Biography
Professor Baker received his B.S. in biochemistry from New Mexico State University in 1992. He earned his Ph.D. in biochemistry from the University of Iowa in 1997 for studying the relationships between structure and thermodynamics in protein binding reactions. During postdoctoral work at Harvard University, as a fellow of the Cancer Research Institute, he investigated the structure, thermodynamics, and kinetics of protein-protein interactions and their role in the immune system. He joined the Notre Dame faculty in August 2001. In 2005 he received a Faculty Career Development Award from the National Science Foundation and a Research Scholar Award from the American Cancer Society.
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Research Interests
Research in our group is focused on the biophysics of macromolecular interactions; principally, how do the structure and dynamics of macromolecules allow interactions to proceed with particular affinities, specificities, kinetics, and environmental dependencies? As these properties ultimately dictate biological activity, the lab is also interested in the relationships between macromolecular biophysical chemistry and biology. An understanding of the biophysics of macromolecular interactions is crucial for the developing field of structure-based drug design, prediction of binding sites and properties from structural or sequence databases, and dissecting the nuances of complex, multi-subunit protein machines and signaling pathways.
Our primary focus is on two important molecules in the immune system: T-cell receptors (TCRs) and their ligands, small peptides bound and "presented" by class I or class II major histocompatibility molecules (peptide/MHCs). These molecules form the foundation of the cellular arm of the mammalian immune system. Detailed studies of macromolecular interactions in the immune system will aid in our understanding of the role of the immune system in health and disease, including such areas as the response to foreign pathogens and cancer immunosurveillance. Furthermore, it will contribute to efforts to design immunologically-based therapeutics and interventions for diseases such as autoimmunity and cancer.
Our laboratory uses primarily structural and biophysical appraoches. We combine the techniques of structural biology (macromolecular X-ray crystallography and NMR) with biophysical methods such as titration calorimetry, surface plasmon resonance, fluorescence spectroscopy, and analytical ultracentrifugation. We also use a number of computational approaches (continuum electrostatics, molecular modeling, and molecular dynamics). We work closely with immunologists at the National Institutes of Health who investigate a variety of immunological phenomena. Our overall goals are to integrate structural, biophysical, and immunological data to generate useful descriptions of how molecular interactions modulate immune reactivity.
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Recent Papers
Full publication list at PubMed
| Armstrong KM, Insaidoo FK, and Baker BM (2008) Thermodynamics of T cell receptor - peptide/MHC interactions: progress and opportunities. J Mol Recog 21 275 Link |
| Borbulevych OY, Insaidoo FK, Baxter TK, Powell D, Johnson L, Restifo NP, & Baker BM (2007) Structures of MART-1 Peptide/HLA-A2 complexes reveal a remarkable disconnect between antigen structural homology and T cell recognition. J Mol Biol 372, 1123 Link |
| Armstrong KM & Baker BM (2007) A comprehensive calorimetric investigation of an entropically driven T cell receptor - peptide/major histocompatibility complex interaction. Biophysical Journal 93, 597 Link |
| Davis-Harrison RL, Insaidoo FK, & Baker BM (2007) T cell receptor binding transition states and recognition of peptide/MHC. Biochemistry 46, 1840 Link |
| Gagnon SJ, Borbulevych OY, Davis-Harrison RL, Baxter TK, Turner RV, Damirjian M, Wojnarowicz A, Biddison WE, & Baker BM (2006) T cell receptor recognition via cooperative conformational plasticity. Journal of Molecular Biology 363, 228 Link |
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