Maria Peña
Short Biography:
Dr. Peña received her B.S. in Biology in 1989 and her M.S. and Ph.D. degrees in Plant Science in 1994 and 1996, respectively, from the University of Santiago de Compostela (Spain). Prior to joining the CCRC in 2003, she was a Postdoctoral Fellow from 1998 to 2002 in the Department of Botany and Plant Pathology of Purdue University (IN). Currently, Dr. Peña is an Associate Research Scientist at the CCRC and funded investigator of the DOE Center for Bioenergy Innovation (CBI).
Dr. Peña has over 60 full publications, 1 book charter and 1 patent.
Research Interests:
Dr. Peña’s research focuses on several topics related to plant cell walls including i) synthesis, structure, and biological function of cell wall polysaccharides, ii) plant biomass deconstruction by microorganisms, and iii) production of plant cell wall-derived biomaterials. This research involves the application of advance mass spectrometry and NMR spectroscopy techniques for the determination of polysaccharide structure, functional characterization of carbohydrate-active enzymes and protein-carbohydrate interactions.
William York
Short Biography:
Dr. York received his B.A. in molecular, cellular, and developmental biology in 1978 from the University of Colorado and his Ph.D. in biochemistry and molecular biology in 1996 from the University of Georgia. He was senior research chemist at the CCRC from 1985-96. Full publications: 96.
Research Interests:
Dr. York’s diverse research interests include the development and application of spectroscopic and computational methods for the structural and conformational analysis of complex carbohydrates, the development of bioinformatics tools to study the roles of carbohydrates in living systems, and the use of these tools to develop realistic models describing the assembly and morphogenesis of the “primary cell walls” that surround the growing cells of higher plants.
His early research focused on the analysis of plant cell walls using a multidisciplinary approach. Extensive spectroscopic analysis of xyloglucan, a load-bearing polysaccharide involved in controlling the rate and orientation of cell wall growth, have been performed in Dr. York’s laboratory. The results of these spectroscopic studies have been summarized in the form of a database that provides chemical shift information taken from the NMR spectra of over 50 xyloglucan oligosaccharides that have been characterized in Dr. York’s laboratory. The organization and user interface of this database facilitates the retrieval of information regarding specific correlations between structural featurres of the oligosaccharides and the chemical shifts of diagnostic resonances in the NMR spectra. The availability of this information makes it possibly to rapidly and accurately identify oligosaccharides that are present in the database and to identify structural features of related oligosaccharides that have not yet been characterized. As a result of Dr. York’s interest in database development and data mining methodology, he has recently initiated a bioinformatics project as part of the Integrated Technology Resource for Biomedical Glycomics funded by the National Center for Research Resources of the NIH.
The Plant Cell Wall. Expansion of the primary cell wall determines the final size and shape of each plant cell, thereby defining the morphology of the entire plant. It is generally accepted that, with the exception of cellulose, the macromolecular components of the primary cell wall are synthesized within the Golgi and exported to the apoplasm. Cellulose, which is synthesized at the plasmalemma, combines with these components to form a cross-linked matrix (the primary cell wall) that expands at a controlled rate in a defined direction. The process of cell wall assembly thus depends on the incorporation and subsequent reorganization of polysaccharides. In order to develop a coherent picture of this complex process, it is necessary to combine information regarding the biosynthetic mechanisms and chemical structures of cell wall polysaccharides, the physical bases for their assembly (i.e., their molecular conformations and dynamics), the nature of their covalent and non-covalent interconnections, the specificity and regulation of enzymes that catalyze the formation and/or cleavage of these interconnections, the overall topology of interconnected polysaccharide networks, and the rheological consequences of these interacting factors. This is a formidable problem demanding a multidisciplinary approach.
York is addressing this problem by examining the structural details of the cell walls of various plants, thereby determining how their primary, secondary, and higher-order structures vary from tissue to tissue and from plant to plant. Conserved features are likely to confer essential functions upon the cell wall. For example, features that are consistently associated with a specific developmental stage or morphogenetic process (e.g., cell elongation) probably play important roles in plant cell differentiation. The abundance of individual oligosaccharide subunits of the polysaccharide may vary, or novel, chemically modified subunits may be produced at specific developmental stages. For further information regarding the mulitdisciplinary study of plant cell walls see the CCRC’s Plant Cell Walls Web Site.
Spectroscopic methods to analyze complex glycans. Although much less sensitive than chromatographic and mass spectral methods, NMR spectroscopy can often provide all of the information necessary to completely define the primary structure of a complex glycan. York and his colleagues have used NMR (along with other techniques) to determine the primary structures of more than 50 oligosaccharides derived from XGs isolated from the cell walls of various plants. These analyses make it possible to identify previously characterized XG oligosaccharides by their NMR spectra and have revealed many correlations between the structural features of XG oligosaccharides and characteristic resonances in their NMR spectra, facilitating the structural analysis of novel XG oligosaccharides. Continued development of this approach will provide crucial information necessary for studying cell wall structure and metabolism, and is a prerequisite for the comprehensive application of chromatographic methods that rely on well characterized standards.
Recently, York and colleagues have developed methods for the selective fragmentaion of pectic polysaccharides based on β-elimination reactions. Effective utilization of this class of reactions to break pectic polysaccharides into well-defined fragments has been a long-standing goal in the plant cell wall research community. The new methods developed in York’s lab have the potential to greatly simplify the characterization of pectic polysaccharides that are modified as plant cells develop.
In collaboration with other scientists at the CCRC (notably the Orlando Laboratory) York has developed new methods using isobaric labeling and multiple mass spectrometry (MSn) techniques to simultaneously identify and quantitate glycans at high sensitivity. The new method, called Quantitation by Isobaric Labeling (QUIBL) can even be used to quantitate mixtures of isomeric glycans, which is extremely difficult using more traditional methods.
The molecular conformations and dynamics of complex glycans. The assembly and expansion of the primary plant cell wall is directed by the conformation and dynamics of the cell wall polysaccharides that must interact during this process. York and co-workers have developed models, based on conformational energy calculations, for the incorporation of XGs into the primary cell wall. These calculations suggest that the XG can adopt specific, low energy conformations that allow all of the side chains to fold onto one face of the XG chain, freeing the other face to interact with cellulose. Rigorous evaluation of this model will require further experimental and computational analyses, and will depend on improvements in the accuracy of molecular force fields.
Polysaccharides and other glycans often exhibit complex dynamic behavior in solution because they can adopt many different low energy conformations, making them difficult to study by crystallographic and spectroscopic techniques. Their flexibility, compared to globular proteins, may paradoxically arise from the rigidity of the glycosyl residues from which they are constructed. Rigid glycosyl residues may not fold into a neatly packed, low energy structure the way the flexible amino acid side chains of a typical protein do. Therefore, it is often proper to define the conformation of a complex glycan in terms of an ensemble of interconverting states. NMR spectroscopy is the most frequently used technique to study these dynamic ensembles, but it rarely provides sufficient information to describe them in detail. Therefore, conformational models must rely on the agreement of computational methods with experimental methods such as NMR. Although these rapidly evolving techniques currently provide a limited picture of the conformational dynamics of complex glycans, they are indispensable tools for elaborating a dynamic structural model of the primary cell wall.
Informatics for glycobiology and glycomics. Dr. York has a long-standing interest in informatics technology that can be applied to complex glycan structures. He was actively involved in the creation of CARBBANK, which was the first worldwide, comprehensive database of glycan structures. More recently, York has been developing methods for the exchange of glycan structural data over the Internet. His most important contribution in this area is GLYDE-II, an XML standard for structural data exchange that has been accepted as the standard protocol by the leading carbohydrate databases in the United States, Germany, and Japan.
Dr. York’s work is supported by the United States Department of Agriculture, the Department of Energy, the National Science Foundation, The National Institutes of Health, and the University of Georgia Research Foundation.
James Prestegard
Short Biography:
Dr. Prestegard received his B.S. in chemistry in 1966 from the University of Minnesota and his Ph.D. in chemistry from the California Institute of Technology in 1971. Prior to joining the CCRC in January 1998, Dr. Prestegard spent 27 years in the Chemistry Department at Yale University where he held positions of assistant professor, associate professor, and professor. In addition to his normal professorial duties, he now directs the regional NMR facilities at the University of Georgia. Dr. Prestegard serves on the editorial boards of several journals, including the Journal of Magnetic Resonance and the Journal of Biomolecular NMR, and is a frequent member of advisory and review panels.
Research Interests:
Dr. Prestegard’s group is applying nuclear magnetic resonance (NMR) spectroscopy to the study of the structure and function of biologically important macromolecular assemblies involving carbohydrates, proteins, and membranes. Research in the Prestegard laboratory focuses on NMR methods development, membrane proteins, cell-surface carbohydrates, protein structure, and protein-protein interactions.
Proteins are large molecules that are targets (receptors) of natural ligands (smaller molecules that bind specifically to the active site of a protein) as well as pharmaceuticals. An essential part of developing any new drug is to determine how that drug will bind to its target protein(s) and to characterize the structures and conformations of the interacting molecules, a particularly difficult task when flexible structures such as carbohydrates are involved. Nuclear magnetic resonance (NMR) spectroscopy is rapidly becoming a major contributor of structural information on how natural ligands and derived drug candidates bind to protein targets. However, progress has been impeded by reliance on short-range interactions (known as NOEs) that are limited in their ability to characterize the relative placement of remote parts of macromolecules or to characterize the average conformation of flexible ligands. These limitations are particularly severe in recognition of carbohydrate-containing ligands because they are inherently flexible and because the proteins that recognize them often function as multimers of loosely connected domains.
The Prestegard group has recently made some important advances in developing non-NOE-based structure determination methods. These methods rely on a more direct NMR measurement that can be made in “ordered” media, in the presence of high magnetic fields. Using these new methods the Prestegard group has succeeded in characterizing the relative orientation of two domains in a carbohydrate-binding protein and in collecting structural data on a flexible trisaccharide (a molecule composed of three sugars) without the use of NOEs. The experiments provide data in a fraction of the time required by the traditional NOE-based approach and can provide a unique structural perspective on which to base the design of new drugs.
NMR methods development. Methods development is closely related to the demands of the applications. For example, some exciting diffusion-edited amide exchange experiments have been developed for the investigation of the energetics and kinetics of protons involved in hydrogen bonds. Hydrogen bonding is important in stabilizing protein structural elements and in protein-carbohydrate recognition, both subjects being studied in the Prestegard group. Neural network-based automated assignment programs for multi-dimensional NMR spectra have been developed, as have statistics-based spectral analysis programs. These programs are essential in achieving less tedious and more precise NMR-based structural analysis.
An ongoing objective of the Prestegard group is to extract new types of information from NMR and related experiments. Current projects involve the use of residual dipolar couplings that occur in molecules oriented by very high magnetic fields and cross-correlation effects that involve chemical shift anisotropies that also become large in high fields. Both topics rely on the design of new experiments and in-depth theoretical analysis of experimental results.
Membrane proteins. The structural analysis of membrane proteins is one of the major challenges in biophysical chemistry today. It is a major challenge because these proteins prefer an environment that is neither crystal nor solution. Unfortunately, crystal and solution phases are the only two phases for which structure determination methods are well established. The Prestegard lab has undertaken the development of NMR-based structure determination methods that are applicable in a medium that mimics the partial, liquid crytalline order of natural membranes. These methods are currently being applied to peptides that present typical membrane protein structural motifs, such as trans bilayer helices and surface-associated amphipathic helices.
Cell-surface carbohydrates. Carbohydrates covalently linked to proteins (glycoproteins) and to lipids (glycolipids) are also present on the surfaces of membranes. In fact, they are the primary mediators in processes that involve interaction of a cell with its external environment. This external environment includes important processes such as cell-cell interactions, hormone stimulation, and invasion by pathogens. Structural characterization of the carbohydrate moieties in their nature environment is essential to understanding and controlling the processes in which they are involved. Many of the NMR methods being developed to characterize membrane proteins are equally applicable to cell-surface carbohydrates. In addition, methods that are more focused on the details of protein-carbohydrate recognition interactions are important. A number of lectins from plant and animal sources are being studied as models for these recognition processes and as a testing ground for methods that can characterize them.
Protein structure and protein-protein interactions. Knowledge of protein structure is essential to understanding a very large number of biochemical processes. However, proteins seldom act alone. They interact with substrates, receptors, and one another to fine tune their activities and specificities. NMR spectroscopy offers the opportunity not only to determine protein structure (in solution, for the cases of interest to the Prestegard group) but to focus on particular regions involved in critical contacts. Isotope-edited NMR experiments are a key component enabling analyses of these special regions. The Prestegard group has implemented a full array of these experiments and is applying them to interesting protein systems. One study involves components of chaperonin systems important to protein folding. Another involves components of multi-enzyme systems important in the synthesis and modification of long chain fatty acids.
Dr. Prestegard’s research is supported by the National Science Foundation, the National Institutes of Health, and the Georgia Research Alliance.
Art Edison
Short Biography:
Art Edison is a Georgia Research Alliance Eminent Scholar and Professor of Genetics and Biochemistry and a member of the Complex Carbohydrate Research Center and Institute of Bioinformatics at the University of Georgia. He received his Ph.D. in biophysics from the University of Wisconsin-Madison, where he developed and applied NMR experimental and theoretical methods for protein structural studies under the supervision of John Markley and Frank Weinhold. He joined the faculty at the University of Florida and the National High Magnetic Field Laboratory in 1996. He advanced from Assistant to Full Professor in the UF Department of Biochemistry & Molecular Biology. Prof. Edison was the founding PI and Director of the NIH-funded Southeast Center for Integrated Metabolomics, and his research focuses on the role of small molecules in biology and disease. In 2015, Edison moved to the University of Georgia where he directs the CCRC NMR facility, which supports research in both metabolomics and structural biology. Edison’s research group collaborates on several metabolomics projects from microbes to humans.
Research Interests:
The Edison lab uses metabolomics to solve problems in biology and biomedicine. Metabolomics is the omics technology that focuses on metabolites in the context of systems biology. As such, we spend a considerable amount of effort on bioinformatics, data integration, and modeling of data. Our primary analytical technology is NMR, but we also regularly use mass spectrometry. We develop new NMR and bioinformatic methods and collaborate extensively with other groups that have interesting applications or complementary technologies.