Molecular bioengineering, applied molecular biology, protein engineering.
My group focuses on biomolecular engineering of proteins for applications in immunology and nanotechnology, and emphasis is placed on directed molecular evolution approaches. All projects apply molecular, cell, and microbiological methods as nontraditional engineering tools. BIOMOLECULAR ENGINEERING APPLICATIONS IN IMMUNE FUNCTION Immunology research has undergone explosive growth in the past ~20 years, catalyzing dramatic improvement in understanding of immune phenomena. Numerous molecular mechanisms have been elucidated; in particular, receptor proteins involved in many aspects of cellular immunity have been described in some detail. The field is therefore poised for substantial breakthroughs in practical applications through the contributions of engineers, and my group seeks to be at the forefront of this new field of immuno-engineering. APPLICATIONS IN BIOSENSORS AND FUSION PROTEINS The ability of proteins to sensitively respond to chemical and other stimuli with high specificity has led to great interest in their use in sensing applications. Furthermore, many proteins demonstrate elegant functional alterations in response to environmental stimuli, frequently including significant and precise conformational changes at the nanoscale. Thus, new methods are required to address the potential of engineering protein functions beyond simple ligand binding (which has been the focus of most protein engineering to date) and enable protein use in functional nanodevices such as sensors and drug and gene delivery vehicles. A major effort in my group pursues such new methods. APPLICATIONS IN PROTEIN IMMOBILIZATION AND MODIFICATION Application of engineered proteins with sensing ability and environmentally triggered functional responses will in many instances require methods to integrate those proteins with synthetic surfaces or materials. We aim to explore novel enzymatic approaches to modify and immobilize proteins; the advantages of our tools relative to existing techniques stem primarily from the combination of high selectivity and the use of gentle conditions compatible with biological molecules, while avoiding the use of large protein fusions potentially confounding facile recombinant protein production. SECRETION AND QUALITY CONTROL IN RECOMBINANT PROTEIN FUSIONS Production of engineered proteins for incorporation into functional devices, as well as use of display technologies for directed evolution, depends on recombinant expression in suitable host organisms. Protein secretion from eukaryotic cells such as yeast has the advantage of in vivo quality control mechanisms putatively ensuring only natively folded, functional proteins are produced. We seek to probe the limits of yeast secretion and quality control for both engineering and production of proteins. RECENT PUBLICATIONS: R. Parthasarathy, S. Subramanian, and E.T. Boder: Sortase A as a novel molecular “stapler” for sequence-specific protein conjugation (submitted). S. Subramanian, E.T. Boder, and D.E. Discher: Phylogenetic Divergence in Human SIRPα-CD47 Interactions Reveals Locus of Species-specificity: Implications for the Binding Site. J. Biol. Chem. (in press). http://www.jbc.org/cgi/doi/10.1074/jbc.M603923200 J.H. Lee, M. Goulian, and E.T. Boder: Autocatalytic Activation of Influenza Hemagglutinin. J. Mol. Biol., 364:275-282 (2006). http://dx.doi.org/10.1016/j.jmb.2006.09.015 L.R. Pepper, D.A. Hammer, and E.T. Boder: Rolling Adhesion of αL I Domain Mutants Decorrelated from Binding Affinity J. Mol. Biol., 360:37-44 (2006). http://dx.doi.org/10.1016/j.jmb.2006.04.049 S. Park, Y. Xu, X.F. Stowell, F. Gai, J.G. Saven, and E.T. Boder: Limitations of yeast surface display in engineering proteins of high thermostability. Prot. Eng. Des. Sel., 19:211-217 (2006). http://dx.doi.org/10.1093/protein/gzl003 P. Derr, E. Boder, and M. Goulian: Genetic selection for new bacterial chemoreceptors. J. Mol. Biol. 355:923-932 (2006). http://dx.doi.org/10.1016/j.jmb.2005.11.025 S. Subramanian, R. Parthasarathy, E.T. Boder, and D.E. Discher: Species-specific adhesive interactions between CD47 and human SIRPα. Blood, 107:2548-2556 (2006). http://dx.doi.org/10.1182/blood-2005-04-1463 R. Parthasarathy, S. Subramanian, E.T. Boder, and D.E. Discher: Post-translational regulation of expression and conformation of an immunoglobulin domain in yeast surface display. Biotechnol. Bioeng., 93:159-168 (2006). http://dx.doi.org/10.1002/bit.20684 R. Parthasarathy, J. Bajaj, and E.T. Boder: Immobilized biotin ligase via surface display of E. coli BirA on Saccharomyces cerevisiae. Biotechnol. Prog., 21:1627-1631 (2005). http://dx.doi.org/10.1021/bp050279t E.T. Boder, J.R. Bill, A.W. Nields, P.C. Marrack, and J.W. Kappler: Yeast surface display of a noncovalent MHC class II heterodimer complexed with antigenic peptide. Biotechnol. Bioeng., 92:485-491 (2005). http://dx.doi.org/10.1002/bit.20616 S. Park, E.T. Boder, and J.G. Saven: Modulating the DNA affinity of Elk-1 with computationally selected mutations. J. Mol. Biol., 348:75-83 (2005). http://dx.doi.org/10.1016/j.jmb.2004.12.062 S.J. Park, H. Kono, W. Wang, E.T. Boder, and J.G. Saven: Progress in the development and application of computational methods for probabilistic protein design. Computers Chem. Eng., 29:407-21 (2005). http://dx.doi.org/10.1016/j.compchemeng.2004.07.037 http://www.jbc.org/cgi/doi/10.1074/jbc.M603923200http://dx.doi.org/10.1016/j.jmb.2006.09.015http://dx.doi.org/10.1016/j.jmb.2006.04.049http://dx.doi.org/10.1093/protein/gzl003http://dx.doi.org/10.1016/j.jmb.2005.11.025http://dx.doi.org/10.1182/blood-2005-04-1463http://dx.doi.org/10.1002/bit.20684http://dx.doi.org/10.1021/bp050279thttp://dx.doi.org/10.1002/bit.20616http://dx.doi.org/10.1016/j.jmb.2004.12.062http://dx.doi.org/10.1016/j.compchemeng.2004.07.037shapeimage_1_link_0shapeimage_1_link_1shapeimage_1_link_2shapeimage_1_link_3shapeimage_1_link_4shapeimage_1_link_5shapeimage_1_link_6shapeimage_1_link_7shapeimage_1_link_8shapeimage_1_link_9shapeimage_1_link_10