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Jarrod B. French

french

Assistant Professor
Department of Biochemistry and Cell Biology

B.Sc. Brock University, St. Catharines, ON, Canada,
2004 Ph.D. Cornell University, Ithaca, NY, 2010
CIHR Postdoctoral Fellow, The Pennsylvania State University, 2011 – 2013

The French Group Website  
E-mail:   jarrod.french@stonybrook.edu

  • Research Description
      Structural Biology, Chemical Biology and Enzymology of Metabolic Pathways and Protein Complexes

    We take a highly interdisciplinary approach to study the structure, function and control of enzymes and enzyme complexes involved in cellular metabolism. We are particularly interested in understanding how multi-protein macromolecular machines provide spatial and temporal control over metabolic pathways in cells. Our long term goal is to characterize the structure, functions and control mechanisms of these protein assemblies and to exploit this information to develop novel treatments for cancer and inflammatory diseases such as rheumatoid arthritis. To this end, we employ a variety of techniques including X-ray crystallography, mechanistic enzymology, microscopy and chemical biology.

    Characterization of multifunctional proteins involved in purine and pyrimidine biosyn

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    thesis in eukaryotes 

    Many enzymes in humans and other eukaryotes catalyze multiple steps in metabolic pathways. These multi-domain enzymes are usually very difficult to characterize due to their inherent flexibility and large size. Often these proteins undergo significant conformational changes in response to ligand binding, post-translational modification or when interacting with other proteins. Understanding the structure of such multi-domain enzymes provides a significant opportunity for drug development. Enzymes involved in purine and pyrimidine biosynthesis are of particular interest as this metabolic pathway has been validated as an     anti-cancer target (greater than 20% of all clinically approved cancer treatments are purine or pyrimidine anti-metabolites).

    Structure and control of the purinosome 

    Recently, a multi-enzyme metabolic machine involved in purine biosynthesis was discovered. This dynamic and reversible protein complex, called the purinosome, forms when cells are depleted of purines and has been demonstrated to be a potential target for anti-cancer chemotherapeutics. We are investigating the structure and assembly process of this protein agglomerate and hope to use this information to understand how such phenomena may help control metabolism in cells. We are also interested in how such complexes may influence metabolic reprogramming in cancer cells.  

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      Drug discovery 

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    One of the long term goals of our research is to use our knowledge of the structure and fun ction of enzymes and protein complexes to develop drugs to treat human disease. Using novel assays, we employ both conventional high-throughput methodologies as well as structure-guided approaches to identify, characterize and optimize lead compounds. 

  • Publications

    31.  A. Gil, S. P. Laptenok, J. N. Iuliano, A. Lukacs, A. Verma, C. R. Hall, E. Yoon, R. Brust, G. Greetham, M. Towrie, J. B. French, S. R. Meech, and P. J. Tonge (2017) Photoactivation of the BLUF protein PixD Probed by the Site-Specific Incorporation of Fluorotyrosine Residues. J. Am. Chem. Soc. 139(41): 14638-14648.

    30.  W. Zhou, Y. Yin, A. Weinheimer, N. Kaur, N. Carpino and J. B. French (2017) Structural and functional characterization of the histidine phosphatase domains of human Sts-1 and Sts-2. Biochemistry, 56(35): 4637-4645.

    29.  I. Chitrakar, D. Kim-Holzapfel, W. Zhou, and J. B. French (2017) Higher Order Structures in Purine and Pyrimidine Metabolism. J. Struct. Biol., 197: 354 – 364.

    28. A. Gil, S. P. Laptenok, J. B. French, J. N. Iuliano, A. Lukacs, C. R. Hall, I. V. Sazanovich, G. M. Greetham, A. Bacher, B. Illarionov, M. Fischer, P. J. Tonge, and S. R. Meech (2017) Femtosecond to Millisecond Dynamics of Light Induced Allostery in the Avena Sativa Lov Domain. J. Phys. Chem. B, 121(5): 1010 – 1019.

    27.  J. B. French *, S. A. Jones, H. Deng, A. M. Pedley, D. Kim, C. Y. Chan, H. Hu, R. J. Pugh, H. Zhao, Y. Zhang, T. J. Huang, Y. Fang*, X. Zhuang*, and S. J. Benkovic* (2016) Spatial Colocalization and Functional Link of Purinosomes with Mitochondria.  Science, 351(6274): 733 - 737 . *Corresponding authors.

    26.  A. Gil, A. Haigney, S. Laptenok, R. Brust, A. Lukacs, J. Iuliano, J. Meng, E. Melief, R. Zhao, E. Yoon, I. Clark, G. Greetham, A. Ng, J. Truglio, J. B. French, S. R. Meech, and P. J. Tonge. (2016) The Mechanism of the AppaBLUF Photocycle Probed by Site-Specific Incorporation of Fluorotyrosine Residues: The Effect of the Y21 pKa on the Forward and Reverse Ground State Reactions. J. Am. Chem. Soc., 138: 926-935

    25.  J. Matarlo, C. Evans, I. Sharma, L. Lavaud, S. Ngo, R. Shek, K. Rajashankar, J. B. French, D. Tan, P. J. Tonge (2015) Mechanism of MenE Inhibition by Acyl-Adenylate Analogues and Discovery of Novel Antibacterial Agents. Biochemistry. 54(42): 6514. Epub 2015 Oct. 15.

    24.  H. Zhao, C. R. Chiaro, L. M. Zhang, P. B. Smith, C. Y. Chan, A. M. Pedley, R. J. Pugh, J. B. French, A. D. Patterson, and S. J. Benkovic (2015) Quantitative Analysis of Purine Nucleotides Reveals that Purinosomes Increase de Novo Purine Biosynthesis. J. Biol. Chem.290(11): 6705-13. PMID: 25605736

    23.  F. Guo, W. Zhou, P. Li, Z. Mao, N. Yennawar, J. B. French * and T. Jun Huang* (2015) Precise manipulation and patterning of protein crystals for macromolecular crystallography using surface acoustic waves. Small. 11(23): 2710. *Corresponding authors. PMID: 25641793        

    22.  C. Y. Chan, H. Zhao, R. J. Pugh, A. M. Pedley, J. B. French, S. A. Jones, X. Zhuang, H. Jinnah, T. J. Huang and S. J. Benkovic (2015) Purinosome formation as a function of the cell cycle. Proc. Natl. Acad. Sci. U.S.A . 112(5): 1368-73. PMID: 25605889

    21. C. T. Liu, J. Layfield, J. B. French, P. Hanoian, J. Ashbury, S. Hammes-Schiffer and S. J. Benkovic (2014) Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for E. coli Dyhydrofolate Reductase. J. Am. Chem. Soc.136(29)10349-10360 . PMID: 4977791

    20.  F. Guo, P. Li, J. B. French, H. Zhao, J. R. Fick, S. J. Benkovic and T. Jun Huang (2015) Controlling Cell-Cell Interactions using Surface Acoustic Waves. Proc. Natl. Acad. Sci. U.S.A. 112(1): 43-8. PMID: 25535339

    19.  D. Ahmed, H. S. Muddana, M. Lu, J.B. French, A. Ozcelik, Y. Fang, P. J. Butler, S. J. Benkovic, A. Manz and T. J. Huang (2014) An acoustofluidic waveform generator for spatiotemporal control of the chemical microenvironments. Anal. Chem . 86(23): 11803-10. PMID: 25405550

    18.  Guo, F., French, J.B., Li, P., Zhao, H., Chan, K.Y., Fick, J.R.,  Benkovic, S.J., and Huang, T.J. (2013) Probing cell-cell communication with microfluidic devices.  Lab on a Chip. 13(16): 3152-62.

    17.  Liu, C.T., Hanoian, P., French, J.B., Pringle, T.H., Hammes-Schiffer, S., and Benkovic, S.J. (2013) Functional Significance of Evolving Protein Sequence in Dihydrofolate Reductase from Bacteria to Humans.   Proc. Natl. Acad. Sci. U.S.A.   110(25): 10159-64.           

    16.  Zhao, Y., Chen, D., Yue, H, French, J.B., Benkovic, S.J. and Huang, T.J. (2013) Single Molecule Studies on Chip.   Lab on a Chip.13(12): 2183-98.

    15.  Zhao, H., French. J.B., Fang, Y. and Benkovic, S.J. (2013) The purinosome, a multi-protein complex involved in the   de novobiosynthesis of purines in humans.   Chem. Comm.   49(40): 4444-4452 .

    14.  French, J.B., Zhao, H., Niessen,S., An, S., Cravatt, B.F., and Benkovic, S.J. (2013) The Hsp90/Hsp70 Chaperone Machinery is Involved in the Assembly of the Purinosome.   Proc. Natl. Acad. Sci. U.S.A.   110(7): 2528-33 .

    13.  Fang, Y., French, J.B., Zhao, H., and Benkovic, S.J. (2013) G protein-coupled receptor regulation of de novo purine biosynthesis: a novel druggable mechanism.   Biotechnol. Genet. Eng.   29(1): 31-48.         

    12.  Deng, Y., Gam, J., French, J.B., Zhao, H. and Benkovic, S.J. (2012) Mapping Protein-Protein Interactions in the Purinosome.    J. Biol. Chem.   287(43): 36201-7 .

    11.  French, J.B.,  Yates, P.A., Soysa, D.R., Boitz, J.M., Carter, N.S., Chang, B., Ullman, B., Ealick, S.E. (2011) The   Leishmania donovani  UMP Synthase is Essential for Promastigote Viability and has an Unusual Tetrameric Structure that Exhibits Substrate-Controlled Oligomerization.    J. Biol. Chem.  286(23): 20930-41.

    10.  French, J.B., Begley, T.P., Ealick, S.E. (2011) Structure of Trifunctional THI20 from Yeast.    Acta Cryst D.  67, 784-791.

    9.   French, J.B., Ealick, S.E. (2011) Structure of 5-Hydroxy Isourate Hydrolase from   Klebsiella pneumoniae  and Mechanistic Implications.  Acta Cryst D.   67(Pt 8): 671-7.

    8.   French, J.B., Neau, D., Ealick, S.E. (2010) Characterization of the Structure and Function of   Klebsiella pneumoniae   Allantoin Racemase.   J. Mol. Biol.  410(3): 447-460.

    7.   French, J.B., Cen, Y., Vrablik, T.L., Xu, P., Allen, E., Hanna-Rose, W., Sauve, A.A. (2010) Chacterization of Nicotinamidases: Steady-State Kinetic Parameters, Class-Wide Inhibition by Nicotinaldehydes and Catalytic Mechanism.   Biochemistry. 49(49): 10421-39.

    6.   French, J.B., Ealick, S.E. (2010) Structural and Mechanistic Studies on  Klebsiella pneumoniae   2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline Decarboxylase.   J. Biol. Chem.  285(46): 35446-54.

    5.   French, J.B.,  Cen, Y., Sauve, A.A., Ealick, S.E. (2010) High Resolution Crystal Structures of   Streptococcus pneumoniaeNicotinamidase with Trapped Intermediates Provide Insights into Catalytic Mechanism and Inhibition by Aldehydes.   Biochemistry49(40): 8803-8812.

    4.   French, J.B., Ealick, S.E. (2010) Biochemical and Structural Characterization of a Ureidoglycine Aminotransferase in the   Klebsiella pneumoniae  Uric Acid Catabolic Pathway.   Biochemistry   (Rapid Report). 49: 5975-7.

    3.   French, J.B., Cen, Y., Sauve, A.A. (2008)   Plasmodium falciparum  Sir2 is an NAD +-dependent deacetylase and an acetyllysine-dependent and acetyllysine-independent NAD +  glycohydrolase.   Biochemistry  47: 10227-39.

    2.   French, J.B., Holland, G., Holland, H.L., Gordon, H.L. (2004) A Comparative Molecular Field Analysis of the Biotransformation of Sulfides by   Rhodococcus erythropolis.   J. Molec. Cat. B: Enzym.  31: 87-96.

    1.   Holland, H.L., Brown, F.M., Barrett, F., French, J., Johnson, D. (2003) Biotransformations of β-ketosulfides to produce chiral β-hydroxysulfoxides.   J. Ind. Microbiol. Biotech.  30: 292-296.

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