Student Publications

Banerjee S , Huber T, Sakmar TP. Rapid Incorporation of Functional Rhodopsin into Nanoscale Apolipoprotein Bound Bilayer (NABB) Particles. J Mol Biol, 377(4) DOI: jmb.2008.01.066 (2008).

Chao X, Muff TJ, Park S, Zhang S, Pollard AM, Ordal GW, Bilwes AM, & Crane BR. A receptor-modifying deamidase in complex with a signaling phosphatase reveals a mechanism of reciprocal regulation. Cell. 124, 561-571 (2006).

Park SY, Chao X, Gonzalez-Bonet G, Beel BD, Bilwes AM & Crane BR. Structure and function of a new family of protein phosphatases: the bacterial chemotaxis proteins CheC and CheX. Mol Cell. 16, 563-574 (2004).

Cisar, J. S.; Tan, D. S. Small molecule inhibition of microbial natural product biosynthesis – An emerging antibiotic strategy. Chem. Soc. Rev., 37, 1320–1329 (2008). PMID: 18568158

Cisar JS, Ferreras JA, Soni RK, Quadri LEN, & Tan DS. Exploiting Ligand Conformation in Selective Inhibition of Non-Ribosomal Peptide Synthetase Amino Acid Adenylation with Designed Macrocyclic Small Molecules. J Am Chem Soc, 129(25),
7752 – 7753 (2007). PMID: 17542590

Song, J.; Cisar, J. S.; Bertozzi, C. R.Functional self-assembling bolaamphiphilic polydiacetylenes as colorimetric sensor scaffolds. J. Am. Chem. Soc., 126, 8459–8465 (2004). PMID: 18568158

Oeffinger M, Wei KE, Rogers R, DeGrasse JA, Chait BT, Aitchison JD & Rout MP, "Comprehensive analysis of diverse ribonucleoprotein complexes". Nature Methods, 4, 951-956 (2007).

Fenyo D, Wang QJ, DeGrasse JA, Padovan JC, Cadene M, Chait BT, "MALDI sample preparation: the ultra thin layer method". Journal of Visualized Experiments Issue 3 (2007).

Tackett AJ, DeGrasse JA, Sekedat MD, Oeffinger M, Rout MP & Chait BT. I-DIRT, A general method for distinguishing between specific and nonspecific protein interactions. J Proteome Res. 4, 1752-1756 (2005).

George EA, Novick RP, Muir TW. Cyclic peptide inhibitors of staphylococcal virulence prepared by Fmoc-based thiolactone peptide synthesis. J Am Chem Soc. 130(14), 4914-24, (2008). PMID: 18335939

Geisinger E, George EA, Muir TW, Novick RP. Identification of ligand specificity determinants in AgrC, the Staphylococcus aureus quorum-sensing receptor. J Biol Chem. 283(14), 8930-8 (2008). PMID: 18222919

George EA, Muir TW. Molecular Mechanisms of agr Quorum Sensing in Virulent Staphylococci. Chembiochem 8(8), 847-55. (2007). PMID: 17457814

Simoneau CA, George EA, and Ganem B. A new approach to four-and five-component Ugi condensations starting from nitriles.  Tet Lett. 47, 1205-1207 (2006).

Cordero J, Cuello L, Zhao Y, Jogini V, Cortes DM, Roux B & Perozo E. Molecular determinants of gating at the potassium channel selectivity filter. Nat Struct Mol Biol. 13, 311-8 (2006).

Jogini V & Roux B. Electrostatics of the intracellular vestibule of K+ channels. J Mol Biol. 354, 272-288 (2005).

Candi E, Paradisi A, Terrinoni A, Pietroni V, Oddi S, Cadot B, Jogini V, Meiyappan M, Clardy J, Finazzi-Agro A & Melina G. Transglutaminase 5 is regulated by guanine-adenine nucleotides. Biochemistry J. 381, 313-319 (2004).

Keppetipola N, Shuman S. A phosphate-binding histidine of binuclear metallophosphodiesterase enzymes is a determinant of 2',3' cyclic nucleotide phosphodiesterase activity.J Biol Chem. (2008). PMID: 18757371

Keppetipola N, Shuman S. Characterization of the 2',3' cyclic phosphodiesterase activities of Clostridium thermocellum polynucleotide kinase-phosphatase and bacteriophage {lambda} phosphatase. Nucleic Acids Res. 35(22), 7721-32 (2007). PMID: 17986465

Keppetipola N, Jain R, Shuman S. Novel triphosphate phosphohydrolase activity of Clostridium thermocellum TTM, a member of the triphosphate tunnel metalloenzyme superfamily. J Biol Chem. 282(16), 11941-9 (2007). PMID: 17303560

Keppetipola N, Nandakumar J, Shuman S. Reprogramming the tRNA-splicing activity of a bacterial RNA repair enzyme. Nucleic Acids Res. (2007). PMID: 17488852

Keppetipola N, Shuman S. Distinct enzymic functional groups are required for the phosphomonoesterase and phosphodiesterase activities of Clostridium thermocellum polynucleotide kinase/phosphatase. J Biol Chem. 281, 19251-9 (2006). PMID: 16675457

Keppetipola N & Shuman S. Mechanism of the phosphatase component of Clostridium thermocellum polynucleotide kinase-phosphatase. RNA. 12, 73-82 (2006). PMID: 16301605

Poe SL; Kobašlija M; McQuade DT. Microcapsule Enabled Multi-Catalyst System. J Am Chem Soc (accepted).

Kobašlija M; McQuad, DT. Removable Color Coatings Based on Calcium Alginate Hydrogels. Biomacromolecules. 7, 2357 (2006).

Kobašlija M; McQuade DT. Polyurea Microcapsules from Oil-in-Oil Emulsions via Interfacial Polymerization. Macromolecules 39, 6371 (2006).

Eliezer D, Barre P, Kobašlija M, Chan D, Li X, Heend L. Residual structure in the repeat domain of tau: echoes of microtubule binding and paired helical filament formation.  Biochemistry. 44, 1026-36 (2005).

Broadwater SJ, Roth SL, Price KE, Kobašlija M & McQuade DT. One-pot multi-step synthesis: A challenge spawning innovation. Org Biomol Chem. 3, 2899-2906 (2005).

Hoelz A, Janz JM, Lawrie SD, Corwin B, Lee A & Sakmar T. Crystal structure of the SH3 domain of betaPIX in complex with a high affinity peptide from PAK2. J Mol Biol. (Volume number not yet available) 1-14 (2006).

Eguez L, Lee A, Chavez JA, Miinea CP, Kane S, Lienhard GE, McGraw TE. Full intracellular retention of GLUT4 requires AS160 Rab GTPase activating protein. Cell Metab. 2, 263-272 (2005).

Lu SX, Alpdogan O, Lin J, Balderas R, Campos R, Wang X, Gao G, Suh D, King C, Chow M, Smith OM, Hubbard VM, Bautista L, Cabrera-Perez J, Zakrzewski J, Kochman A, Chow A, Altan-Bonnet G, van den Brink MR. STAT-3 and ERK 1/2 phosphorylation are critical for T cell alloactivation and Graft-Versus-Host-Disease Blood. In press (August 2008).

Alpdogan O, Lu SX, Patel N, McGoldrick S, Suh D, Budak-Alpdogan T, Smith OM, Grubin J, King C, Goldberg G, Hubbard VM, Kochman A, van den Brink MR.  Rapidly Proliferating CD44hi Peripheral T cells Undergo Apoptosis and Delay Post-transplant T cell Reconstitution After Allogeneic Bone Marrow Transplantation" Blood. In press (August 2008).

Zakrzewski JL, Suh D, Markley JC, Smith OM, King C, Goldberg GL, Jenq R, Holland AM, Grubin J, Cabrera-Perez J, Brentjens RJ, Lu SX, Rizzuto G, Sant'Angelo DB, Riviere I, Sadelain M, Heller G, Z-Pflcker JC, Lu C, van den Brink MR. Tumor immunotherapy across MHC barriers using allogeneic T-cell precursors. Nat Biotechnol. 26(4), 453-61 (2008). PMID: 18376399

Ramirez-Montagut T, Chow A, Kochman AA, Smith OM, Suh D, Sindhi H, Lu S, Borsotti C, Grubin J, Patel N, Terwey TH, Kim TD, Heller G, Murphy GF, Liu C, Alpdogan O, van den Brink MR.  IFN-gamma and Fas ligand are required for graft-versus-tumor activity against renal cell carcinoma in the absence of lethal graft-versus-host disease.  J Immunol. 179(3), 1669-80 (2007). PMID: 17641033

Borsotti C, Keating A, Lu SX, Kim TD, Smith OM, Suh D, King CG, Chow A, Liu C, Alpdogan O, van den Brink MR. Absence of donor T cell derived soluble TNF decreases graft-versus-host-disease without impairing graft-versus-tumor activity. Blood. (2007) [Epub ahead of print]

Waldman E, Lu SX, Hubbard VM, Kochman AA, Eng JM, Terwey TH, Muriglan SJ, Kim TD, Heller G, Murphy GF, Liu C, Alpdogan O & van den Brink MR. Absence of the b7 integrin results in less graft-versus-host disease due to decreased homing of alloreactive T cells to intestine. Blood. 107, 1703-1711 (2006).

Alpdogan O, Hubbard VM, Smith OM, Patel N, Lu S, Goldberg GL, Gray DH, Feinman J, Kochman AA, Eng JM, Suh D, Muriglan SJ, Boyd RL & van den Brink MR. Keratinocyte growth factor (KGF) is required for postnatal thymic regeneration. Blood. 107, 2453-2460 (2006).

Ramirez-Montagut T, Chow A, Hirschhorn-Cymerman D, Terwey TH, Kochman AA, Lu S, Miles RC, Sakaguchi S, Houghton AN, van den Brink MR. Glucocorticoid-induced TNF receptor family related gene activation overcomes tolerance/ignorance to melanoma differentiation antigens and enhances antitumor immunity. J Immunol. 176, 6434-42 (2006).

Zakrzewski JL, Kochman AA, Lu SX, Terwey TH, Kim TD, Hubbard VM, Muriglan SJ, Suh D, Smith OM, Grubin J, Patel N, Chow A, Cabrera-Perez J, Radhakrishnan R, Diab A, Perales MA, Rizzuto G, Menet E, Pamer EG, Heller G, Zuniga-Pflucker JC, Alpdogan O, van den Brink MR. Adoptive transfer of T-cell precursors enhances T-cell reconstitution after allogeneic hematopoietic stem cell transplantation. Nat Med. 12, 1039-47 (2006).

Terwey TH, Kim TD, Kochman AA, Hubbard VM, Lu S, Zakrzewski JL, Ramirez-Montagut T, Eng JM, Muriglan SJ, Heller G, Murphy GF, Liu C, Budak-Alpdogan, T, Alpdogan O & van den Brink, MR. CCR2 is required for CD8-induced graft-versus-host disease. Blood. 106, 3322-3330 (2005).

Potuzak JS, Moilanen SB & Tan DS. Stereocontrolled synthesis of spiroketals via a remarkable methanol-induced kinetic spirocyclization reaction. J Am Chem Soc. 127, 13796-13797 (2005).

Moilanen SB & Tan DS. Enantioselective synthesis of erythro-4-deoxy-glycals as scaffolds for target- and diversity-oriented synthesis: new insights into glycal reactivity. Org Biomol Chem. 3, 798-803 (2005).

Potuzak JS, Moilanen SB & Tan DS. Discovery and applications of small molecule probes for studying biological processes. Biotechnol Genet Eng Rev. 21, 11-78 (2004).

Yuhong Du, Moulick K, Rodina A, Aguirre J, Felts S, Dingledine R, Haian Fu, Chiosis G. High-throughput screening fluorescence polarization assay for tumor-specific hsp90.Biomol Screen. Oct;12(7):915-24 (2007).

Rodina A, Vilenchik M, Moulick K, Aguirre J, Kim J, Chiang A, Litz J, Clement CC, Kang Y, She Y, Wu N, Felts S, Wipf P, Massague J, Jiang X, Brodsky JL, Krystal GW, Chiosis G. Selective compounds define Hsp90 as a major inhibitor of apoptosis in small-cell lung cancer. Nat Chem Biol.
Aug;3(8):498-507 (2007).

Luo W, Dou F, Rodina A, Chip S, Kim J, Zhao Q, Moulick K, Aguirre J, Wu N, Greengard P, Chiosis G. Roles of heat-shock protein 90 in maintaining and facilitating the neurodegenerative phenotype in tauopathies. Proc Natl Acad Sci U S A. May 29;104(22) (2007).

Chiosis G, Rodina A &  Moulick K. Emerging Hsp90 inhibitors: from discovery to clinic. Anticancer Agents Med Chem 6, 1-8 (2006).

Moulick K, Clement CC, Aguirre J, Kim J, Kang Y, Felts S & Chiosis G. Synthesis of a red-shifted fluorescence polarization probe for Hsp90. Bioorg Med Chem Lett. 16, 4515-8 (2006).

Nomikos M, Mulgrew-Nesbitt A, Pallavi P, Mihalyne G, Zaitseva I, Swann K, Lai FA, Murray D, McLaughlin S. Binding of phosphoinositide-specific phospholipase C-zeta (PLC-zeta) to phospholipid membranes: potential role of an unstructured cluster of basic residues. 
J Biol Chem. Jun 1;282(22):16644-53 (2007).

Mulgrew-Nesbitt A,  Diraviyam K, Wang J, Singh S, Murray P, Li Z, Rogers L, Mirkovic N & Murray D. The role of electrostatics in protein­membrane interactions. Bioch Biophys Acta. 1761, 812-826 (2006).

Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S. Structural Basis for  Nick Recognition by a Minimal Pluripotent DNA Ligase Nat. Struct Mol. Biol In press.

Keppetipola N, Nandakumar J, Shuman S. Reprogramming the tRNA-splicing activity of a bacterial RNA repair enzyme. Nucleic Acids Res. May 8 (2007). PMID: 17488852 [PubMed - as supplied by publisher]

Nandakumar J, Nair PA, Shuman S. Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate. Mol Cell. Apr 27;26(2):257-71 (2007).

Nandakumar J, Shuman S, Lima CD. RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. Cell. Oct 6;127(1):71-84 (2006).

Zhu H, Nandakumar J, Aniukwu J, Wang LK, Glickman MS, Lima CD, Shuman S. Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D. PNAS. Feb 7;103(6):1711-6. Epub Jan 30 (2006).

Nandakumar J, Shuman S, Lima CD. RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. Cell. 127, 71-84 (2006).

Nandakumar J, Shuman S. Dual mechanisms whereby a broken RNA end assists the catalysis of its repair by T4 RNA ligase 2. J Biol Chem. Jun 24;280(25):23484-9 (2005).

Nandakumar J, Ho CK, Lima CD & Shuman S. RNA substrate specificity and structure-guided mutational analysis of bacteriophage T4 RNA ligase 2. J Biol Chem. 279, 31337-31347 (2004).

Nandakumar J & Shuman S. How an RNA ligase discriminates RNA versus DNA damage. Mol Cell. 16, 211-221 (2004).

Brennan IM, Peters U, Kapoor TM, Straight AF. Polo-like kinase controls vertebrate spindle elongation and cytokinesis. PLoS ONE. May 2;2(5):e409 (2007).

Peters U, Cherian J, Kim JH, Kwok BH, Kapoor TM. Probing cell-division phenotype space and Polo-like kinase function using small molecules. Nat Chem Biol. 2, 618-26 (2006).

Llauger L, He H, Kim J, Aguirre J, Rosen N, Peters U, Davies P & Chiosis G. Evaluation of 8-arylsulfanyl. J Med Chem. 48, 2892-2905 (2005).

Marcus A, Peters U, Thomas SL, Garrett S, Zelnak A, Kapoor TM & Giannakakou P. Mitotic kinesin inhibitors induce mitotic arrest and cell death in Taxol-resistant and -sensitive cancer cells. J Biol Chem. 280, 11569-11577 (2005).

Oaksmith JM, Peters U & Ganem B. Three-component condensation leading to b-amino acid diamides: Convergent assembly of b-peptide analogues. J American Chem. Soc. 126, 13606-13607 (2004).

Peters U & Kapoor TM. New probes for microtubule dynamics. Chem Biol. 1,14-16 (2004).

Frank CG, Sanyal S, Rush JS, Waechter CJ, Menon AK. Does Rft1 flip an N-glycan lipid precursor? Nature. 454, (7204):E3-4; discussion E4-5. (2008). PMID: 18668045

Sanyal S, Frank CG, Menon AK. Distinct flippases translocate glycerophospholipids and oligosaccharide diphosphate dolichols across the endoplasmic reticulum.
Biochemistry. 47(30), 7937-46 (2008). PMID: 18597486

Sutterwala SS, Creswell CH, Sanyal S, Menon AK, Bangs JD. De novo sphingolipid synthesis is essential for viability, but not for transport of glycosylphosphatidylinositol-anchored proteins, in African trypanosomes. Eukaryot Cell. Mar;6(3):454-64. (2007)

Onwueme KC, Vos CJ, Zurita J, Ferreras JA & Quadri LE. The dimycocerosate ester polyketide virulence factors of mycobacteria. Prog Lipid Res. 44, 259-302 (2005).

Onwueme KC, Vos CJ, Zurita J, Soll CE & Quadri LE. Identification of phthiodiolone ketoreductase, an enzyme required for production of mycobacterial diacyl phthiocerol virulence factors. J Bacteriol. 187, 4760-4766 (2005).

Chung JY, Lu M, Yin Q and Wu H. Structural revelation of TRAF2 function in TNF Receptor Signaling Pathway. In press, and published online at eurekah.com. (2006).

Chung JY, Lu M, Yin Q, Lin S-C and Wu H. Molecular basis for the unique specificity of TRAF6. In TNF receptor associated factors. In press, and published online on eurekah.com. (2006).

Zoltowski BD, Schwerdtfeger C, Widom J, Loros JJ, Bilwes AM, Dunlap JC, Crane BR. Conformational Changes in the Fungal Light Sensor Vivid. Science. 316, 1054-1057 (2007).