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Rhinovirus [Return to top]


1.
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.

 
  2.
Goncalves, R. B., Mendes, Y. S., Soared, 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.


3.
Thomas, J., Katpally, U., Chase, E., Harris, K., Siuzdak, G., Smith, T. J., (2003) Human Rhinovirus dynamics is controlled by canyon flexibility. Virol. 314:34-44.
  4. Smith, T. J., (2003) Structural studies on antibody-virus complexes. In Advances in Protein Chemistry (Chiu, W., ed.) 64:445-490.
  5. Smith, T. J., (2002) Antibody recognition of human rhinovirus. In Molecular Biology of Picornaviruses (Wimmer, E., and Semler, B., eds) ASM Press, Washington, D.C. pp 39-49.
  6. 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.
  7. 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.
  8. 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.
  9. Smith, T. J. and Baker, T. (1999) Picornaviruses: epitopes, canyons, and pockets. Adv. Virus Res. 52: 1-23.
pdf 10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. Rossmann, M.G., Smith, T.J., and Rueckert, R.R. (1993) The structure of human rhinovirus 14. Structure Introductory Issue: xxiv-xxv.
  22. 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.
  23. 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.
  24. Smith, T.J., and Chase, E.S. (1992) Purification and crystallization of intact human rhinovirus complexed with a neutralizing Fab Virology 191:600-606.
  25. Smith, T. (1992) Purification of mouse antibodies and Fab fragments. In Asai, D. (ed.), Methods in Cell Biology Chapter 4, pp 75-93.
  26. 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.
  27. 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.


28.
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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
Glutamate Dehydrogenase [Return to top]


1.
Li, M., Allen, A., Smith, T. J. (2007) High throughput screening reveals several new classes of glutamate dehydrogenase inhibitors.  Biochemistry  (in press)


2.
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.



 
  3.

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 43:14431-14443.
  4.
Banerjee, S., Schmidt, T., Fang, J., Stanley, C. A., Smith, T. J. (2003) Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation.  Biochemistry, 42:3446-3456.
 
5.

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.
pdf
6.
Fang, J., Hsu, B.Y., Macmullen, C., Poncz, M., 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.
pdf 7.


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
  8.

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.
  9.

Peterson, P. and Smith, T. J. (1999) The structure of bovine glutamate dehydrogenase provides insights into the mechanism of allostery. Structure 7: 769-782.
  10. Peterson, P., Pierce, J., Smith, T. J. (1997) Crystallization and characterization of bovine glutamate dehydrogenase. J. Struc. Biol. 120:73-77.
  11.

Smith, T.J., and Bell, J. (1985) Investigation of the effects of crosslinking glutamate dehydrogenase with dimethylpimelimidate Arch. Biochem. Biophys. 239:63-73.
  12. 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.
  13.

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.
 
ABC Transporters [Return to top]


1.
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.




2.
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.

 
  2.
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.


4.
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.
  5. Banerjee, S., Wei, B., Bhattacharyya-Pakrasi, M., Pakrasi, H. B., Smith, T. J. (2003) Structural determinants of metal specificity in the zinc transporter ZnuA from Synechocystis 6803. J. Mol. Biol. 333:1061-1069.
  Plant Viruses [Return to top]


1.
Kakani, K., Reade, R., Katpally, U., Smith, T. J., Rochon, D. (2007) Induction of particle polymorphism by Cucumber necrosis virus coat protein in vivo. J. Virol. (in press).

 
  2.
Katpally, U., Kakani, K., Reade, R., Rochon, D., Smith, T. J. (2007) Structures of T=1 and T=3 Cucumber necrosis particles:  evidence of internal scaffolding.  J. Mol. Biol. 365:502-512.


  3.
Asurmendi, S., Berg, R. H., Smith, T. J., Beachy, R. N. (2007) TMV stacked disk aggregates play an important role in coat-protein mediated resistance. Virology 336:98-106.


4.
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.
  5. Bowman, V. D., Chase, E. S., Franz, A. W. E., Chipman, P. R., Zhang, X., Perry, K. L., Baker, T. S., Smith, T. S. (2002) An antibody to the putative aphid recognition site on cucumber mosaic virus recognizes pentons but not hexons.  J. Virol 76:12250-12258.


6.
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.


7.
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.
Caliviruses [Return to top]


1.
Katpally, U., Wobus, C. E., Dryden, K., Virgin, H. W. IV, and Smith, T. J. (2007) Unexpected structural differences between authentic norovirus and virus like particles. J. Virol. (in press).


MolView [Return to top]


1.
Smith, TJ. (2004) MolViewX:  a molecular visualization program for the Macintosh OS X system.  J. App. Cryst.37:654-657.
  2. Smith, TJ. (1995) MolView, freeware for analyzing and viewing atomic structures. SciTech Journal 5:24-25.
  3. Smith, TJ. (1995) MolView: a program to analyze and display atomic structures on the Macintosh personal computer. J. Molecular Graphics 13:122-125.
  4. 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.
  5. Smith, T.J. (1990) MacInPlot - a program to display electron density and atomic models on the Macintosh personal computer J. Appl. Cryst. 23:141-142.
Fungal Toxins [Return to top]


1.
Allen, A., Snyder, A. K., Preuss, M., Nielsen, E. E., Shah, D. M., Smith, T. J. (2007) Plant and virally encoded fungal toxins inhibit plant root growth. Planta (in press).


2.
Spelbrink, R., Dilmac, N., Allen, A., Smith, T. J., Shah, D. M., Hockerman, G. (2004) The plant defensin from alfalfa blocks a mammalian calcium channel.  Plant Physiol. 135:2055-2067.
  3. 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.
pdf 4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
Alphaviruses [Return to top]
  1. 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.
  2. 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.


3.
Boege, U., Cygler, M., Wengler, G., Tsao, J., Luo, M., Dumas, P., Smith, T.J., and Rossmann, M.G. (1989) Sindbis virus nucleocapsid core protein crystals J. Mol. Biol. 208:79-82.
Other Papers [Return to top]
  1. Saraswat, N., Alleman, J.E., and Smith, T.J. (1994) Enzyme immunoassay detection of Nitrosomonas europaea. Appl. and Environ. Microbiol. 60:1969-1973.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. Smith, T.J., and Bell, J.E. (1986) An exponential gradient maker for use with minigel polyacrylamide electrophoresis systems Anal. Biochem. 152:74-77.