The hyperthermophilic archaeon Pyrococcus furiosus (Pf) grows optimally at 100°C by fermenting peptides and sugars. It also reduces elemental sulfur to hydrogen sulfide. From Pf we are purifying and characterizing a range of metal-containing, oxidoreductase-type enzymes and redox proteins that are involved in unusual catabolic pathways. In addition, all ORFs in the Pf genome (1.9 Mb) are being cloned and expressed in an NIH-funded structural genomics initiative with the goal of obtaining 3D structures on all Pf proteins. The function of all Pf ORFs are being assessed using DNA microarrays and proteomic approaches in conjunction with metabolic and physiological analyses.

Heme is a key and essential compound for the vast majority of living organisms. Heme, as a cofactor in a variety of proteins, is widely acknowledged to be essential for gas transport, respiration, xenobiotic detoxification, peroxide production and destruction, fatty acid desaturation, and a variety of one electron transfer reactions. Over the past decade the number of roles identified for heme has grown substantially. It has become clear that heme is also an important intracellular regulatory ligand. Among the list of biological processes for which higher eucaryotic heme-binding proteins have now been implicated is regulation of circadian rhythm, adipogenesis, glucose homeostasis, microRNA processing, gas sensing, control of ion channels, and intra- and intercellular signal transduction. The list of bacterial heme-binding sensors seems to grow with each new journal publication, and the role of the heme-containing DevS-DevR proteins of Mycobacterium tuberculosis as regulators of passage into the dormant stage has attracted considerable attention for obvious biomedical reasons. Dietary heme also serves as a significant source of iron for many organisms including pathogenic bacteria. A search of PubMed for “heme” yields over 2500 listed publications in the past year. The Dailey lab’s research focuses on the enzymes responsible for heme biosynthesis. Current studies involve structure/function investigations of the terminal enzymes of heme biosynthesis and their relationship to the human genetic diseases known as porphyrias, biochemical characterization of the enzymes from both eukaryotic and prokaryotic organisms, identification and characterization of novel and previously unidentified genes involved in heme synthesis and transport, protein-protein interactions among heme synthesis enzymes, and regulation of expression and translocation of heme synthetic enzymes.

The Edison lab develops new approaches in metabolomics and natural products research. Our primary research tool is NMR spectroscopy, but we regularly collaborate with experts in mass spectrometry. A major focus is on data integration between NMR, MS, and other quantitative measurements. We have numerous applications, primarily through collaborations.
 

We study how protein glycosylation affects cellular communication as well as protein folding using biochemical, cell biological and animal studies. The forms of glycosylation we study affect development, birth defects, and cancer.
 

Research in my lab is at the intersection of genome biology, evolutionary biology and computational structural biology. We combine techniques and approaches from these diverse disciplines to understand the underlying mechanisms of signaling proteins in atomic detail.

Heme is a cofactor found in essentially all aerobic organisms and a majority of anaerobes and facultative organisms. Most organisms that possess heme synthesize it themselves. With the exception of Caenorhabditis elegans and related helminthes, heme acquired via dietary sources is generally degraded to release free iron and is not utilized as a source of cellular heme. While the traditional textbook roles for heme as a cofactor include hemo- and myoglobins, cytochromes and a handful of enzymes, considerable evidence has emerged that demonstrates a central role for heme in regulation of gene transcription, as a gas sensor, in the regulation of circadian rhythm, during development and in RNAi processing. Disordered heme metabolism can have profound developmental and health consequences. Our laboratory is exploring these mechanisms in atomic detail in order to provide a better foundation for future drug and therapy development.

Understanding intracellular and intercellular heme transport

My research focuses on the use of mass spectrometry to answer biological / biomedical questions. The majority of our projects involve characterizing the post-translational modifications (e.g., glycosylation, phosphorylation) present in the protein of interest. For example, we are currently investigating the in vivo changes that occur in human eye lenses upon normal aging and cataract formation. We hope that this research ultimately will provide a mechanism to prevent cataracts. We also conduct research into developing new methodologies to increase the amount of information obtained from these MS experiments and to reduce the quantity of material needed for analysis.

The Prestegard group applies Nuclear Magnetic Resonance (NMR) spectroscopy to the investigation of structural and functional properties of biologically important systems. Systems of interest include carbohydrate binding proteins, metallo-proteins and membrane associated proteins. These systems play important roles in cell signalling, cell differentiation, and cell-cell interaction. As such, they become targets for rational drug design. NMR provides a useful tool for these investigations. However, NMR is also an evolving tool, limited both by current experimental approaches and data analysis procedures. To push back limits of applicability the group also devotes considerable effort to method development.

X-ray structural biology, the mitochondrial inner membrane space transport system, structure based vaccine and therapeutic design, improved/automated methods for synchrotron SAD data collection and structure determination.

Biophysical analysis of metallobiochemical systems using X-ray absorption spectroscopy; systems biology approaches to discovery of transcriptional regulation of microbiological hydrogen production as part of an alternative energy project.

Our research focuses on protein structure and function and protein-protein interactions. We employ an approach combining modern analytical, biophysical and molecular biology techniques, with an emphasis on biomolecular NMR spectroscopy. Our core projects include the study of gene regulation and novel regulators of transcription initiation in bacteria, oxidative stress and calcium signaling, steroid hormone (estrogen) receptor activation, and regulation of biofilm formation and pathogenesis in Pseudomonas aeruginosa. These projects are important fundamentally, and they important biomedically with respect to antibiotic target development, oxidative stress and biological aging, and diseases such as breast cancer and cystic fibrosis.

Structure-function studies by X-ray diffraction, transcription proteins, structural genomics, phasing methods

Our laboratory is interested in how post-translational modifications of proteins increase functional diversity. Primarily, we are interested in glycosylation, with a focus regarding: 1. O-GlcNAc in Type II diabetes and stem cell biology 2. O-Mannosylation in Congenital Muscular Dystrophy and viral entry into host cells 3. Glycoproteins as biomarkers in human disease, specifically pancreatic cancer and metabolic syndrome 4. Development of technology-based approaches, primarily mass-spectrometry, for quantitive proteomics/ glycomics/ glycoproteomics.

Glycosylation regulates the activities of proteins via multiple intrinsic and extrinsic mechanisms. A remarkable example, in our laboratory’s view, is the glycosylation of a subunit of the E3(SCF)ubiquitin ligases, Skp1. Skp1 glycosylation, which depends on its prior oxygen-dependent prolyl hydroxylation, promotes assembly and presumably the activities of this enzyme family toward the degradation of a whole host of cell regulatory factors. This mechanism underlies oxygen-sensing by a variety of unicellular organisms, including the social amoebaDictyostelium and the human pathogen Toxoplasma gondii. Our multidisciplinary approaches to understand this mechanism, and exploit our understanding to control parasite virulence, embrace structural biology, metabolomics, bioinformatics, molecular genetics, enzymology, cell and developmental biology, and parasitology.

X-ray crystallographic and biochemical studies of nucleotide sugar metabolism

The focus of my group's research is to examine the relationships between carbohydrate conformation and biological recognition and activity. We are particularly interested in the mechanisms of carbohydrate recognition in the immune system. Current research projects include examinations of bacterial antigen-antibody interactions, as well as other carbohydrate-protein interactions. The carbohydrate antigens associated with bacteria, such as Salmonella paratyphi B and group B Streptococcus are being studied in order to quantify the contributions made by hydrophobic and hydrophilic interactions. In conjunction with experimental methods (NMR and X-ray), we apply molecular dynamics simulations with the GLYCAM parameters and the AMBER force field.

Cancer Computational and Systems Biology: We are interested in developing integrated computational and omic techniques for (a) identification of biomarkers for a number of human cancers, detetable through analyses of serum/urine samples, and (b) understanding the relationships between molecular signatures and cancer formation & development. Our work involves microarray gene expression data generation and analyses, comparative genome analyses and analyses of other experimental data. Computational Study of Plant Cell-wall Synthesis Genes and Pathways : We are interested in developing computational prediction and analysis techniques for inference of genes involved in cell wall synthesis in plants and regulatory elements of these genes & their relevant biochemical pathways. Our work currently involves prediction and analyses of protein-protein interactins relevant to cell wall synthesis, prediction of Golgi-residing proteins, bi-clustering analyses of microarray gene expression data and co-evolutionary analyses of cell-wall synthesis genes. Study of Microbial Genome Structure and Application to Pathway & Network Inference: We are interested in understanding both the micro- and macro-structures of microbial genomes through computational studies and experimental validation, and in understanding why microbial genomes are organized the way they are. We are also interested applying the knowledge and information gained through such studies to prediction of pathways and networks in microbes. Computational Methods for Protein Structure Prediction and Modeling: We are interested in developing effective computational methods for protein fold recognition, protein structure prediction and modeling, and protein complex prediction; and applying these tools to solve real structural biology problems. We are also interested in developing hybrid methods for protein structure solution using information from derived from computational tools and partial experimental data, including NMR and X-ray crystallograpohic data. Our research work is currently sponsored by NSF, DOE, NIH, Georgia Research Alliance, Georgia Cancer Coalition and the University of Georgia. In addition, our work had been generously supported by Oak Ridge National Lab and Pacific Northwest National Lab.

The "primary" cell wall, which surrounds growing plant cells, plays a key role in plant development. One of its most important functions is to control the rate and orientation of cell expansion. Polysaccharide networks in the wall expand by gradually yielding under osmotic stress, allowing the cell to grow in a controlled, oriented fashion. This process determines the morphology of each cell, which ultimately determines the shape of the entire plant. Research in my laboratory is aimed at characterizing the molecular dynamics and topology that lead to the assembly and controlled expansion of the cell wall.