cytochrome oxidase.  This center may also be involved in H+ translocation within cytochrome oxidase. Subunit II can be expressed as an isolated protein.  The Hunsicker-Wang lab is exploring how the histidines in this protein may function to pump H+ using chemical modification and site-directed mutagenesis.  We are also exploring how the CuA protein and the Rieske protein (from all three species), are modified by endogenously produced molecules, such as 4-hydroxy nonenal (HNE) and 4-oxo nonenal (ONE).  These molecules are produced in membranes in the presence of reactive oxygen species such as peroxide.  We are exploring how these molecules will react with amino acids of important metalloproteins involved in the respiration process. 

Maeder Lab

Biochemistry & Molecular Biology

Professor: Corina Maeder, Ph.D.

Overview: Research in the Maeder Lab centers on understanding the mechanisms involved in gene expression, specifically that of pre-messenger RNA splicing. In eukaryotes, initially, RNA transcribed from DNA may have intervening non-protein coding sequences, or introns. These sequences must be removed for accurate protein translation. The removal of these introns must be precisely coordinated to avoid inaccuracies that can result in many diseases, including cancer and retinitis pigmentosa. This process is known as pre-messenger RNA splicing.

Research focus: A large macromolecular complex of RNA and proteins called the spliceosome facilitates splicing. The mechanism of pre-mRNA splicing involves large-scale rearrangements of protein-RNA complexes, which must be regulated to ensure both splicing timing and accuracy. Our research focuses on understanding these large-scale rearrangements within the spliceosome. The spliceosome is composed of five small nuclear ribonucleoprotein complexes (snRNPs).  Dynamic rearrangements occur both within and between the snRNPs during the splicing cycle. These rearrangements are indicators that splicing is proceeding accurately. The ramifications of improper splicing are severe. In humans, improper splicing can lead to a range of diseases, including retinitis pigmentosa, on which our lab focuses. Our research aims to dissect the molecular interactions that stimulate spliceosome assembly and activation.  Specifically, we are currently focused on how the interactions of splicing proteins Dib1, Prp6 and Prp31 help progress spliceosome assembly. Dib1, Prp6 and Prp31are essential for cell viability and splicing and are conserved from yeast to humans.  We have identified amino acids in each protein that are important for splicing. We are now trying to further characterize the interactions using biochemical and molecular biology techniques in order to understand how the interactions between proteins help to maintain particular splicing complexes. For example, a change to an amino acid in the Dib1 may cause the protein to not interact as well with Prp6 resulting in weakened interaction that stall spliceosome assembly. Overall, our work aims to build a molecular model for how these splicing proteins at the core of the splicing machinery help regulate spliceosome assembly directly or indirectly. Our studies on the spliceosome are quite interdisciplinary. In our lab, we use a variety of biochemical, molecular biological, and genetics techniques to dissect the importance of protein-nucleic acid and protein-protein interactions in the spliceosome. Students have opportunities in 1) biochemistry, including gel based binding assays for protein-RNA and protein-protein interactions, and structural studies using circular dichroism, 2) molecular biology, using protein purifications, DNA cloning, and RNA transcription and purification and 3) genetics using Saccharomyces cerevisiae (Baker’s yeast) and mouse and human cell culture and 4) fluorescence microscopy skills. 

Cooley Lab

Chemical Synthesis, Bioinorganic Chemistry and Polymer Chemistry

Professor: Christina Cooley, Ph.D.

Overview: 

Research in the Cooley lab applies the power of synthetic organic chemistry to solve problems in biology and human health. Students in my lab will have the opportunity to design and synthesize new molecules and assess their ability to detect and treat human disease under the following two major project areas.

Our primary research area is in the development of new methods to amplify molecular signals as a way to detect biomolecular interactions and potentially, disease. We have developed fluorogenic monomers that are not fluorescent in monomer form, but glow when incorporated into a polymer synthesized by various methods, for example by atom transfer radical polymerization (ATRP). Polymer fluorescence is quantifiable by fluorescence readers or visible to the naked eye, and tracks with the concentration of polymerization initiator, which serves a model analyte.

This fluorogenic polymerization subgroup has many current research directions ranging from fundamental organic synthesis and polymerization studies to detection applications. Current projects are aimed toward the synthesis of new monomers to improve physical properties such as water solubility, development and evaluation of alternative light-initiated fluorogenic polymerization platforms, optimization of the fluorogenic polymerization approaches for analyte detection, and application to the direct detection of proteins and biomolecular interactions. Students working in this area will apply a range of organic, polymer and biochemical techniques, from the chemical synthesis of small molecules and free-radical polymerization techniques initiated by various methods from metal catalysts to irradiation with visible light, to analysis and characterization of the polymers formed by gel permeation chromatography, nuclear magnetic resonance spectroscopy, and fluorescence analysis methods.

The Cooley lab has a second subgroup in the general field of therapeutic drug delivery, utilizing the sensing of reactive oxygen species (ROS) for prodrug activation and therapeutic release in diseased tissues. A prodrug is a “caged” version of a drug that is inactive until release to the free drug is achieved under specific biological conditions. We have synthesized and evaluated prodrugs of AA 147, which activates a stress-responsive signaling pathway as a therapeutic target for treatment following reperfusion events such as heart attacks and strokes. These prodrugs of AA 147 are selectively uncaged by the presence of reactive oxygen species (ROS), which occur at high levels during reperfusion events. We are also exploring other types of releasable AA 147 prodrugs to improve pharmacodynamics properties for in vivo animal studies, and the synthesis of fluorogenic ROS sensors for collaborative chemical applications. Students in this area will gain experience with small-molecule synthesis and characterization, and analyze their therapeutic release profile under biological conditions.

Lambert Lab

Organic Chemistry

Professor: Joseph B. Lambert, Ph.D.

Amber is the fossilized end product of resinous materials exuded by plants millions of years ago.  It is found on every continent except Antarctica.  There are at least five chemically distinct types of amber, depending on the botanical material from which the original exudate came from.  Nuclear magnetic resonance (NMR) spectroscopy can distinguish these different botanical sources and provide a means of determining authenticity of amber and learning about its geographical sources.

More generally, exudates are complex mixtures of organic compounds produced by plants, usually as the result of injury or disease.  Secreted as liquids, exudates may harden to solids in hours to months on the surface of the plant.  These materials have found numerous practical applications throughout human history, and they provide a molecular window to the classification of plants (taxonomy).  We have found that exudates are remarkably robust and consistent in their molecular constitution within a single plant and from plant to plant within a given species.  There are several, distinct chemical constitutions of exudates.  Resins, which can form amber through fossilization, are composed of terpenoid compounds.  Gums are made of polysaccharides.  Gum resins like frankincense and myrrh contain both materials.  Kinos contain phenols.  Although these four chemical groups are the largest, there are several other smaller but distinct chemical groups.

We are carrying out a worldwide survey of plant exudates from all plant families, and of amber, necessitating field acquisition of materials and analysis by NMR in the lab.  We also are examining the effect of heat on the molecular structure of amber and its slightly younger colleague, copal.  Heat has been used to alter the properties of amber prior to carving.  Spectroscopic examination of artificially heated samples may clarify how structure change with heating.

Shearer Lab

Inorganic Chemistry; Computational Chemistry; X-ray Spectroscopy

Type: Inorganic Chemistry
Professor: Jason Scherer, Ph.D.

Research in the Shearer Group is broadly centered on understanding how the electronic structure of biologically and industrially relevant transition metal species contribute to their reactivity and physical properties. Central to our work is the synergistic use of synthetic, spectroscopic and computational chemistry. Although we perform some work with naturally occurring biological systems or industrial catalysts, we primarily study synthetic systems to probe a specific aspect of their chemistry. Briefly outlined below are two projects currently being undertaken by the Shearer Group.

 1. High-Valent “Oxo” Complexes of Late First Row Transition Metals. Nature uses transition metal-oxo species to facilitate a large variety of biosynthetic transformations including water oxidation to O2, methane hydroxylation to methanol, alkene epoxidations and cellulose degradation to simple sugars. Manganese, iron and copper are employed in these biological transformation, yet nature does not use cobalt or nickel. To understand why we have been investigating the properties of CoO and NiO complexes in high oxidation states in collaborations with other research groups from the US, Europe and Asia. The key questions we seek to address are: a) how can one stabilize Co/Ni-O complexes, b) what is the fundamental nature of the Co/Ni-O moiety, and c) how are different structures and bonding schemes about the Co/Ni-O moiety influencing the stability and reactivity of the resulting complexes. To these ends we prepare high-valent metal-oxo complexes (see Figure) and subject them to spectroscopic, mechanistic and computational studies to understand their fundamental properties. It is hoped that an understanding of the structure-function relationships in such species will inform on the design of molecular oxidation catalysts. 

2. Understanding Transition Metal Ligand Bonds Through the Lens of Valence Bond Theory. In modern chemical physics quantum mechanical descriptions of chemical bonding are described through three main models: molecular orbital, density functional, and valence bond (VB) theory. All of these approaches have distinct benefits and disadvantages. VB theory has the advantage of placing bonding in terms that chemists understand (covalent vs ionic bonding), and thus yields intuitive descriptions of bonding. However, it has only been in the past decade that VB theory methods have advanced to the point where larger systems of chemical interest can be tackled at a sufficiently high level of theory to yield accurate solutions. We have taken advantage of these recent advances in VB theory to explore the bonding, energetics, and reactivity of transition metal complexes involved in organometallic transformations. For example, we have recently investigated reductive elimination from [CuR4]– complexes (R = alkyl) and discovered a number of “hidden” features concerning the chemistry of such species. For example, one surprising aspect of such reactions is that they are not reductive eliminations in any physically meaningful sense of the word; instead they can be viewed as admixtures of radical C-C couplings and simple Lewis acid/base reactions. 

Urbach Research Group

Organic Synthesis, Chemical Biology

Professor: Adam Urbach, Ph.D.

The chemistry of pharmaceuticals and medical diagnostics depends on the ability of a molecule to recognize a specific protein in a complex mixture, such as blood, and to stick to that protein. Pharmaceuticals block the normal function of that protein. Medical diagnostics measure the quantity of that protein. The Urbach Research Group develops new chemistry that enables the recognition of specific proteins, and we apply this new knowledge to address current biomedical problems.

The group has established a set of rules for protein recognition that is predictable from the sequence of amino acids, and we are working to expand these rules and to develop new applications. Current research directions in the group include: 1) synthesis of artificial receptors for site-specific labeling of proteins; 2) synthesis of artificial receptors for ultra-high affinity binding of proteins; and 3) using artificial receptors to direct protein folding.  These projects is funded by an external grant from the Welch Foundation, National Institutes of Health, and Research Corporation for Science Advancement, respectively.  Dr. Urbach is always interested in discussing new ideas with students.

Students in the group are involved in all aspects of the research, including experimental design and implementation, problem solving, data analysis, presentation, and publication. Students learn a wide range of techniques, including organic synthesis, NMR spectroscopy, mass spectrometry, microcalorimetry, fluorescence spectroscopy, circular dichroism spectroscopy, high performance liquid chromatography, and X-ray crystallography.  This year, all students will focus on the synthesis of new molecules and the study of their interactions with proteins.  This combination of experimental approaches and methodology offers students a breadth of technique and depth of study that is an excellent foundation for graduate school and for employment in biotech, pharmaceuticals, diagnostics, and quality control.

Harrison Research Group

Spectroscopy and Photochemistry of Atmospheric Aerosols

Focus:  Analytical, Physical and Atmospheric Chemistry
Professor:  Aaron W. Harrison, Ph.D.

Overview: Aerosols are microscopic solid or liquid particles suspended in the atmosphere, ranging in size from a few nanometers to several microns. The atmosphere contains a diverse mix of aerosols from biogenic and anthropogenic sources, including carbonaceous particles (brown carbon, secondary organic aerosols), sea salt, dust, and bioaerosols like viruses and pollen. Aerosols play central roles in atmospheric chemistry by providing surfaces and condensed phases for chemical reactions and serving as cloud condensation nuclei. However, elevated aerosol concentrations also contribute to poor air quality, with links to respiratory and cardiovascular health issues. Understanding the sources, chemical composition, and oxidative transformations of atmospheric aerosols is critical for addressing challenges at the intersection of climate change, air quality, and human health. 

Research focus:
Research in the Harrison Group focuses on development and application of advanced spectroscopic techniques and computational analysis to characterize the composition, photochemistry, and optical properties of atmospheric aerosols. A central tool in our work is fluorescence spectroscopy, which enables the identification and classification of aerosol types in both laboratory and field studies. Despite its utility, significant difficulties remain in accurately characterizing chemically complex aerosols, leading to potential misidentifications in environmental settings. To address this challenge, research in our group explores the combined use of energy- and time-resolved fluorescence to more reliably distinguish aerosol types, with applications in atmospheric field studies and remote sensing.

In addition, our research leverages fluorescent probe molecules to directly investigate particle characteristics such as pH and viscosity which are key factors that control chemical reactivity and gas-particle partitioning. These properties are difficult to measure due to the size and variability of atmospheric particles. However, by applying laser-induced fluorescence spectroscopy, this research provides insight into how these properties change with composition and humidity and the microenvironment within aerosol particles. 

Photochemistry is another major focus of our research. Many light-absorbing compounds including quinones, aromatic ketones, and oxygenated or nitrated polycyclic aromatic hydrocarbons (PAHs) partition into condensed atmospheric phases such as aerosols and cloud water. Sunlight initiates secondary chemistry in these systems through the production of reactive species, yet the ability of these molecules to act as photosensitizers remains poorly quantified under atmospherically relevant conditions. Our work seeks to close this knowledge gap by directly probing photosensitization processes in aerosol proxy matrices.

Rapf Lab

Photochemistry in Complex Aqueous Environment

Type: Physical Chemistry
Professor: Rebecca Rapf, Ph.D.

Overview: The Sun is the largest source of energy to the planet, and it controls, directly or indirectly, the vast majority of physical, chemical, and biological processes that take place on Earth. Photochemical processing of material drives the engine of atmospheric and environmental chemistry in planetary environments, largely through the formation and subsequent reactions of radical species. The reactivity of these radicals is controlled and mediated by the surrounding environmental conditions under which they were generated. Photochemically-generated organic radicals are particularly interesting because they offer an abiotic pathway to make larger, more complex organic molecules, which has applications to atmospheric chemistry, prebiotic chemistry, and astrobiology. This research is grounded in fundamental physical chemistry but is inherently interdisciplinary, drawing on organic chemistry, environmental chemistry, biophysics, and planetary science.

The Rapf lab examines the direct aqueous photochemistry of organic molecules under conditions relevant to planetary environments, including the modern and ancient Earth as well as other potentially habitable worlds. We conduct detailed photochemical experiments that allow us to examine, mechanistically, changes in reactivity that occur as a function of reaction conditions, including photon flux, atmospheric composition, and solution conditions (e.g. pH and salinity). Using model chemical systems, we can systematically increase the complexity of model systems to investigate the origins of emergent behavior.

In tandem with photochemical studies, we also explore how intermolecular interactions mediate chemistry, both through orientation and concentration at interfaces and through the formation of supramolecular assemblies. This is motivated by the repeated observations that in many cases the chemistry of single species in a bulk environment cannot be used to predict the reactivity of those species either in confined environments or in concert with other molecules. Of particular interest are recent literature reports that molecules at aqueous interfaces can undergo photochemistry that is not seen in the bulk. We explore how photochemistry is mediated by surface films composed of insoluble surfactants, such as long-tailed fatty acids like stearic and palmitic acid, using photochemical-initiator species, such as pyruvic acid.

Students will conduct photochemical experiments, which are analyzed using a combination of mass spectrometry, optical spectroscopy, and surface tension measurements. Students will also have opportunities for instrument development, as we build surface sensitive spectroscopic techniques to probe interfacial photochemistry directly.