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Smith's Research Lab

Publications

PubMed: Recent publications for Thomas Smith

TJ Smith Publications

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  • 2024-2020
    2024-2020
    1. Sherman M, Cox F, Smith H, Habib MH, Karst S, Wobus CE, Smith TJ. The reversible activation of norovirus by metal ions. J Virol. 2024 Jan 18:e0173523. doi: 10.1128/jvi.01735-23.
    2. Sanfaçon H, Alam SB, Ghoshal B, Ghoshal K, Hui E, Jackson AO, Kakani K, Morris TJ, Nagy PD, Simon AE, Sit TL, Smith TJ, White KA, Xiang Y. D'Ann Rochon (1955-2022), a life of passion for plant virology. Virology. 2023 Oct;587:109874. doi: 10.1016/j.virol.2023.109874.
      3. Creutznacher R, Maass T, Dülfer J, Feldmann C, Hartmann V, Lane MS, Knickmann J, Westermann LT, Thiede L, Smith TJ, Uetrecht C, Mallagaray A, Waudby CA, Taube S, Peters T. Distinct dissociation rates of murine and human norovirus P-domain dimers suggest a role of dimer stability in virus-host interactions. Commun Biol. 2022 Jun 9;5(1):563. doi: 10.1038/s42003-022-03497-4.
    3. Helm EW, Peiper AM, Phillips M, Williams CG, Sherman MB, Kelley T, Smith HQ, Jacobs SO, Shah D, Tatum SM, Iyer N, Grodzki M, Morales Aparicio JC, Kennedy EA, Manzi MS, Baldridge MT, Smith TJ, Karst SM. Environmentally-triggered contraction of the norovirus virion determines diarrheagenic potential. Front Immunol. 2022 Nov 1;13:1043746. doi: 10.3389/fimmu.2022.1043746.
    4. Sherman MB, Williams AN, Smith HQ, Pettitt BM, Wobus CE, Smith TJ. Structural Studies on the Shapeshifting Murine Norovirus. Viruses. 2021 Oct 26;13(11):2162. doi: 10.3390/v13112162.
    5. Ng JCK, Peng JHC, Chen AYS, Tian T, Zhou JS, Smith TJ. Plasticity of the lettuce infectious yellows virus minor coat protein (CPm) in mediating the foregut retention and transmission of a chimeric CPm mutant by whitefly vectors. J Gen Virol. 2021 Sep;102(9):001652. doi: 10.1099/jgv.0.001652.
    6. Williams AN, Sherman MB, Smith HQ, Taube S, Pettitt BM, Wobus CE, Smith TJ. Multiple Signals in the Gut Contract the Mouse Norovirus Capsid To Block Antibody Binding While Enhancing Receptor Affinity. J Virol. 2021 Oct 27;95(22):e0147121. doi: 10.1128/JVI.01471-21.
    7. Williams AN, Sherman MB, Smith HQ, Taube S, Pettitt BM, Wobus CE, Smith TJ. A norovirus uses bile salts to escape antibody recognition while enhancing receptor binding. J Virol. 2021 Apr 7:JVI.00176-21. doi: 10.1128/JVI.00176-21.
    8. Sherman MB, Smith HQ, Smith TJ. The Dynamic Life of Virus Capsids. Viruses. 2020, 12(6):618. doi: 10.3390/v12060618.
    9. Sherman MB, Guenther R, Reade R, Rochon D, Sit T, Smith TJ. Near-Atomic-Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus: Evolutionary Divergence at the Icosahedral Three-Fold Axes. J Virol. 2020, 94(2):e01439-19. doi: 10.1128/JVI.01439-19.
      10.
  • 2019-2010
    2019-2010
    1. Nassar OM, Wong KY, Lynch GC, Smith TJ, Pettitt BM. (2019) Allosteric Discrimination at the NADH/ADP Regulatory Site of Glutamate Dehydrogenase. Protein Sci.(12):2080-2088. doi: 10.1002/pro.3748.
    2. Hoffpauir ZA, Sherman E, Smith TJ. (2019) Dissecting the Antenna in Human Glutamate Dehydrogenase: Understanding Its Role in Subunit Communication and Allosteric Regulation. Biochemistry. 58(41):4195-4206. doi: 10.1021/acs.biochem.9b00722.
    3. Sherman MB, Williams AN, Smith HQ, Nelson C, Wilen CB, Fremont DH, Virgin HW, Smith TJ. (2019) Bile Salts Alter the Mouse Norovirus Capsid Conformation: Possible Implications for Cell Attachment and Immune Evasion. J Virol. 93(19). pii: e00970-19. doi: 10.1128/JVI.00970-19.
    4. Smith HQ, Smith TJ (2019) The Dynamic Capsid Structures of the Noroviruses. Viruses. 11(3). pii: E235. doi: 10.3390/v11030235.
    5. Nassar OM, Li C, Stanley CA, Pettitt BM, Smith TJ. (2019) Glutamate dehydrogenase: Structure of a hyperinsulinism mutant, corrections to the atomic model, and insights into a regulatory site. Proteins. 87(1):41-50. doi: 10.1002/prot.25620.
    6. Smith HQ, Li C, Stanley CA, Smith TJ (2019) Glutamate Dehydrogenase, a Complex Enzyme at a Crucial Metabolic Branch Point. Neurochem Res. 44(1):117-132. doi: 10.1007/s11064-017-2428-0.
    7. Warner BE, Ballinger MJ, Yerramsetty P, Reed J, Taylor DJ, Smith TJ, Bruenn JA. PeerJ. (2018) Cellular production of a counterfeit viral protein confers immunity to infection by a related virus. 6:e5679. doi: 10.7717/peerj.5679.
    8. Nelson CA, Wilen CB, Dai YN, Orchard RC, Kim AS, Stegeman RA, Hsieh LL, Smith TJ, Virgin HW, Fremont DH. (2018) Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor. Proc Natl Acad Sci U S A. 115(39):E9201-E9210. doi: 10.1073/pnas.1805797115.
    9. Rotem A, Serohijos AWR, Chang CB, Wolfe JT, Fischer AE, Mehoke TS, Zhang H, Tao Y, Lloyd Ung W, Choi JM, Rodrigues JV, Kolawole AO, Koehler SA, Wu S, Thielen PM, Cui N, Demirev PA, Giacobbi NS, Julian TR, Schwab K, Lin JS, Smith TJ, Pipas JM, Wobus CE, Feldman AB, Weitz DA, Shakhnovich EI. (2018) Evolution on the Biophysical Fitness Landscape of an RNA Virus. Mol Biol Evol. 35(10):2390-2400. doi: 10.1093/molbev/msy131.
    10. Kirkpatrick CL, Parsley NC, Bartges TE, Cooke ME, Evans WS, Heil LR, Smith TJ, Hicks LM. (2018) Fungal Secretome Analysis via PepSAVI-MS: Identification of the Bioactive Peptide KP4 from Ustilago maydis. J Am Soc Mass Spectrom. 29(5):859-865. doi: 10.1007/s13361-017-1880-z. Epub 2018 Feb 5. Erratum in: J Am Soc Mass Spectrom. 2018 Sep;29(9):1940.
    11. Kolawole AO, Smith HQ, Svoboda SA, Lewis MS, Sherman MB, Lynch GC, Pettitt BM, Smith TJ, Wobus CE. (2017) Norovirus Escape from Broadly Neutralizing Antibodies Is Limited to Allostery-Like Mechanisms. mSphere. 2(5). pii: e00334-17. doi: 10.1128/mSphere.00334-17.
    12. Sherman MB, Kakani K, Rochon D, Jiang W, Voss NR, Smith TJ. (2017) Stability of Cucumber Necrosis Virus at the Quasi-6-Fold Axis Affects Zoospore Transmission. J Virol.91(19). pii: e01030-17. doi: 10.1128/JVI.01030-17.
    13. Dong Y, Liu Y, Jiang W, Smith TJ, Xu Z, Rossmann MG. (2017) Antibody-induced uncoating of human rhinovirus B14. Proc Natl Acad Sci U S A. 114(30):8017-8022. doi: 10.1073/pnas.1707369114.
    14. Barrosse-Antle M, Su C, Chen P, Boodhansingh KE, Smith TJ, Stanley CA, De León DD, Li C. (2017) A severe case of hyperinsulinism due to hemizygous activating mutation of glutamate dehydrogenase. Pediatr Diabetes. 18(8):911-916.
    15. Smith HQ, Smith TJ. (2016) Identification of a Novel Activator of Mammalian Glutamate Dehydrogenase. Biochemistry. 55(47):6568-6576.
    16. Fischer AE, Wu SK, Proescher JB, Rotem A, Chang CB, Zhang H, Tao Y, Mehoke TS, Thielen PM, Kolawole AO, Smith TJ, Wobus CE, Weitz DA, Lin JS, Feldman AB, Wolfe JT. (2015) A high-throughput drop microfluidic system for virus culture and analysis. J Virol Methods. 213:111-7.
    17. Kolawole, A. O., Xia, C., Li, M., Gamez, M., Yu, C., Rippinger, C. M., Yucha, R. E., Smith, T. J., Christiane E. Wobus (2014) Newly isolated mAbs broaden the neutralizing epitope in murine norovirus. J. Gen. Virol. 95:1958-1968.
    18. Kolawole, A. O., Li, M., Xia, C., Fischer-Hesselbrock, Giacobbi, N. S., Rippinger, C. M., Proescher, J. B. G., Wu, S. K., Bessling, S. L., Garnez, M., Yu, C., Pipas, J. M., Wolfe, J. T., Feldman, A. B., Smith, T. J., Wobus, C. E. (2014) Flexibility in surface exposed loops in the virus capsid mediates escape from antibody neutralization. J. Virol. 88:4543-4557.
    19. Li, M., Li, C., Allen, A., Stanley, C. A., Smith, T. J. (2014) Glutamate dehydrogenase; structure, allosteric regulation, and role in insulin homeostasis. Neurochem. Res. 39: 433-445. DOI:10.1007/s11064-013-1173-2.
    20. Li, M., Kakani, K., Katpally, U., Johnson, S., Rochon, D., Smith, T. J. (2013) Atomic structure of cucumber necrosis virus and the role of the capsid in vector transmission. J. Virol. 87:12166-12175.
    21. Sagaram, U. S., El-Mounadi, K., Buchko, G. W., Berg, H. R., Kaur, J., Pandurangi, R. S., Smith, T. J., Shah, D. M. (2013) Structural and functional studies of a phosphatidic acid-binding antifungal plant defensing MtDef4: identification of an RGFRRR motif governing fungal cell entry. PloS One 8:e82485.
    22. Allen, A., Chatt, E., Smith, T. J. (2013) The atomic structure of the virally encoded antifungal protein, KP6. J. Mol. Biol. 452:609-621.
    23. Allen, A., Islamovic, E., Kaur, J., Gold, S., Shah, D. Smith, T. J. (2013) The virally-encoded killer proteins from Ustilago maydis. Fungal Biology Reviews. 26:166-173. (http://dx.doi.org/10.1016/j.fbr.2012.10.001).
    24. Cameron, E.A., Maynard, M., Smith, C. J., Smith, T. J., Koropatkin, N., Martens, E. (2012) Multi-domain carbohydrate-binding proteins involved in Bacteroides thetaiotaomicron starch metabolism. JBC 287:34614-34625.
    25. Smith, T. J. (2012) Green tea and control of glutamate dehydrogenase activity. In Tea in health and disease prevention. (ed. Preedy, V. R.). pp. 1029-1038.
    26. Smith, T. J. (2012) Glutamate dehydrogenase: structure regulation, and its role in insulin homeostasis. In Monogenic Hyperinsulinemic Hypoglycemia Disorders. Frontiers in Diabetes Vol. 21. (Eds. C. A. Stanley and D. D. De Leon) Karger Publishers, Unionville, CT. pp 87-99.
    27. Hansman, G. S., Taylor, D. W., McLellan, J. S., Smith, T. J., Tame, J. R. H., Park, S.-Y., Yamazaki, M., Gondaira, F., Miki, M., Katayama, K., Murata, K., Kwong, P. D. (2012) Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle. J. Virol. 86:3635-3646.
    28. Strong, D. W., Thackray, L. B., Smith, T. J., Virgin, H. W. (2012) Protruding domain of capsid protein is necessary and sufficient to alter murine norovirus replication and pathogenesis in vivo. J. Virol. 86:2950-2958.
    29. Li, M., Li, C., Allen, A., Stanley, C. A., Smith, T. J. (2012) The structure and allosteric regulation of glutamate dehydrogenase. Arch. Biochem. Biophys. 519:69-80. DOI:10.1016/j.abb.2011.10.015.
    30. Smith, T. J. and Stanley, C. A. (2012) Glutamate Dehydrogenase in Amino Acids in Human Nutrition and Health, D'Mello, ed., CAB International, UK, Chapter 1, pp. 3-23.
    31. Li, C., Li, M., Chen, P., Narayan, S., Matschinsky, F. M., Bennett, M. J., Stanley, C. A., Smith, T. J. (2011) Green tea polyphenols control dysregulated glutamate dehydrogenase in transgenic mice by hijacking the ADP activation site. J. Biol. Chem 286:34164-34174 (DOI: 10.1074/jbc.M111.268599)
    32. Smith, T. J. (2011) Structural studies on antibody recognition and neutralization of viruses. Current Opinion in Virology, 1:150-156 (DOI:10.1016/j.coviro.2011.05.020).
    33. Smith, T. J. (2011) Development of fungal resistance in crop plants using genetic engineering and antifungal proteins from viruses. ISB News Report, May 2011.
    34. Bailey, J., Powell, L., Sinanan, L., Neal, J., Li, M., Smith, T. J., Bell, J. E. (2011) A novel mechanism of V type zinc inhibition of glutamate dehydrogenase results from disruption of subunit interactions necessary for efficient catalysis. FEBS J. 278:3140-3151. (DOI: 10.1111/j.1742-4658.2011.08240.x.)
    35. Sagaram, U. S., Pandurangi, R., Kaur, J., Smith, T., Shah, D. (2011) Structure-activity determinants in two different antifungal plant defensins that have different modes of action. PLoS One. 2011; 6(4): e18550.
    36. Allen, A., Islamovic, E., Kaur, J., Gold, S., Shah, D., Smith, T. J. (2011) Transgenic maize plants expression the Totivirus antifungal protein, KP4, are highly resistant to corn smut. Plant Biotech. J. 9:857-864; DOI: 10.1111/j.1467-7652.2011.00590.x).
    37. Koropatkin, N., Pakrasi, H.B., Smith, T.J. (2011) Iron binding protein FutA1. In Handbook of Metalloproteins, A. Messerschmidt (ed.), Chichester, UK: John Wiley & Sons, Ltd, pp 336-341.
    38. Pakrasi, H.B., and Smith, T.J. (2011) Zinc binding protein, ZnuA. In Handbook of Metalloproteins, A. Messerschmidt (ed.), Chichester, UK: John Wiley & Sons, Ltd, pp 746-754.
    39. Higashi, Y., Kutchen, T. M., Smith, T. J. (2011) The atomic structure of salutaridine reductase from the opium poppy Papaver somniferum. J. Biol. Chem. 286:6532-6541.
    40. Smith, T.J. (2011) Green tea polyphenols in drug discovery - a success or failure? Expert Opinion on Drug Discovery, 6:589-595.
    41. Li, M., Li, C., Allen, A., Stanley, C. A., Smith, T. J. (2011) The structure and allosteric regulation of glutamate dehydrogenase. Neurochem. Int. 59:445-455 (doi:10.1016/j.neuint.2010.10.017).
    42. Smith, T.J. (2010) Structural studies on antibody/virus complexes. In Structural Virology Monographs, Agbandje-McKanna, M. and McKenna, R. (eds.), Royal Society of Chemistry, UK, Chapter 14, pp. 261-283.
    43. Li, C., Chen, P., Palladino, A., Narayan, S., Russell, L. K., Sayed, S., Xiong, G., Chen, J., Stokes, D., Butt, Y. M., Jones, P. M., Collins, H. W., Cohen, N. A., Cohen, A. S., Smith, T. J., Strauss, A. W., Matschinsky, F. M., Bennett, M. J., Stanley, C. A. (2010) Mechanism of hyperinsulinism in short-chain 3-hydroxyacyl-CoA dehydrogenase deficiency involves activation of glutamate dehydrogenase. J. Biol. Chem. 285:31806-31818.
    44. Taube, S., Rubin, J. R., Smith, T. J., Kendall, A., Stuckey, J., Wobus, C. E. (2010) High resolution X-ray structure and functional analysis of murine norovirus (MNV)-1 capsid protein protruding domain. J. Virol. 84: 5695-5705.
    45. Katpally, U., Voss, N. R., Cavazza, T., Taube, S., Rubin, J. R., Young, V. L., Stuckey, J., Ward, V. K., Virgin, H. W., Wobus, C. E., Smith, T. J. (2010) High-resolution cryo-electron microscopy structures of MNV-1 and RHDV reveals marked flexibility in the receptor binding domains. J. Virol. 84:5836-5841.
    46. Higashi, Y. Smith, T.J., Jez, J., Kutchen, T.M. (2010) Crystallization and preliminary X-ray diffraction analysis of salutaridine reductase from Papaver somniferum. Acta Cryst. F66: 163-166.
    47. Koropatkin, N., Smith, T.J. (2010) SusG: a unique cell membrane associated a-amylase from a prominent human gut symbiont targets complex starch molecules. Structure 18:200-215.
    48. Katpally, U. and Smith, T.J. (2010) The Caliciviruses. Current Topics in Microbiology and Immunology 343:23-41.
  • 2009-2000
    2009-2000
    1. Smith, T.J. (2009) Glutamate dehydrogenase; structure, evolution, regulation, and role in insulin homeostasis. Amino Acids 37: S119.
    2. Martens, E.C., Koropatkin, N.M., Smith, T.J., Gordon, J.I. (2009) Complex glycan catabolism by the human gut Bacteroidetes: the Sus-like paradigm. J. Biol. Chem. 284:24673-24677.
    3. Katpally, U., Fu, T., Freed, D.C., Casimiro, D.R., Smith, T.J. (2009) Antibodies to the buried N-terminus of rhinovirus VP4 exhibit cross-serotypic neutralization. J. Virol. 83:7040-7048.
    4. Koropatkin, N., Martens, E.C., Gordon, J.I., Smith, T.J. (2009) Structure of a SusD homologues, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont. Biochemistry 48: 1532-1542.
    5. Li, M., Smith, C.J., Walker, M.C., Smith, T.J. (2009) Novel inhibitors complexed with glutamate dehydrogenase: allosteric regulation by control of protein dynamics. J. Biol. Chem. 284: 22988-23000.
    6. Smith, T.J., and Stanley, C. (2008) Untangling the glutamate dehydrogenase allosteric nightmare. TiBS 33: 557-564.
    7. Koropatkin, N.M., Martens, E.C., Gordon, J.I., Smith, T.J. (2008) Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 16: 1105-1115.
    8. Katpally, U., Wobus, C.E., Dryden, K., Virgin, H.W. IV, and Smith, T.J. (2008) Structure of antibody-neutralized murine norovirus and unexpected differences from virus like particles. J. Virol. 82: 2079-2088.
    9. Kakani, K., Reade, R., Katpally, U., Smith, T.J., Rochon, D. (2008) Induction of particle polymorphism by Cucumber necrosis virus coat protein mutants in vivo. J. Virol. 82: 1547-1557.
    10. Allen, A., Snyder, A.K., Preuss, M., Nielsen, E.E., Shah, D.M., Smith, T.J. (2008) Plant defensins and virally encoded fungal toxin KP4 inhibit plant root growth. Planta. 227: 331-339.
    11. Li, M., Allen, A., Smith, T.J. (2007) High throughput screening reveals several new classes of glutamate dehydrogenase inhibitors. Biochemistry 46: 15089-15102.
    12. Katpally, U., Kakani, K., Reade, R., Rochon, D., Smith, T.J. (2007). Structures of T=1 and T=3 particles of Cucumber necrosis virus: evidence of internal scaffolding. J. Mol. Biol. 365: 502-512.
    13. 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.
    14. 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.
    15. 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 366: 98-106.
    16. 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.
    17. Katpally, U., Smith, T.J. (2007) Pocket factors are unlikely to play a major role in the life cycle of human rhinovirus. J. Virol. 81: 6307-6315.
    18. 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. Mol. Biol. Edu. 35: 410-415.
    19. 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.
    20. 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.
    21. 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.
    22. 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.
    23. 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. Plant Phys. 135: 2055-2067.
    24. Smith, T.J. (2004) MolViewX: a molecular visualization program for the Macintosh OS X system. J. Appl. Cryst. 37: 654-657.
    25. Allen, A., Kwagh, J., Fang, J., Stanley, C.A., Smith, T.J. (2004) Evolution of glutamate dehydrogenase regulation of insulin homeostasis is an example of molecular exaptation. Biochemistry 43: 14431-14443.
    26. Smith, T.J. (2003) Structural studies on antibody-virus complexes. (Chiu, W., ed.) In Advances in Protein Chemistry, 64: 409-443.
    27. 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. Biochemistry 42: 3446-3456.
    28. Thomas, J., Katpally, U., Chase, E., Harris, K., Siuzdak, G., Smith, T.J. (2003) Human rhinovirus capsid dynamics is controlled by canyon flexibility. Virology 314: 34-44.
    29. 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.
    30. 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) allosteric regulatory mutations. Biochem. J. 363: 81-87.
    31. Smith, T.J., Schmidt, T., Fang, J., Wu, J., Siuzdak, G., Stanley, C.A. (2002) The structure of apo human glutamate dehydrogenase details subunit communication and allostery. J. Mol. Biol. 318: 765-777.
    32. 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.
    33. Smith, T.J. (2002) Antibody recognition of human rhinovirus. (Wimmer, E. and Semler, B., eds.) In Molecular Biology of Picornaviruses. pp. 39-49.
    34. Bowman, V.D. and Chipman, P.R. and Smith, T.J. and Chase, E.S. and Franz, A.W.E. and Perry, K.L. and Baker, T.S., (2002). "Cucumber mosaic virus-fab complex examined by electron cryo-microscopy and three-dimensional image reconstruction", Microscopy and Microanalysis, vol. 8, no. SUPPL. 2, pp. 852-853.
    35. Bowman, V.D., Chase, E.S., Franz, A.W., Chipman, P.R., Zhang, X., 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.
    36. 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.
    37. 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 USA 98: 2274-2277.
    38. 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.
    39. MacMullen C., Fang J., Hsu B.Y., Kelly A., de Lonlay-Debeney P., Saudubray J.M., Ganguly A., Smith T.J., Stanley C.A. (2001) The hyperinsulinism/hyperammonemia contributing investigators. hyperinsulinism/hyperammonemia syndrome in children with regulatory mutations in the inhibitory guanosine triphosphate-binding domain of glutamate dehydrogenase. J. Clin. Endocrin. Metab. 86(4): 1782-1787.
    40. Gage, M.J., Bruenn, J., Fischer, M., Sanders, D., Smith, T.J. (2001) KP4 fungal toxin inhibits growth in Ustilago maydis by blocking calcium uptake.  Mol. Microbiol. 41(4): 775-785.
    41. Smith, T.J., Chase, E., Schmidt, T., Perry, K.L. (2000) The structure of cucumber mosaic virus and comparison to cowpea chlorotic mottle virus. J. Virol. 74: 7578-7586.
  • 1999-1990
    1. 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. Biophys. J. 76: 1270-1279.
    2. Smith, T.J. and Baker, T. (1999) Picornaviruses: epitopes, canyons, and pockets. Adv. Virus Res. 52: 1-23.
    3. Peterson, P.E. and Smith, T.J. (1999) The structure of bovine glutamate dehydrogenase provides insights into the mechanism of allostery. Structure 7: 769-782.
    4. 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. Struct. Biol. 125:166-175.
    5. 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.
    6. Lewis, J.K., Bothner, B., Smith, T.J., Siuzdak, G. (1998) Antiviral agent blocks breathing of the common cold virus. PNAS USA 95: 6774-6778.
    7. Lewis, J.K., Bendahmane, M., Smith, T.J., Beachy, R.N. Siuzdak, G. (1998) Identification of viral mutants by mass spectrometry. PNAS USA 95: 8596-8601.
    8. Smith, T.J., and Mosser, A.G. (1997) Antibody-mediated neutralization of picornaviruses. In Chiu, W., Burnett, R., and Garcea, R. (eds.), Structural Biology of Viruses. Oxford University Press, NY, pp. 134-156.
    9. Rossmann, M.G., Greve, J.M., Kolatkar, P.R., Olson, N.H., Smith, T.J., McKinlay, M.A., Rueckert, R.R. (1997) Rhinovirus attachment and cell entry. In Chiu, W., Burnett, R., and Garcea, R. (eds.), Structural Biology of Viruses. Oxford University Press, NY, pp. 105-133.
    10. Peterson, P., Pierce, J., Smith, T.J. (1997) Crystallization and characterization of bovine glutamate dehydrogenase. J. Struct. Biol. 120: 73-77.
    11. 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, NY (Parker, M., ed.) pp. 291-303.
    12. T.J. Smith, N.H. Olson, Z. Che, E. Chase, A. Mosser, D. Leippe, H. Cheng, R.R. Rueckert, T.S. Baker. (1996) Structural studies on virus-antibody interactions. Cold Spring Harbor Symposium Proceedings -Vaccines96. 161-167.
    13. T.J. Smith, E.S. Chase, T.J. Schmidt, N.H. Olson, T.S. Baker. (1996) Neutralizing antibody to human rhinovirus 14 penetrates the receptor-binding canyon. Nature (London) 383:350-354.
    14. Cheng, R.H., Kuhn, R.J., Olson, N.H., Rossmann, M.G., Choi, H., Smith, T.J., Baker, T.S. (1995) Nucleocapsid and glycoprotein organization in an enveloped virus. Cell 80:1-20.
    15. Smith, T.J. (1995) MolView: a program to analyze and display atomic structures on the Macintosh personal computer. J. Mol. Graph. 13:122-125.
    16. Smith, T.J. Mosser, A.G, and Baker, T.S. (1995) Structural studies on the mechanisms of antibody-mediated neutralization of human rhinovirus. Semin. Virol. 6:233-242.
    17. Smith, T.J. (1995) MolView, freeware for analyzing and viewing atomic structures. SciTech Journal 5:24-25.
    18. 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.
    19. 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 alphaviruses as visualized by cryo-electron microscopy. PNAS USA 92:10648-10652.
    20. Smith, T.J. (1995) Introduction: Antibody recognition in viruses. Semin. Virol. 6: 217-218.
    21. Liu, H., Smith, T.J., Lee, W.M., Mosser, A.G., Rueckert, R.R., Olson, N.H., Cheng, R.H., and Baker, T.S. (1994) Structure determination of an FAB fragment that neutralizes human rhinovirus 14 and analysis of the Fab-virus complex. J. Mol. Biol. 240: 127-137.
    22. Chiu, W., and Smith, T.J. (1994) Structural studies of virus-antibody complexes by electron cryomicroscopy and X-ray crystallography. Cur. Opin. Struct. Biol. 4:219-224.
    23. Saraswat, N., Alleman, J.E., and Smith, T.J. (1994) Enzyme immunoassay detection of Nitrosomonas europaea. Appl. and Environ. Microbiol. 60:1969-1973.
    24. 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.
    25. 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., 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.
    26. Smith, T.J., Olson, N.H., Cheng, R.H., Liu, H., Chase, E.S., 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.
    27. Smith, T.J., Olson, N.H., Cheng, R.H., Chase, E.S., Baker, T.S. (1993) Structure of a human rhinovirus-bivalently bound antibody complex: Implications for virus neutralization and antibody flexibility. PNAS USA 90:7015-7018.
    28. 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.
    29. Rossmann, M.G., Smith, T.J., and Rueckert, R.R. (1993) The structure of human rhinovirus 14. Structure Introductory Issue: xxiv-xxv.
    30. Olson, N.H., Smith, T.J., Kolatkar, P.R., Oliveira, M.A., Rueckert, R.R., Greve, J.M., Rossmann, M.G., 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.
    31. Smith, T.J. (1992) Purification of mouse antibodies and Fab fragments. In Asai, D. (ed.), Methods in Cell Biology, Chapter 4, pp 75-93.
    32. Smith, T.J., and Chase, E.S. (1992) Purification and crystallization of intact human rhinovirus complexed with a neutralizing Fab. Virology 191:600-606.
    33. Tsao, J., Chapman, M.S., Agbandje, M., Keller, W., Smith, K., Wu, H., Luo, M., Smith, T.J., Rossmann, M.G., Compans, R.W., Parrish, C.R. (1991) The three-dimensional structure of canine parvovirus and its functional implications. Science 251: 1456-1464.
    34. Prongay, A.J., Smith, T.J., Rossmann, M.G., Ehrlich, L.S., Carter, C.A., McClure, J. (1990) Preparation and crystallization of a human immunodeficiency virus p24-Fab complex. PNAS USA 87:9980-9984.
    35. Willingmann, P., Krishnaswamy, S., McKenna, R., Smith, T.J., Olson, N.H., Rossmann, M.G., Stow, P.L., Incardona, N.L. (1990) Preliminary investigation of the phage fX174 crystal structure. J. Mol. Biol. 212:345-350.
    36. 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., Shepard, D. (1990) Crystallographic and pharmacological studies of antiviral agents against human rhinovirus. In Bugg, C.E., and Ealick, S.E., (eds.), Crystallographic and modeling methods in molecular design, Springer-Verlag, New York, pp. 9-28.
    37. 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.
    38. Kim, S., Boege, U., Krishnaswamy, S., Minor, I., Smith, T.J., Luo, M., Scraba, D.G., 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.
  • 1989-1980
    1. 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.
    2. Diana, G.D., Pevear, D.C., Otto, M.J., McKinlay, M.A., Rossmann, M.G., Smith, T.J., Badger, J. (1989) Inhibitors of viral uncoating Pharmacol. Therapeut. 42:289-305.
    3. Boege, U., Cygler, M., Wengler, G., Dumas, P., Tsao, J., Luo, M., Smith, T.J., Rossmann, M.G. (1989) Sinbis virus nucleocapsid core protein crystals. J. Mol. Biol. 208:79-82.
    4. Badger, J., Minor, I., Oliveira, M.A., Smith, T.J., Rossmann, M.G. (1989) Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses. Proteins 6:1-19.
    5. Heinz, B.A., Rueckert, R.R., Shepard, D.A., Dutko, F.J., McKinlay, M.A., Fancher, M., Rossmann, M.G., Badger, J., Smith, T.J. (1989) Genetic and molecular analyses of spontaneous mutants of human rhinovirus 14 resistant to an antiviral compound. J. Virol. 63:2476-2485.
    6. Kim, S., Smith, T.J., Chapman, M.S., Rossmann, M.G., Peavear, D.C., Dutko, F.J., Felock, P.J., Diana, G.D., McKinlay, M.A. (1989) The crystal structure of human rhinovirus serotype 1A (HRV1A). J. Mol. Biol. 210:91-111.
    7. Diana, G.D., Otto, M.J., Treasurywala, A.M., McKinlay, M.A., Oglesby, R.C., Maliski, E.G., Rossmann, M.G., Smith, T.J. (1988) Enantiomeric effects of homologues of disoxaryil on the inhibitory activity against human rhinovirus-14. J. Med. Chem. 31:540-544.
    8. Badger, J., Minor, I., Kremer, M.J., Oliveira, M.A., Smith, T.J., Griffith, J.P., Guerin, D.M., Krishnaswamy, S., Luo, M., Rossmann, M.G., McKinlay, M.A., Diana, G.D., Kutko, F.J., Fancher, M., Rueckert, R.R., Heinz, B.A. (1988) Structural analysis of a series of antiviral agents complexed with human rhinovirus 14. PNAS USA 85:3304-3308.
    9. 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.
    10. 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., 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.
    11. 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., 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.
    12. 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., Otto, M. (1987) Common cold viruses. Trends Biochem. Sci. 12:313-318.
    13. Smith, T.J., Kremer, M.J., Luo, M., Vriend, G., Arnold, E., Kamer, G., Rossmann, M.G., McKinlay, M.A., Diana, G.D., Otto, M.J. (1986) The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating. Science 233:1286-1293.
    14. Smith, T.J., and Bell, J.E. (1986) An exponential gradient marker for use with minigel polyacrylamide electrophoresis systems. Anal. Biochem. 152:74-77.
    15. Smith, T.J., and Bell, J.E. (1985) Investigation of the effects of crosslinking glutamate dehydrogenase with dimethylpimelimidate. Arch. Biochem. Biophys. 239:63-73.
    16. Holt, J.T., Arvan, D.A., Mayer, T., Smith, T.J., 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.
    17. 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.