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[ Phd Program: Chemistry ]

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NameEmailPhd ProgramResearch InterestsPublications
Allbritton, Nancy email , , , , publications

The overall focus of the laboratory is to quantitatively measure the activity of proteins in cellular signaling networks to understand the relationships of these intracellular pathways in regulating cell health and disease. These networks are composed of interacting proteins and small molecules that work together in a concerted manner to regulate the cell in response to its environment. Despite the importance of these key signaling molecules in controlling the behavior of cells, most of these proteins and metabolites can not be quantified in single cells. There is a need throughout biology for new technologies to identify and understand the molecular circuits within single cells. A research goal is to develop new methods that will broaden the range of measurements possible at the single-cell level and then to utilize these methods to address fundamental biologic questions. We are pursuing this task by bringing to bear diverse techniques from chemistry, physics, biology and engineering to develop new analytical tools to track signal transduction within individual cells. Our research is a multidisciplinary program for the development and application of new analytical methods with two main focus areas: 1) techniques to monitor cellular signaling, and 2) microfabricated cellular analysis systems.

Berkowitz, Max email , , , , publications

We use computational techniques (multiscale molecular dynamics computer simulations) to study interactions of proteins and peptides with membranes and to study interactions of shock waves with membranes of neural cells. Specifically, we study the interaction of antimicrobial peptides with bacterial membranes to understand how they destroy such membranes.  In our study of shock wave interacting with brain tissue we investigate the importance of cavitation effect (collapse of bubbles) created by shock waves. Detailed molecular level knowledge of the processes we investigate using computational methodology is very helpful in understanding processes such as TBI (traumatic brain injury).  The computational methodology we use is also playing now an important role in the filed of drug design.  Member of the Molecular & Cellular Biophysics Training Program.

Brustad, Eric M email , , , publications

The Brustad group is interested in applying chemical principles to expand biological systems beyond Nature’s design. We make use of developing technologies such as unnatural amino acid mutagenesis and non-natural cofactor design to increase the chemical functionality available to proteins. Current efforts are directed towards the genetic incorporation of organocofactor mimics as well as heme protein engineering through the incorporation of orthogonal metalloporphyrin scaffolds. We combine methods in synthetic chemistry, molecular biology, X-ray crystallography, and directed evolution to optimize the function of our protein engineering efforts.

DeSimone, Joseph M. email , , , , publications

The direct fabrication and harvesting of monodisperse, shape-specific nano-biomaterials are presently being designed to reach new understandings and therapies in cancer prevention, diagnosis and treatment.  Students interested in a rotation in the DeSimone group should not contact Dr. DeSimone directly.  Instead please contact Chris Luft at jluft@email.unc.edu.

Erie, Dorothy email , , , , publications

The research in my lab is divided into two main areas – 1) Atomic force microscopy and fluorescence studies of protein-protein and protein-nucleic acid interactions, and 2) Mechanistic studies of transcription elongation. My research spans the biochemical, biophysical, and analytical regimes.

Hicks, Leslie M. email , , , , publications

Research in the Hicks lab focuses on development and implementation of mass spectrometric approaches for protein characterization including post-translational modifications, as well as the identification of bioactive peptides/proteins from plants. Keywords: proteins / peptides, proteomics, PTM, enzymes, analytical chemistry, mass spectrometry, separations / chromatography, plants, algae

Lawrence, David S email , , , , , , publications

Living cells have been referred to as the test tubes of the 21st century. New bioactive reagents developed in our lab are designed to function in cells and living organisms. We have prepared enzyme inhibitors, sensors of biochemical pathways, chemically-altered proteins, and activators of gene expression. In addition, many of these agents possess the unique attribute of remaining under our control even after they enter the biological system. In particular, our compounds are designed to be inert until activated by light, thereby allowing us to control their activity at any point in time.

Li, Bo email , , , , publications

Our research focuses on the discovery and design of new gene-encoded bioactive small molecules from bacteria.  We are interested in understanding enzymes involved in their biosynthesis, their therapeutic mechanisms of action, and implications in health and diseases, in particular with respect to the human microbiome.  This work is driven by intensive development of new metabolomics and genomics technologies.  We subsequently manipulate and engineer these biosynthetic pathways to make new and improved molecules as potential therapeutics such as antibiotics.

Lockett, Matthew Ryen email , , , publications

Research in the Lockett group focuses on the development of analytical model systems to: i) chemically modify the surface of thin films, and study chemical and biochemical reactions occurring on those surfaces; ii) study drug metabolism in an environment that closely mimics the human liver; iii) measure tumor invasion in an environment that closely mimics human tissue. /  / While these problems require techniques found in analytical chemistry, biochemistry, molecular biology, bioengineering, and surface science we are particularly interested in the technologies that allow us to quantitatively measure reactions and analytes.

Pielak, Gary J. email , , , , , publications

My graduate students and I use the formalism of equilibrium thermodynamics and the tools of molecular biology and biophysics to understand how nature designs proteins.

Redinbo, Matt email , , , , , , , publications

The Redinbo Laboratory examines dynamic cellular processes using structural, chemical, molecular and cell biology. Our goals are to discover new drugs and to elucidate molecular pathways essential to human disease.  Current projects include developing the first drugs that target the human microbiome, unraveling the nature of innate immunity in the human lung, and discovering how microbial systems exchange genes, including those that encode antibiotic resistance.

Thompson, Nancy email , , publications

The immune system is a network of interacting biological cells. The molecular events that lead to the activation and regulation of these cells often occur at the cell surface. However, little is known about the arrangement, motions and interactions of the participating cell-surface molecules. To examine these phenomena, we construct model cell membranes on planar supports from purified or synthesized molecules.  Recently developed techniques in laser-based fluorescence microscopy can then be employed to examine the behavior of select fluorescently labeled molecules at or near the supported planar membranes.  This research is significant not only in the basic understanding of the immune system, but also in other areas of cell-cell communication and cell membrane biophysics, in the physics of two-dimensional fluids, and in biotechnology.

Waters, Marcey email , , publications

Our research focuses on several different aspects of biomolecular recognition, including (1) protein post-translational modifications, (2) protein-nucleic acid interactions, and (3) protein-protein interactions that are important in a number of different biological areas, including epigenetics and cancer.  We use bio-organic chemistry combined with peptide design and biophysical chemistry to study these interactions and to develop new tools for inhibition and/or sensing of these biomolecular interactions.

Weeks, Kevin email , , , , , , publications

The Weeks group invents novel chemical microscopes for understanding the structure and function of RNA and then applies these technologies to leading, and previously intractable, problems in biology. Most projects in the laboratory span fundamental chemistry or technology development and ultimately lead to practical applications in virology (especially HIV), next-generation structure analysis, drug design, and understanding RNA structure in living cells.  Collectively, this work has led to extensive recognition of graduate student colleagues in the laboratory.

Wolfenden, Richard email , , publications

Enzymes allow organisms to channel the flow of matter to their own advantage, allowing some reactions to proceed rapidly compared with other reactions that offer no selective advantage to the organism. After a substrate is bound at an enzyme’s active site, its half-life is usually a small fraction of 1 s. Rapid turnover is necessary if any enzyme is to produce a significant rate of reaction at the limited concentration (<10(-5) M) at which enzymes are present within the cell. Many enzymes are known to have evolved to work nearly as efficiently as is physically possible, with second order rate constants that approach their rates of encounter (10(9) M(-1)s(-1) with the substrate in solution. How rapidly would biological reactions occur if an enzyme were not present? Until recently, some reactions were known to require several years, and everyday experience suggests that some reactions are slower still. The survival of paper documents and ancient ships for long periods under water implies that the glycosidic bonds of cellulose, for example, are very resistant to hydrolysis in the absence of cellulases that catalyze their hydrolysis. Why would one wish to know the rate of a biological reaction in the absence of an enzyme? That information would allow biologists to appreciate what natural selection has accomplished in the evolution of enzymes as proficient catalysts and would enable chemists to compare enzymes with artificial catalysts produced in the laboratory. Such information would also be of value in considering the design of enzyme antagonists: the greater the rate enhancement that an enzyme produces, the greater is its affinity for the altered substrate in the transition state compared with its relatively modest affinity for the substrate in the ground state. That principle has furnished a basis for the design of transition state analogues, extremely powerful inhibitors that resemble the transition state and take advantage of that special affinity. Examples have now been discovered for enzymes of every class, including inhibitors that are already used to control hypertension, the spread of HIV, the maturation of insects and the growth of weeds. By allowing snapshots of enzymes in action, transition state analogues have also provided valuable tools for investigating enzyme structures and mechanisms, most recently that of the peptide bond forming center of the ribosome. Those enzymes that produce the largest rate enhancements and transition state affinities should offer the most sensitive targets for inhibitor design. Particularly remarkable are those enzymes that act as simple protein catalysts, without the assistance of metals or other cofactors. To determine the extent to which one such enzyme, human uroporphyrinogen decarboxylase, enhances the rate of substrate decarboxylation; we examined the rate of spontaneous decarboxylation of pyrrolyl-3-acetate. Extrapolation of first-order rate constants measured at elevated temperatures indicates that this reaction proceeds with a half-life of 2.3 x 10(9) years, approaching the age of the Earth. This enzyme shows no significant structural or sequence homology with yeast orotidine 5′-monophosphate decarboxylase, another cofactorless enzyme that catalyzes a very slow reaction. To uncover the mechanisms of action of these remarkable molecules, we are studying these and other enzymes by kinetic and structural methods, site-directed mutation and the study of model reactions. In addition to more traditional methods, these projects make extensive use of new methods that include high-field NMR, isothermal calorimetry, and kinetic experiments in water and other solvents in sealed tubes at very high temperatures.