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Topics: Protein and nucleic acid structure and dynamics; molecular recognition; gene regulation; enzyme catalysis; NMR spectroscopy; molecular biophysics; thermodynamics; kinetics.
Approach: Understanding how the structure and mobility of biological molecules influence their function is one of the most exciting and rewarding research objectives in biochemistry, and is the main focus of my laboratory's efforts. Biological processes are coordinated via complex molecular interactions involving proteins, nucleicacids (DNA, RNA) and small molecules. These molecules are not rigid, but rather undergo dynamic conformational changes to achieve their functions. High-resolution NMR spectroscopy is ideally suited to our principle objective of understanding these motions, as it is the only method that allows us to study both the structural and dynamic properties of macromolecules at atomic resolution. Our group enjoys access to excellent NMR facilities, which include fields up to 800 MHz, equipped with cryogenically cooled triple-resonance probes. While NMR spectroscopy is one major research tool in the laboratory, our projects are fundamentally multidisciplinary and collaborative, merging components of molecular biology, protein engineering and biochemistry, NMR spectroscopy and computation. As a result, members of the laboratory have the opportunity, and are encouraged, to become competent in diverse creative approaches for solving biochemical problems. Group members obtain rigorous training in basic research by studying the fundamental principles that govern biomolecular function, and emerge with scientific skills to pursue careers in either academics or private industry.
Mechanisms of Gene Regulation. Cells react to physiological stimuli via a cascade of biomolecular interactions involving cell-surface receptors, biological sensors, kinases, phosphatases and signaling molecules that relay information from the surface to the interior of the cell where internal conditions determine the appropriate response. Responses can include inflammation (lysis), proliferation (growth and division), quiescence (resting) or apoptosis (suicide). These responses are often carried put the transcription or degradation of specific proteins. Malfunction of signaling processes can have dire consequences: cancer, muscular dystrophy and autoimmune diabetes are well-recognized disorders that result from improper cellular response. Our work seeks to reveal how regulatory macromolecules recognize the appropriate signal and pass it on down the next step in the cascade.
Enzyme structure and dynamics. Enzymes catalyze chemical reactions by binding the appropriate substrates in a conformation that lowers the energetic activation barrier, and then releases the products, at the appropriate rate. While the structures of many different enzymes are known, little is generally known about the molecular motions that enable enzymes to carry out their function. This lack of understanding severely limits our ability to design drugs to specifically inhibit the enzymes, or to design new enzymes to carry out novel chemistries. We seek to understand of the mode of action of select enzymes by characterizing their solution behavior (structure and dynamics) and to examine the effects of inhibitor and substrate binding.
Xu Y, Oruganti SV, Gopalan V, Foster MP. "Thermodynamics of Coupled Folding in the Interaction of Archaeal RNase P Proteins RPP21 and RPP29." (2012) Biochemistry 51 (4):926–935. doi: 10.1021/bi201674d
Kleckner IR, Foster MP. "GUARDD: User-friendly MATLAB software for rigorous analysis of CPMG RD NMR data." (2012) J Biomol NMR 52:11-22. doi: 10.1007/s10858-011-9589-y
Kleckner IR, Gollnick P, Foster MP. "Mechanisms of Allosteric Gene Regulation by NMR Quantification of μs-ms Protein Dynamics." (2012) J Mol Biol 415(2): 372-381. doi: 10.1016/j.jmb.2011.11.019
Crowe BL, Bohlen CJ, Wilson RC, Gopalan V, Foster MP. "Assembly of the Complex between Archaeal RNase P Proteins RPP30 and Pop5." (2011) Archaea 2011: Article ID 891531. doi:10.1155/2011/891531, (PDF)
Chen WY, Xu Y, Cho IM, Oruganti SV, Foster MP, Gopalan V. "Cooperative RNP assembly: complementary rescue of structural defects by protein and RNA subunits of archaeal RNase P." (2011) J Mol Biol. 411(2):368-83.doi:10.1016/j.jmb.2011.05.012 (PubMed)
Kleckner IR, Foster MP. "An Introduction to NMR-based Approaches for Measuring Protein Dynamics." (2010) BBA - Proteins and Proteomics. Special Issue: Protein Dynamics.1841(8):942-968 (http://dx.doi.org/10.1016/j.bbapap.2010.10.012)
Sachleben JR, McElroy CA, Gollnick P, Foster MP. "Mechanism for pH-dependent gene regulation by amino-terminus-mediated homooligomerization of Bacillus subtilis anti-trp RNA-binding attenuation protein." (2010) Proc Natl Acad Sci U S A 107(35):15385-90 doi: 10.1073/pnas.1004981107
Xu Y, Amero CD, Pulukkunat DK, Gopalan V, Foster MP. "Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions." (2009) J Mol Biol. 393(5):1043-55. (PDF, http://dx.doi.org/10.1016/j.jmb.2009.08.068; PMC2782587)
Amero CD, Byerly DW, McElroy CA, Simmons A, Foster MP. "Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase." (2009) Biochemistry. 48(32):7595-607. DOI: 10.1021/bi900600b (PDF, SI). Addendum.
Amero CD, Boomershine WP, Xu Y, Foster M. "Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner." (2008) Biochemistry. 47(45):11704-10. DOI: 10.1021/bi8015982 (PDF, html)
Kamadurai HB, Jain R and Foster MP, "Crystallization and structure determination of the core-binding domain of bacteriophage lambda integrase." (2008) Acta Crystallographica F, 64(6):470-473. (PDF, doi:10.1107/S174430910801381X)
Amero CD, Arnold JJ, Moustafa IM, Cameron CE, and Foster MP, "Identification of the oriI-binding site of poliovirus 3C protein by NMR spectroscopy." (2008) J Virol, 82(9):4363-70, PMID: 18305026. (PubMed, doi:10.1128/JVI.02087-07, PDF)
Kamadurai HB, Foster MP, "DNA recognition via mutual-induced fit by the core-binding domain of bacteriophage lambda integrase." (2007) Biochemistry, 46(49):13939-47. (PubMed, PDF) DOI: 10.1021/bi700974t
Subramaniam S, Kamadurai HB, Foster MP, "Trans Cooperativity by a Split DNA Recombinase: The Central and Catalytic Domains of Bacteriophage Lambda Integrase Cooperate in Cleaving DNA Substrates When the Two Domains Are not Covalently Linked." (2007) J Mol Biol. 370(2):303 - 314. (PubMed, PDF) doi:10.1016/j.jmb.2007.04.024