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Thomas Smith's Laboratory

 

Publications

2008

  • Smith, T. J., Stanley, C. A. (2008) Untangling the glutamate dehydrogenase allosteric nightmare. TiBS (in press).
  • Koropatkin, N. M., Martins, E. C., Gordon, J. I., Smith, T. J. (2008) Starch catabolism by a prominent human symbiont is directed by the recognition of amylose helices. Structure 16:1105-1115.
  • Katpally, U., Wobus, C. E., Dryden, K., Virgin, H. W. IV, and Smith, T. J. (2008) Unexpected structural differences between authentic norovirus and virus like particles. J. Virol. 82:2079-2088.
  • Kakani, K., Reade, R., Katpally, U., Smith, T. J., Rochon, D. (2008) Induction of particle polymorphism by Cucumber necrosis virus coat protein in vivo. J. Virol. 82:1457-1557.
  • Allen, A., Snyder, A. K., Preuss, M., Nielsen, E. E., Shah, D. M., Smith, T. J. (2008) Plant and virally encoded fungal toxins inhibit plant root growth. Planta. 227: 331-339.

2007

  • Li, M., Allen, A., Smith, T. J. (2007) High throughput screening reveals several new classes of glutamate dehydrogenase inhibitors. Biochemistry 46: 15089-15102.
  • Katpally, U., Kakani, K., Reade, R., Rochon, D., Smith, T. J. (2007).  Structures of T=1 and T=3 Cucumber necrosis virus particles:  evidence of internal scaffolding. J. Mol. Biol.  365:  502-512.
  • Koropatkin, N. M., Koppenaal, D. W., Pakrasi, H. B., Smith, T. J. (2007) The structure of a cyanobacterial bicarbonate transport protein, CmpA.  J. Biol. Chem. 282:  2606-2614.
  • Goncalves, R. B., Mendes, Y. S., Soares, M. R., Katpally, U., Smith, T. J., Silva, J. L., Oliveira, A. C. (2007) VP4 protein from human rhinovirus 14 is released by pressure and locked in the capsid by the antiviral compound WIN.  J. Mol. Biol. 366:  295-306.
  • Asurmendi, S., Berg, R. H., Smith, T. J., Bendhamane, M., Beachy, R. N. (2007) Aggregation of TMV CP plays a role in CP functions and in coat-protein mediated resistance. Virology 336:98-106.
  • Wei, B., Randich, A. M., Bhattacharyya-Pakrasi, M., Pakrasi, H. B., Smith, T. J. (2007) Possible regulatory role for the histidine-rich loop in the zinc transport protein, ZnuA.  Biochemistry 46: 8734-8743.
  • Katpally, U., Smith, T. J. (2007) Pocket factors unlikely play a major role in the life cycle of human rhinovirus.  J. Virol. 81:  6307-6315.
  • Jez, J., Schachtman, D. P., Berg, R. H., Taylor, C. G., Chen, S., Hicks, L. M., Smith, T. J., Nielsen, E., Pikaard, C. S. (2007). Developing a new interdisciplinary lab course for undergraduate and graduate students:  plant cells and proteins. Biochem. and Mol. Biol. Edu. 35:410-415.
  • Bhattacharyya-Pakrasi, M., Ogawa, T., Smith, T. J., Si, X.-M., Pakrasi, H. (2007)  FEMS Letters. (Submitted).
  • Koropatkin, N. M., Randich, A. M., Bhattacharyya-Pakrasi, M., Pakrasi, H. B., Smith, T. J. (2007) The structure of the iron binding protein, FutA1, from Synechocystis 6803. J. Biol. Chem. 282:27468-27477.

2006

  • Li, C., Allen, A., Kwagh, J., Doliba, N. M., Qin, W., Najafi, H., Collins, H. W., Matschinsky, F. M., Stanley, C. A., Smith, T. J. (2006) Green tea polyphenols modulate insulin secretion by inhibiting glutamate dehydrogenase.  J. Biol. Chem.281:  10214-10221.
  • Koropatkin, N. M., Pakrasi, H. B., Smith, T. J. (2006) Atomic structure of a nitrate-binding protein crucial for photosynthetic productivity. PNAS 103:9820-9825.

2004

  • Ke, J., Schmidt, T., Chase, E., Bozarth, R. F., Smith, T. J. (2004) Structure of Cowpea Mottle Virus: a consensus in the genus Carmovirus. Virology 321:349-358.
  • Spelbrink, R., Dilmac, N., Allen, A., Smith, T. J., Shah, D. M., Hockerman, G. (2004) Differential antifungal and calcium channel-blocking activity among structurally related plant defensins. 135:2055-2067.
  • Smith, T. J. (2004) MolViewX: a molecular visualization program for the Macintosh OS X system. J. Appl. Cryst.  37:654-657.
  • Allen, A., Kwagh, J., Fang, J., Stanley, C., Smith, T. J. (2004) Evolution of glutamate dehydrogenase regulation of insulin homeostasis is an example of molecular exaptation. Biochemistry: 14431-14443.

2003

  • Smith, T. J., (2003) Structural studies on antibody-virus complexes. (Chiu, W., ed.) In Advances in Protein Chemistry, 64:409-443.
  • Banerjee, S., Schmidt, T. J., Fang, J., Stanley, C. A., Smith, T. J. (2003) Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation.  Biochem. 42:3446-3456.
  • Thomas, J., Katpally, U., Chase, E., Harris, K., Siuzdak, G., Smith, T. J. (2003) Human rhinovirus capsid dynamics is controlled by canyon flexibility.  Virol. 314:34-44.
  • Banerjee, S., Wei, B., Bhattacharyya-Pakrasi, M., Pakrasi, H. B., Smith, T. J. (2003) Structural determinants of metal specificity in the zinc transport protein ZnuA from Synechocystis 6803. J. Mol. Biol. 333:1061-1069. 

2002

  • Fang, J., Macmullen, C., Smith, T. J., Stanley, C. A. (2002) Expression, purification, and characterization of human glutamate dehydrogenase (GDH) regulatory mutations associated with a dominantly-expressed congenital hyperinsulinism / hyperammonemia syndrome. Biochem. J. 363:81-87.
  • Smith, T.J., Schmidt, T., Fang, J., Wu, J., Siuzdak, G., Stanley, C. (2002) The structure of apo human glutamate dehydrogenase details subunit communication and allostery. J. Mol. Biol.  318:765-777.
  • Gage, M. J., Rane, S. G., Hockerman, G. H., Smith, T. J. (2002) The virally encoded fungal toxin KP4 specifically blocks L-type voltage-gated calcium channels. Mol. Pharmacol. 61:936-944.
  • Smith, T. J., (2002) Antibody recognition of human rhinovirus. (Wimmer, E., and Semler, B., eds) In Molecular Biology of Picornaviruses. pp 39-49.
  • Bowman, V. D., Chase, E. S., Franz, A. W. E., Chipman, P. R., Perry, K. L., Baker, T. S., and Smith, T. J. (2002) An antibody to the putative aphid recognition site on cucumber mosaic virus recognizes pentons but not hexons.  J. Virol. 76:12250-12258.

2001

  • Smith, T., J. (2001) Antibody interactions with rhinovirus; lessons for mechanisms of neutralization and the role of immunity in viral evolution. In Current topics in microbiology and immunology; Antibodies in Viral Infection.  Burton, D. R. ed. (Springer, New York) pp 1-28.
  • Broo, K., Wei, J., Marshall, D., Brown, F., Smith, T. J., Johnson, J. E., Schneeman, A., Siuzdak, G. (2001) Viral capsid mobility:  a dynamic conduit for inactivation. PNAS 98:2274-2277.
  • Smith, T. J., Peterson, P. E., Schmidt, T., Fang, J., Stanley, C. A. (2001) Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation. J. Mol. Biol 307: 707-720.
  • MacMullen C. Fang J. Hsu BY. Kelly A. de Lonlay-Debeney P. Saudubray JM. Ganguly A. Smith TJ. Stanley CA. (2001) The Hyperinsulinism/hyperammonemia Contributing Investigators. Hyperinsulinism/hyperammonemia syndrome in children with regulatory mutations in the inhibitory guanosine triphosphate-binding domain of glutamate dehydrogenase. Journal of Clinical Endocrinology & Metabolism. 86(4):1782-1787
  • Gage, M. J., Bruenn, J., Fisher, M., Sanders, D., Smith, T. J. (2001) KP4 fungal toxin inhibits growth in Ustilago maydis by blocking calcium uptake.  Mol. Microbiol 41(4):775-786.

2000

  • Smith, T. J., Chase, E., Schmidt, T., Perry, K (2000) The structure of cucumber mosaic virus and comparison to cowpea chlorotic mottle virus.  J. Virol. 74: 7578-7586.

1999

  • Oliveira, A. C., Ishimaru, D., Goncalves, R. B., Smith, T. J., Mason, P., Sá-Carvalho, D., Silva, J. L. (1999) Low temperature and pressure stability of picornaviruses: implications for virus uncoating.  Biophysical Journal 76:1270-1279.
  • Smith, T. J. and Baker, T. (1999) Picornaviruses: epitopes, canyons, and pockets. Adv. Virus Res. 52: 1-23.
  • Peterson, P. and Smith, T. J. (1999) The structure of bovine glutamate dehydrogenase provides insights into the mechanism of allostery.  Structure 7: 769-782.
  • Belnap, D. M., Kumar, A., Folk, J. T., Smith, T. J., Baker, T. S. (1999) Low-resolution density maps from atomic models: how stepping 'back' can be a step 'forward.' J. Struc. Biol. 125:166-175.

1998

  • Che, Z., Olson, N. H., Leippe, D., Lee, W.-M., Mosser, A., Rueckert, R. R., Baker, T. S., Smith, T. J. (1998) Antibody-mediated neutralization of human rhinovirus 14 explored by means of cryo-electron microscopy and X-ray crystallography of virus-Fab complexes. J. Virol. 72:4610-4622.
  • Lewis, J. K., Bothner, B., Smith, T. J., Siuzdak, G. (1998) Antiviral agent blocks breathing of the common cold virus.  Proc. Natl. Acad. Sci. 95:6774-6778.
  • Lewis, J. K., Bendahmane, M., Smith, T. J., Beachy, R. N. Siuzdak, G. (1998) Identification of Viral Mutants by Mass Spectrometry. Proc. Natl. Acad. Sci. USA 95:8596-8601.

1997

  • Smith, TJ, and Mosser, AG. (1997) Antibody-mediated neutralization of picornaviruses. In  Chiu, W., Burnett, R., and Garcea, R. (eds.), Structure Biology of Viruses. Oxford University Press, New York pp. 134-156.
  • Rossmann, M.G., Greve, J.M., Kolatkar, P.R., Olson, N.H., Smith, T.J., McKinlay, M.A., and Rueckert, R.R. (1997) Rhinovirus attachment and cell entry. In Chiu, W., Burnett, R., and Garcea, R. (eds.), Structure Biology of Viruses. Oxford University Press, New York. pp.105-133. 
  • Peterson, P., Pierce, J., Smith, T. J. (1997)  Crystallization and characterization of bovine glutamate dehydrogenase.  J. Struc. Biol. 120:73-77.

1996

  • Gu, F., Khimani, A., Rane, S. G., Flurkey, W. H., Bozarth, R. F., Smith, T. J. (1996) The Structure of a Virally Encoded Fungal Toxin from Ustilago maydis that Inhibits Fungal and Mammalian Ca2+ Channels.  In Protein Toxin Structure . Springer, New York (M. Parker, ed.) pp.291-303.
  • Thomas J. Smith, Norman H. Olson, Zhiwei Che, Elaine Chase, Anne Mosser, Donna Leippe, Holland Cheng, Roland R. Rueckert, and Timothy S. Baker.  (1996) Structural Studies on Virus-Antibody Interactions.  Cold Spring Harbor Symposium Proceedings -Vaccines96. 161-167.
  • Thomas J. Smith, Elaine S. Chase, Timothy J. Schmidt, Norman H. Olson, Timothy S. Baker. (1996) Neutralizing antibody to human rhinovirus penetrates the receptor-binding canyon. Nature (London), 383:350-354.

1995

  • Cheng, R.H., Kuhn, R.J., Olson, N.H., Rossmann, M.G., Choi, H., Smith, T.J., and Baker, T.S. (1995)  Nucleocapsid and glycoprotein organization in an enveloped virus.  Cell 80:1-20.
  • Smith, TJ. (1995)  MolView:  a program to analyze and display atomic structures on the Macintosh personal computer.  J. Molecular Graphics 13:122-125.
  • Smith, TJ, Mosser, AG, and Baker, TS. (1995)  Structural Studies on the Mechanisms of  Antibody-Mediated Neutralization of Human Rhinovirus.  Seminars in Virology 6:233-242.
  • Smith, TJ. (1995)  MolView, freeware for analyzing and viewing atomic structures.  SciTech Journal  5:24-25.
  • Gu, F., Khimani, A., Rane, S. G., Flurkey, W. H., Bozarth, R. F., Smith, T. J. (1995) Structure and function of a virally encoded fungal toxin from Ustilago maydis: a fungal and mammalian Ca2+ channel inhibitor.  Structure 3:805-814.
  • Smith, T. J., Cheng, R. H., Olson, N. H., Peterson, P., Chase, E., Kuhn, R. J., Baker, T. S. (1995) Putative receptor binding sites on enveloped viruses as visualized by cryo-electron microscopy.  Proc. Natl. Acad. Sci (USA) 92:10648-10652.

1994

  • Liu, H., Smith, T.J., Lee, W.M., Leippe, D, Mosser, A., and Rueckert, R.R. (1994)  The purification, crystallization, and structure determination of an Fab fragment that Neutralizes Human Rhinovirus 14  J. Mol. Biol. 240:127-137.
  • Chiu, W., and Smith, T.J. (1994) Structural studies of virus-antibody complexes by electron cryomicroscopy and X-ray crystallography.  Cur. Opin. in Struc. Biol. 4:219-224.
  • Saraswat, N., Alleman, J.E., and Smith, T.J. (1994)  Enzyme immunoassay detection of Nitrosomonas europaea.  Appl. and Environ. Microbiol. 60:1969-1973.
  • Gu, F., Sullivan, T.S., Che, Z., Ganesa, C., Flurkey, W.H., Bozarth, R.F., and Smith, T.J. (1994)  The characterization and crystallization of a virally encoded Ustilago Maydis KP4 toxin.  J. Mol. Biol. 243:792-795.
  • Cheng, R.H., Caston, J.R., Wang, G., Gu, F., Smith, T.J., Baker, T.S., Bozarth, R.F., Trus, B.L., Cheng, N., Wickner, R.B., and Steven, A.C. (1994)  Fungal virus capsids:  cytoplasmic compartments for the replication of double-stranded RNA formed as icosahedral shells of asymmetric Gag dimers.  J. Mol. Biol. 244:255-258.

1993

  • Smith, T.J., Olson, N.H., Cheng, R.H., Liu, H., Chase, E., Lee, W.M., Leippe, D.M., Mosser, A.G., Ruekert, R.R., and Baker, T.S. (1993) Structure of human rhinovirus complexed with Fab fragments from a neutralizing antibody  J. Virol. 67: 1148-1158.
  • Smith, T.J., Olson, N.H., Cheng, R.H., Chase, E.S., and Baker, T.S. (1993)  Structure of a human rhinovirus-bivalent antibody complex: Implications for virus neutralization and antibody flexiblity.  Proc. Natl. Acad. Sci. USA 90:7015-7018.
  • Smith, T.J. (1993)  MacInPlot II-an updated program to display electron density and atomic models on the MacIntosh personal computer  J. Appl. Cryst. 26:496-498.
  • Rossmann, M.G., Smith, T.J., and Rueckert, R.R. (1993) The structure of human rhinovirus 14.  Structure Introductory Issue: xxiv-xxv.

1992

  • Olson, N.H., Smith, T.J., Kolatkar, P.R., Oliveira, M.A., Rueckert, R.R., Greve, J.M., Rossmann, M.G., and Baker, T.S. (1992)  Cryoelectron microscopy of complexes of human rhinovirus with a monoclonal Fab and the viral cellular receptor.  Proc.  Elect. Microsc. Soc. of Amer. 50:524-525.
  • Smith, T. (1992) Purification of mouse antibodies and Fab fragments. In  Asai, D. (ed.), Methods in Cell Biology  Chapter 4, pp 75-93.
  • Smith, T.J., and Chase, E.S. (1992) Purification and crystallization of intact human rhinovirus complexed with a neutralizing Fab  Virology 191:600-606.

1982-1991

  • Tsao, J., Chapman, M.S., Agbandje, M., Keller, W., Smith, K., Wu, H., Luo, M., Smith, T. J., Rossmann, M. G., Compans, R. W., and Parrish, C. R. (1991) The three-dimensional structure of canine parvovirus and its functional implications.  Science 251: 1456-1464.
  • Prongay, A.J., Smith, T.J., Rossmann, M.G., Ehrlich, L.S., Carter, C.A., and McClure, J. (1990)  Preparation and Crystallization of a Human Immunodeficiency Virus p24-Fab Complex  Proc. Natl. Acad. Sci. USA 87:9980-9984.
  • Willingmann, P., Krishnaswamy, S., McKenna, R., Smith, T.J., Olson, N.H., Rossmann, M.G., Stow, P.L., and Incardona, N.L. (1990)  Preliminary investigation of the phage fX174 crystal structure. J. Mol. Biol. 212:345-350.
  • Smith, T.J., Badger, J., Kremer, M., Oliveira, M., Rossmann, M.G., McKinlay, M.A., Diana, G.D., Pavear, D.C., Dutko, F.J., Rueckert, R.R., Heinz, B., and Shepard, D. (1990) Crystallographic and pharmacological studies of antiviral agents against human rhinovirus.  In  Bugg, C.E., and Ealick, S.E., (eds.), Crystallographic and modelling methods in molecular design Springer-Verlag, New York, pp. 9-28.
  • Smith, T.J. (1990)  MacInPlot - a program to display electron density and atomic models on the Macintosh personal computer  J. Appl. Cryst. 23:41-142.
  • Kim, S., Boege, U., Krishnaswamy, S., Minor, I., Smith, T.J., Luo, M., Scraba, D.G., and Rossmann, M.G. (1990) Conformational variability of a picornavirus capsid: pH-dependent structural changes of Mengo virus related to its host receptor attachment site and disassembly.  Virology 175:176-190.
  • Smith, T.J. (1989) Approaches to antiviral drug design. In Perun, T.J., and Propst, C.L., (eds.), Computer-aided drug design.  Methods and applications  Mercel Dekker, New York, pp. 371-403.
  • Diana, G.D., Pevear, D.C., Otto, M.J., McKinlay, M.A., Rossmann, M.G., Smith, T.J., and Badger, J. (1989)  Inbitors of viral uncoating  Pharmacol. Therapeut. 42:289-305.
  • Boege, U., Cygler, M., Wengler, G., Tsao, J., Luo, M., Dumas, P., Smith, T.J., and Rossmann, M.G. (1989)  Sinbis virus nucleocapsid core protein crystals  J. Mol. Biol. 208:79-82.
  • Badger, J., Minor, I., Oliveira, M.A., Smith, T.J., and Rossmann, M.G. (1989)  Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses.  Proteins 6:1-19.
  • Heinz, B.A., Rueckert, R.R., Shepard, D.A., Dutko, F.J., McKinlay, M.A., Francher, M., Rossmann, M.G., Badger, J., and Smith, T.J. (1989)  Genetic and molecular analysis of spontaneous mutants of human rhinovirus 14 resistant to an antiviral compound.  J. Virol. 63:2476-2485.
  • Kim, S., Smith, T.J., Chapman, M.S., Rossmann, M.G., Peavear, D.C., Dutko, F.J., Felock, P.J., Diana, G.D., and McKinlay, M.A. (1989)  The crystal structure of human rhinovirus serotype 1A (HRV1A)  J. Mol. Biol. 210:91-111.
  • Diana, G.D., Otto, M.J,. Treasurywala, A.M., McKinlay, M.A., Oglesby, R.C., Maliski, E.G., Rossmann, M.G., and Smith, T.J. (1988)  Enantiomeric effects of homologues of disoxaryil on the inhibitory activity against human rhinovirus-14  J. Med. Chem. 31:540-544.
  • Badger, J., Minor, I., Kremer, M.J., Oliveira, M.A., Smith, T.J., Griffith, J.P., Guerin, M.A., Krishnaswamy, S., Luo, M., Rossmann, M.G., McKinlay, M.A., Dlana, G.D., Kutko, F.J., Fancher, M., Rueckert, R.R., and Heinz, B.A. (1988)  Structural analysis of a series of antiviral agents complexed with human rhinovirus 14  Proc. Natl. Acad. Sci. U.S. 85:3304-3308.
  • Smith, T.J. (1987)  The isolation of the two electrophoretic forms of cowpea mosaic virus using fast protein liquid chromatography  J. Virol. Meth. 16:263-269.
  • Rossmann, M.G., Arnold, E., Kamer, G., Kremer, M.J., Luo, M., Smith, T.J., Vriend, G., Rueckert, R.R., Mosser, A.G., Sherry, B., Boege, U., Scraba, D.G., McKinlay, M.A., and Diana, G.D. (1987) Structure and function of human rhinovirus 14 and Mengo virus:  Neutralizing antigenic sites, putative receptor binding site, neutralization by drug binding. In  Brinton, M.A., and Rueckert, R.R., (eds.), Positive strand RNA viruses  Alan R. Liss, New York, pp. 59-77.
  • Rossmann, M.G., Arnold, E., Kamer, G., Kremer, M.J., Luo, M., Smith, T.J., Vriend, G., Rueckert, R.R., Mosser, A.G., Sherry, B., Boege, U., Scraba, D.G., McKinlay, M.A., and Diana, G.D. (1987) Viral particles at atomic resolution. In Bercoff, R.P. (ed.), The molecular basis of viral replication  Plenum Press, New York, pp.25-44.
  • Rossmann, M.G., Arnold, E., Griffith, J.P., Kamer, G., Luo, M., Smith, T.J., Vriend, G., Rueckert, R.R., Sherry, B., McKinlay, M.A., Diana, G., and Otto, M. (1987)  Common cold viruses  Trends Biochem. Sci. 12:313-318.
  • Smith, T.J., Kremer, M.J., Luo, M., Vriend, G., Arnold, E., Kamer, G., Rossmann, M.G., McKinlay, M.A., Diana, G.D., and Otto, M.J. (1986)  The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating  Science  233:1286-1293.
  • Smith, T.J., and Bell, J.E. (1986)  An exponential gradient maker for use with minigel polyacrylamide electrophoresis systems  Anal. Biochem. 152:74-77.
  • Smith, T.J., and Bell, J. (1985)  Investigation of the effects of crosslinking glutamate dehydrogenase with dimethylpimelimidate  Arch. Biochem. Biophys. 239:63-73.
  • Holt, J.T., Arvan, D.A., Mayer, T., Smith, T.J., and Bell, J.E. (1983)  Glutamate dehydrogenase in Reye's syndrome: Evidence for the presence of an altered enzyme in serum with increased susceptibility to inhibition by GTP  Biochim. Biophys. Acta. 749:42-46.
  • Smith, T.J. and Bell, J.E. (1982)  The mechanism of hysteresis in bovine glutamate dehydrogenase: The role of subunit interactions  Biochemistry . 21:733-737.

 
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