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 Professor, Born 1954 A.B. 1976, University of California - Berkeley Ph.D. 1981, Stanford University Room: 4209aPhone: 608-263-2594 Email: smith@chem.wisc.edu Position: Professor Selected Publications
| Research DescriptionResearch in the Smith group is directed towards the development of powerful new technologies to drive biological research. The work is multi-faceted and highly interdisciplinary and collaborative in nature. Two major areas of interest are surface chemistries, particularly those related to the development and use of various sorts of biomolecule arrays, and mass spectrometry. An emerging area of interest is in the field of synthetic biology, which has as its goal the development of a sufficient understanding and control of the fundamental processes of life to be able eventually to create self-replicating and sustainable entities.
Surfaces. The advent of high-density DNA arrays in the early ‘90s demonstrated the power of the array concept for genome-wide analyses of biological systems. Through a collaboration with Professor Franco Cerrina in the Department of Electrical Engineering and Computer Science, our group has acquired a Maskless Array Synthesizer, which allows any high-density DNA array of interest (up to 786,000 individual DNA features) to be designed and fabricated overnight (1). Recently we have developed a novel lamellar substrate for such DNA array fabrication, consisting of a thin layer of amorphous carbon deposited on a gold thin film over glass (2). The gold thin film supports the generation of surface plasmons, which are collective oscillations of electron density within the gold layer, and thereby allows the technique of surface plasmon resonance (SPR) imaging to be utilized for label-free detection on these carbon surfaces. Carbon attachment chemistry that we have developed over the last several years in collaboration with Professor Bob Hamers of the Department of Chemistry, permits biomolecule arrays of unprecedented chemical stability to be made on these surfaces. We are actively exploring applications of these new materials for the parallel analysis of DNA:DNA, DNA:RNA, DNA:protein, and protein:small molecule interactions. Together with Professor Helen Blackwell of the Department of Chemistry, we are developing and applying such tools to study quorum-sensing pathways in gram-negative pathogens such as Pseudomonas aeruginosa. Mass Spectrometry. Biology has entered a new era with the recent sequencing of the human and many other genomes. With thousands of genome sequences now readily accessible in databases, research paradigms have fundamentally changed. One of the best examples of this new approach is in the field of proteomics, where tandem mass spectrometric analyses of complex protein mixtures depend upon whole genome database search algorithms to identify proteins. This approach exploits synergies between genome analysis, bioinformatics, and rapidly evolving instrumentation and chemistries for mass spectrometry. As powerful as this technology has become, we believe that the field of biological mass spectrometry is still in its infancy. Mass spectrometry as it currently exists is a relatively inefficient process, in which typically only one out of 107 to 1010 molecules in a sample being analyzed actually give rise to a detection event. This is because of ion losses that occur throughout a mass spectrometry system, in the ion source, the mass analyzer, and at the detector. Although the resolution for low m/z species can be extremely high, at larger m/z values corresponding to low charge states of large biomolecules and biomolecular complexes, both resolution and detection efficiency are extremely poor. Our group is interested in addressing the fundamental issues that limit biological mass spectrometry. We have active projects to improve ionization processes, reduce ion suppression and matrix effects, develop a new generation of highly sensitive ion detectors, and develop approaches for the determination of accurate masses of proteins in complex mixtures. We are also actively engaged in a variety of proteomics collaborations, such as the analysis of prenylated G proteins in Dictyostelium (w. Professor Ted Cox, Princeton University), identification of proteins associated with the proteasome complex in Arabidopsis (Professor Rick Vierstra, Department of Genetics at UW MSN), the human embryonic stem cell proteome (Professor James Thomson, Genome Center of Wisconsin), the study of angiogenesis (Professors Michael Olivier and Andrew Greene, Medical College of Wisconsin), and several others. We are also engaged in the development and application of new strategies for "metabolomics", the analysis of the expression of small molecules in biological systems. These real-world projects keep us at the cutting edge of the rapidly evolving world of biological mass spectrometry, while helping to provide important information essential to understanding these fascinating and important biological systems.
Synthetic biology. A new area of interest in our group is synthetic biology. This project is based upon the work of Professor Brian Fox in the Department of Biochemistry. He and his group have developed a novel approach to the expression of membrane proteins in artificial membrane systems, based upon the use of cell-free translation systems. They have shown that simply adding an RNA encoding a membrane protein of interest to the cell-free translation system, in the presence of synthetic vesicles, results in expression of the properly folded and functional membrane protein in the vesicle. We are interested in using this new technology to build up functional multi-component systems in artificial membranes. Exciting projects in this area include coupling light-sensitive membrane proteins such as bacteriorhodopsin to other energy-dependent processes such as intracellular signaling cascades and flagellar motor assemblies. In the long term, it may eventually be possible to combine this technology with the artificial genomes to create self-replicating entities, the ultimate goal of biological engineering.
Updated: 2.24.09
Awards
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