Fall 2013 Courses
Organic Chemistry II
Biochemistry: Protein Structure and Enzymology
I began studying chemistry at Temple University and had my first research experience in the lab of Grant Krow. There, I worked on a hetero-Diels Alder reaction and regioselective alkene functionalization towards the synthesis of homo-epibatidine. After Temple, I began graduate work at Princeton in the lab of Kevan Shokat. There I did work on protein engineering to alter the nucleotide substrate preference of protein tyrosine kinases to identify their downstream signaling partners as well as design and synthesis of histone deacetylase inhibitors.
Research in Biological Chemistry
There are several projects ongoing in the lab, all of which involve using chemistry to elucidate or control biological systems. Undergraduate students in my lab often learn various techniques such as organic synthesis, protein expression/purification and enzymology.
Research Group Alumni
Alumni have often gone on to graduate and medical schools. Below is a list of some of my former students and where they went after IC:
- Kevin Litwin, PhD program at the Scripps Research Institute
- James Annand, scientist at Ironwood Pharmaceuticals
- Nate Heldt, MD/PhD aspirant.
- Leah Graham, PhD student at Tufts University
- Cornell Conca- Medical School at New York Medical College
- Alyson Waring- Vet School
- Bryan Stefek- Medical School at New York Medical College
- Leona Leung- Medical School at the University of West Virginia
- Dr. Nicky Stephenson- PhD in Chemistry from the University of Wisconsin-Madison
- Dr. Mike MaCauley- Graduate of Penn State Medical School at Hershey
- Dr. Chris Roessler- PhD in Biochemistry at the University of Arizona
- Dr. Mark Hedglin- PhD in Chemical Biology, at the University of Michigan
- Dr. Sam Oliver- PhD in Biochemistry, University of Wisconsin-Madison
- Keris KrennHrubec- MPH from the University of Michigan
- Colleen O'Loughlin- PhD student in Molecular Biology at Princeton
- Dr. Mike Clarke- Graduate of the University of Minnesota Medical School
- Dr. Sarah Boyce- Graduate of the Chemical Biology program at UCSF
Shimazu T, Hirschey MD, Newman J, He W, Shirakawa K, Le Moan N, Grueter CA, Lim H, Saunders LR, Stevens RD, Newgard CB, Farese RV Jr, de Cabo R, Ulrich S, Akassoglou K, Verdin E. "Suppression of oxidative stress by β-hydroxybutyrate, an endogenous histone deacetylase inhibitor." Science. 2013 Jan 11;339(6116):211-4 link
Magadalena Karolczak-Bayatti, Michele Sweeney, Joanna Cheng, Lydia Edey, Stephen C. Robson, Scott M. Ulrich, Achim Treumann, Michael J. Taggart, and G. Nicholas Europe-Finner "Acetylation of heat shock protein 20 (Hsp20) regulates human myometrial activity" J. Biol. Chem. 2011 doi: 10.1074/jbc.M111.278549 link
Tao Su, David M. Bryant, Frédéric Luton, Marcel Vergés, Scott M. Ulrich, Kirk C. Hansen, Anirban Datta, Dennis J. Eastburn, Alma L. Burlingame, Kevan M. Shokat Keith E. Mostov "A kinase cascade leading to Rab11-FIP5 controls transcytosis of the polymeric immunoglobulin receptor" Nature Cell Biology 2010 DOI: doi:10.1038/ncb2118
Swem L, Swem D, O'Loughlin C*, Gatmaitman R*, Ulrich SM, Bassler B. A Quorum Sensing Antagonist that Targets Both Membrane-Bound and Cytoplasmic Receptors Controls Bacterial Pathogenicity Molecular Cell 35 (2) 143-153, 31 July 2009 link
Oehme I, Deubzer HE, Wegener D, Pickert D, Linke J, Hero B, Kopp-Schneider A, Westermann F, Ulrich SM, von Deimling A, Fischer M, and Olaf Witt. "Histone Deacetylase 8 in NeuroblastomaTumorigenesis" Clinical Cancer Research 91 15(1) January 1, 2009 link
Ulrich SM "Chemistry and Roles of Protein Kinases and Dephosphorylases" 2007 Wiley Encyclopedia of Chemical Biology link
KrennHrubec K*, Marshal B, Hedglin M*, Verdin E and Ulrich SM. "Design and Evaluation of Linkerless Hydroxamic Acids and Selective HDAC8 Inhibitors" 2007 March 30 Bioorganic and Medicinal Chemistry Letters link
***this paper was one of the 50 most cited papers in BMCL between 2003-2010***
Ulrich SM, Kenski DM, Shokat KM. "Engineering a 'methionine clamp' into Src family kinases enhances specificity toward unnatural ATP analogues" Biochemistry. 2003 Jul 8;42(26):7915-21.
Ulrich SM, Sallee NA, Shokat KM. "Conformational restraint is a critical determinant of unnatural nucleotide recognition by protein kinases" Bioorg Med Chem Lett. 2002 Nov 4;12(21):3223-7.
Ulrich S, Shokat K. "Green fluorescent protein-based protein kinase biosensor substrates" Methods Mol Biol. 2002;183:275-85
Bradley, Alexander Z.; Ulrich, Scott M.; Jones, Maitland, Jr.; Jones, Stephanie M. "Teaching the Sophomore Organic Course without a Lecture. Are You Crazy?" Journal of Chemical Education 2002, 79, 514. link
Bishop A, Buzko O, Heyeck-Dumas S, Jung I, Kraybill B, Liu Y, Shah K, Ulrich S, Witucki L, Yang F, Zhang C, Shokat KM. "Unnatural ligands for engineered proteins: new tools for chemical genetics" Annu Rev Biophys Biomol Struct. 2000;29:577-606
Grant R. Krow, Osbert H. Cheung, Zilun Hu, Qiuli Huang, John Hutchinson, Nian Liu, Kevin T. Nguyen, Scott Ulrich, Jing Yuan, Yushi Xiao, Donna M. Wypij, Fangming Zuo, Patrick J. Carroll. "Nitrogen-bridge homoepibatidines: syn-6 and syn-5-(chloro-3-pyridyl) isoquinuclidines" Tetrahedron 1999; (55) 7747-7756.
- "Chemical Inhibition of Cell-Cell Communication in Bacteria" Mount Holyoke College, April 2011
- "Chemical Inhibition of Cell-Cell Communication in Bacteria" Hobart and William Smith Colleges, 4/30/09
- "Chemical Inhibition of Quorum Sensing Signaling in Chromobacterium violaceum" SUNY School of Environmental Science and Forestry, 2/27/09
- "Chemical Inhibition of Bacterial Quorum Sensing" Colby College, 9/15/07
- "Chemical Genetic Analysis of Histone Deacetylation" Hobart and William Smith Colleges, 9/22/05
- "Peer-led, problem-based learning in organic chemistry", National ACS meeting, Phila PA, August 2004
By Ithaca College undergraduates:
- Kevin Litwin and Carina Chittim "Design and synthesis of aza- and sulfonium analogs of carbocation intermediates of epi-isozizaene synthase" ACS meeting, New Orleans 2013
- James Annand "Synthesis of transition state analogs of a quorum sensing synthase" ACS meeting, New Orleans 2013
- Leah Graham "Design and synthesis of photo-crosslinking analogs of 968, a Glutaminase C inhibitor" NCUR 2012
- Kevin Litwin and James Annand " Design and synthesis of aza-analogs of terpene synthase carbocation intermediates" NCUR, March 2012
- Cornell Conca and Leah Graham "Chemical inhibition of bacterial quorum sensing" NCUR, April 1 2011.
- Bryan Stefek "Characterization of toxic factors regulated by quorum sensing in Chromobacterium violacium" Rochester section of the American Chemical Society, April 2009
- Colleen O'Loughlin "Design and synthesis of electrophilic LuxS inhibitors" ACS National Meeting, Chicago, March 2007
- Keris KrennHrubec "Design and Evaluation of Linkerless Hydroxamic Acids and Selective HDAC8 Inhibitors" ACS National Meeting, Chicago, March 2007
- Colleen O'Loughlin: "Peptidoglycan Deacetylase 'PgdA' as a New Antibiotic Drug Target" West Nottingham Academy, May 2006
- Keris KrennHrubec: "Development of HDAC8-selective inhibitors" Ithaca College Whalen Symposium, April 2006.
- Nicky Stephenson and Mike MaCauley: "LuxS as an antibacterial drug target." National ACS Meeting, San Diego March 2005
- Mark Hedglin: "Engineering drug sensitive HDAC alleles" National ACS Meeting, San Diego March 2005
- Nicky Stephenson: "LuxS as an antibacterial drug target." Rochester Academy of Sciences
- Chris Roessler: "Development of allele-specific histone deacetylase inhibitors." C-STEP State Meeting, Lake George, NY, April 2004.