Gerald Stubbs , D.Phil.
Professor of Biological Sciences, Emeritus

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Phone Number: 615-322-2018

Email Address:

Stubbs, Gerald's picture

Office Address   Mailing Address

5260-A MRB III

Box 1634-B 37235

Research Keywords
x-ray fiber diffraction, cryo-electron microscopy, protein structure, structural biology, prion structure, amyloid structure, virus structure

Research Description
Although I am not currently taking new students, my laboratory maintains a vigorous program of research into the structures of filamentous biological assemblies such as amyloids and viruses.

Knowing the detailed three-dimensional structure of biological macromolecules and assemblies is essential to an understanding of their functions, including control of their activity. We are studying the molecular structure of prions and other amyloids, as well as filamentous plant viruses. We use x-ray fiber diffraction, cryo-electron microscopy, and other biophysical methods of structure determination.

Prions are responsible for such diseases as Creutzfeldt-Jacob disease and "mad cow disease"; they are infectious amyloids, misfolded proteins with no nucleic acid component. It is now widely recognized that the amyloid peptides associated with many diseases, especially neurodegenerative diseases such as Alzheimer's and Parkinson's diseases and chronic traumatic encephalopathy, should be understood as prions. We obtained the first diffraction data from mammalian prions, and we are developing structural models for these and several other amyloids. In studies of the mammalian prion protein PrP, the Alzheimer's-associated peptide A-beta, the fungal prion HET-s, and others, we have shown that prion self-propagation requires an obligatory level of structural complexity beyond simple generic amyloid structures.

We determined the structure of tobacco mosaic virus at 2.9 A resolution in the 1980s. This enabled us to understand the mechanism of control of assembly of this virus. Through collaborations with molecular geneticists, we designed and studied mutations of the virus that affect viral assembly, disassembly, transport and host defense mechanisms. We studied several viruses related to TMV, as well as a number of more flexible viruses, particularly those in the potexvirus, potyvirus, and closterovirus groups. We showed that flexible filamentous plant viruses all share common structural features; these data have important implications both for basic understanding of viral structure and evolution, and for agriculture and biotechnology.

We have developed new methods in fiber diffraction, particularly for use in disordered filamentous assemblies.

Kurouski, D, Lu, X, Popova, L, Wan, W, Shanmugasundaram, M, Stubbs, G, Dukor, RK, Lednev, IK, Nafie, LA. Is supramolecular filament chirality the underlying cause of major morphology differences in amyloid fibrils. J Am Chem Soc, 136(6), 2302-12, 2014.

Wan, W, Stubbs, G. Fungal prion HET-s as a model for structural complexity and self-propagation in prions. Proc Natl Acad Sci U S A, 111(14), 5201-6, 2014.

Wan, W, Stubbs, G. Heterogeneous seeding of HET-s(218-289) and the mutability of prion structures. Prion, 8(2), , 2014.

Wan, W, Stubbs, G. Fiber Diffraction of the Prion-Forming Domain HET-s(218-289) Shows Dehydration-Induced Deformation of a Complex Amyloid Structure. Biochemistry, 53(14), 2366-70, 2014.

Kendall, A, Bian, W, Maris, A, Azzo, C, Groom, J, Williams, D, Shi, J, Stewart, PL, Wall, JS, Stubbs, G. A common structure for the potexviruses. Virology, 436(1), 173-8, 2013.

Kendall, A, Williams, D, Bian, W, Stewart, PL, Stubbs, G. Barley stripe mosaic virus: structure and relationship to the tobamoviruses. Virology, 443(2), 265-70, 2013.

Wan, W, Bian, W, McDonald, M, Kijac, A, Wemmer, DE, Stubbs, G. Heterogeneous seeding of a prion structure by a generic amyloid form of the fungal prion-forming domain HET-s(218-289). J Biol Chem, 288(41), 29604-12, 2013.

Groscurth, S, M??ller, B, Schwan, S, Menzel, M, Diekstall, F, Senft, M, Kendall, A, Kommor, BA, Neumann, U, Kalischuk, M, Kawchuk, LM, Krzyzanek, V, Heilmann, A, Stubbs, G, Twyman, RM, Pr??fer, D, Noll, GA. Artificial forisomes are ideal models of forisome assembly and activity that allow the development of technical devices. Biomacromolecules, 13(10), 3076-86, 2012.

McDonald, M, Box, H, Bian, W, Kendall, A, Tycko, R, Stubbs, G. Fiber diffraction data indicate a hollow core for the Alzheimer''s a?? 3-fold symmetric fibril. J Mol Biol, 423(3), 454-61, 2012.

Stubbs, G, Kendall, A. Helical viruses. Adv Exp Med Biol, 726, 631-58, 2012.

Wan, W, Wille, H, St??hr, J, Baxa, U, Prusiner, SB, Stubbs, G. Degradation of fungal prion HET-s(218-289) induces formation of a generic amyloid fold. Biophys J, 102(10), 2339-44, 2012.

Tewary, SK, Oda, T, Kendall, A, Bian, W, Stubbs, G, Wong, SM, Swaminathan, K. Structure of hibiscus latent singapore virus by fiber diffraction: a nonconserved his122 contributes to coat protein stability. J Mol Biol, 406(3), 516-26, 2011.

McDonald, M, Kendall, A, Bian, W, McCullough, I, Lio, E, Havens, WM, Ghabrial, SA, Stubbs, G. Architecture of the potyviruses. Virology, 405(2), 309-13, 2010.

Wille, H, Bian, W, McDonald, M, Kendall, A, Colby, DW, Bloch, L, Ollesch, J, Borovinskiy, AL, Cohen, FE, Prusiner, SB, Stubbs, G. Natural and synthetic prion structure from X-ray fiber diffraction. Proc Natl Acad Sci U S A, 106(40), 16990-5, 2009.

Wille, H, Shanmugam, M, Murugesu, M, Ollesch, J, Stubbs, G, Long, JR, Safar, JG, Prusiner, SB. Surface charge of polyoxometalates modulates polymerization of the scrapie prion protein. Proc Natl Acad Sci U S A, 106(10), 3740-5, 2009.

Bromley, KM, Patil, AJ, Perriman, AW, Stubbs, G, Mann, S . Preparation of high quality nanowires by tobacco mosaic virus templating of gold nanoparticles. J Mater Chem, 18, 4796-4801, 2008.

Kendall, A, McDonald, M, Bian, W, Bowles, T, Baumgarten, SC, Shi, J, Stewart, PL, Bullitt, E, Gore, D, Irving, TC, Havens, WM, Ghabrial, SA, Wall, JS, Stubbs, G. Structure of flexible filamentous plant viruses. J Virol, 82(19), 9546-54, 2008.

Kendall, A, Bian, W, Junn, J, McCullough, I, Gore, D, Stubbs, G. Radial density distribution and symmetry of a Potexvirus, narcissus mosaic virus. Virology, 357(2), 158-64, 2007.

Kendall, A, McDonald, M, Stubbs, G. Precise determination of the helical repeat of tobacco mosaic virus. Virology, 369(1), 226-7, 2007.

Bian, W., Wang, H., McCullough, I., and Stubbs, G. WCEN: a computer program for initial processing of fiber diffraction patterns. J. Appl. Cryst. , 39, 752-756, 2006.

Kendall, A., and Stubbs, G. Oriented sols for fiber diffraction from limited quantities or hazardous materials. J. Appl. Cryst., 39, 39-41, 2006.

Parker, L, Kendall, A, Berger, PH, Shiel, PJ, Stubbs, G. Wheat streak mosaic virus--structural parameters for a Potyvirus. Virology, 340(1), 64-9, 2005.

Shanmugam, G, Polavarapu, PL, Kendall, A, Stubbs, G. Structures of plant viruses from vibrational circular dichroism. J Gen Virol, 86(Pt 8), 2371-7, 2005.

Stubbs, G., Parker, L., Junn, J., and Kendall, A. Flexible filamentous virus structures from fiber diffraction. Fibre Diffraction Review, 13, 38-42, 2005.

Dujardin, E., Peet, C., Stubbs, G., Culver, J.N., and Mann, S. Organization of metallic nanoparticles using tobacco mosaic virus templates. Nano Letters, 3, 413-417, 2003.

Parker, L, Kendall, A, Stubbs, G. Surface features of potato virus X from fiber diffraction. Virology, 300(2), 291-5, 2002.

Chandrasekaran, R., and Stubbs, G. Fiber diffraction. International Tables for Crystallography, Vol. F: Macromolecular Crystallography (Rossman, M.G., and Arnold, E., eds. ) Int. Union of Crystallography, F, , 2001.

Fowler, C.E., Shenton, W., Stubbs, G. and Mann, S. Tobacco mosaic virus liquid crystals as templates for the interior design of silica mesophases and nanoparticles. Adv. Materials, 13, 1266-1269, 2001.

Stubbs, G. Fibre diffraction studies of filamentous viruses. Reports on Progress in Physics, 64, 1389-1425, 2001.

Bunick, C, North, AC, Stubbs, G. Evaporative microdialysis: an effective improvement in an established method of protein crystallization. Acta Crystallogr D Biol Crystallogr, 56(Pt 11), 1430-1, 2000.

Stubbs, G., Ferrell, G., Reams, M. and Fletcher, N. Fibre diffraction and diversity in filamentous plant virus structure. Fibre Diffraction Rev., 9, 24-28, 2000.

Shenton, W., Douglas, T., Young, M., Stubbs, G. and Mann, S. (1999). Inorganic-organic nanotube composites from template mineralization of tobacco mosaic virus. Adv. Materials 11, 253-256.

Stubbs, G. Developments in fiber diffraction. Curr Opin Struct Biol, 9(5), 615-9, 1999.

Stubbs, G. Tobacco mosaic virus particle structure and the initiation of disassembly. Philos Trans R Soc Lond B Biol Sci, 354(1383), 551-7, 1999.

Lu, B, Stubbs, G, Culver, JN. Coat protein interactions involved in tobacco mosaic tobamovirus cross-protection. Virology, 248(2), 188-98, 1998.

Lu, B, Taraporewala, F, Stubbs, G, Culver, JN. Intersubunit interactions allowing a carboxylate mutant coat protein to inhibit tobamovirus disassembly. Virology, 244(1), 13-9, 1998.

Wang, H, Planchart, A, Stubbs, G. Caspar carboxylates: the structural basis of tobamovirus disassembly. Biophys J, 74(1), 633-8, 1998.

Chen, J, Torrance, L, Cowan, GH, Macfarlane, SA, Stubbs, G, Wilson, TM. Monoclonal antibodies detect a single amino Acid difference between the coat proteins of soilborne wheat mosaic virus isolates: implications for virus structure. Phytopathology, 87(3), 295-301, 1997.

Stubbs, G. and Wang, H. Carboxylate groups in the disassembly of tobamoviruses. Proceeding of the 22nd International Symposium, Division of Biophysics, The Tanaguchi Foundation. Structure And Function of Macromolecular Assembly. (Namba, K., ed.), Matsushita, Japan, , 165-174, 1997.

Wang, H, Culver, JN, Stubbs, G. Structure of ribgrass mosaic virus at 2.9 A resolution: evolution and taxonomy of tobamoviruses. J Mol Biol, 269(5), 769-79, 1997.

Lu, B, Stubbs, G, Culver, JN. Carboxylate interactions involved in the disassembly of tobacco mosaic tobamovirus. Virology, 225(1), 11-20, 1996.

Culver, JN, Dawson, WO, Plonk, K, Stubbs, G. Site-directed mutagenesis confirms the involvement of carboxylate groups in the disassembly of tobacco mosaic virus. Virology, 206(1), 724-30, 1995.

Dawson, W.O., Lindbeck, A.G.C., Lewandowski, D.J., Culver, J.N., Hilf, M.E., and Stubbs, G. Precise interactions between tobamoviruses and plants. Biotechnology and Plant Protection. Viral Pathogenesis and Disease Resistance. (Bills, D.D. And Kung, S., eds.) World Scientific, New Jersey, , 277-295, 1995.

Culver, JN, Stubbs, G, Dawson, WO. Structure-function relationship between tobacco mosaic virus coat protein and hypersensitivity in Nicotiana sylvestris. J Mol Biol, 242(2), 130-8, 1994.

Wang, H, Stubbs, G. Structure determination of cucumber green mottle mosaic virus by X-ray fiber diffraction. Significance for the evolution of tobamoviruses. J Mol Biol, 239(3), 371-84, 1994.

Wang, H, Planchart, A, Allen, D, Pattanayek, R, Stubbs, G. Preliminary X-ray diffraction studies of ribgrass mosaic virus. J Mol Biol, 234(3), 902-4, 1993.

Wang, H, Stubbs, G. Molecular dynamics in refinement against fiber diffraction data. Acta Crystallogr A, 49(3), 504-13, 1993.

Zhang, H, Todderud, E, Stubbs, G. Crystallization and preliminary X-ray analysis of papaya mosaic virus coat protein. J Mol Biol, 234(3), 885-7, 1993.

Pattanayek, R, Elrod, M, Stubbs, G. Characterization of a putative calcium-binding site in tobacco mosaic virus. Proteins, 12(2), 128-32, 1992.

Pattanayek, R, Stubbs, G. Structure of the U2 strain of tobacco mosaic virus refined at 3.5 A resolution using X-ray fiber diffraction. J Mol Biol, 228(2), 516-28, 1992.

Sosnick, T., Charles, S., Stubbs, G., Yau, P., Bradbury, E.M., Timmins, P. and Trewhella, J. Orienting rigid and flexible biological assemblies in ferrofluids for small-angle neutron scattering studies. Biophys. J., 60, 1178-1189, 1991.

Stubbs, G. Molecular structures of filamentous viruses derived from fiber diffraction data. Comments Mol. Cell. Biophys., 7, 353-374, 1991.

Lobert, S, Stubbs, G. Fiber diffraction analysis of cucumber green mottle mosaic virus using limited numbers of heavy-atom derivatives. Acta Crystallogr A, 46 ( Pt 12), 993-7, 1990.

Lyne, JE, Carter, DC, He, XM, Stubbs, G, Hash, JH. Preliminary crystallographic examination of a novel fungal lysozyme from Chalaropsis. J Biol Chem, 265(12), 6928-30, 1990.

Stubbs, G. Molecular structures of viruses from the tobacco mosaic virus group. Seminars in Virology, 1, 405 -412, 1990.

Hayter, JB, Pynn, R, Charles, S, Skjeltorp, AT, Trewhella, J, Stubbs, G, Timmins, P. Ordered macromolecular structures in ferrofluid mixtures. Phys Rev Lett, 62(14), 1667-1670, 1989.

Jeng, TW, Crowther, RA, Stubbs, G, Chiu, W. Visualization of alpha-helices in tobacco mosaic virus by cryo-electron microscopy. J Mol Biol, 205(1), 251-7, 1989.

Namba, K, Pattanayek, R, Stubbs, G. Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction. J Mol Biol, 208(2), 307-25, 1989.

Stubbs, G. The probability distributions of X-ray intensities in fiber diffraction: largest likely values for fiber diffraction R factors. Acta Crystallogr A, 45 ( Pt 3), 254-8, 1989.

Stubbs, G. Protein-nucleic acid interactions in tobacco mosaic virus. Topics in Molecular and Structural Biology, Vol. X: Protein-Nucleic Acid Interaction. (Saenger, W. and Heinemann, U., eds. ), Macmillan, London, , 87-109, 1989.

Stubbs, G. Virus structure. Prediction of Protein Structure and Principles of Protein Conformation (Fasman, G., ed.), Plenum, New York, , 117-148, 1989.

Namba, K, Caspar, DL, Stubbs, G. Enhancement and simplification of macromolecular images. Biophys J, 53(4), 469-75, 1988.

Beese, L, Stubbs, G, Cohen, C. Microtubule structure at 18 A resolution. J Mol Biol, 194(2), 257-64, 1987.

Beese, L, Stubbs, G, Thomas, J, Cohen, C. Structure of microtubules with reduced hydration. Comparison of results from X-ray diffraction and electron microscopy. J Mol Biol, 196(3), 575-80, 1987.

Lobert, S, Heil, PD, Namba, K, Stubbs, G. Preliminary X-ray fiber diffraction studies of cucumber green mottle mosaic virus, watermelon strain. J Mol Biol, 196(4), 935-8, 1987.

Namba, K. and Stubbs, G. Isomorphous replacement in fiber diffraction using limited numbers of heavy-atom derivatives . Acta Cryst , A43, 64-69, 1987.

Namba, K. and Stubbs, G. Difference Fourier syntheses in fiber diffractionl. Acta Cryst, A43, 533-539, 1987.

Namba, K, Stubbs, G. Structure of tobacco mosaic virus at 3.6 A resolution: implications for assembly. Science, 231(4744), 1401-6, 1986.

Stubbs, G, Namba, K, Makowski, L. Application of restrained least-squares refinement to fiber diffraction from macromolecular assemblies. Biophys J, 49(1), 58-60, 1986.

Namba, K, Caspar, DL, Stubbs, GJ. Computer graphics representation of levels of organization in tobacco mosaic virus structure. Science, 227(4688), 773-6, 1985.

Cross, TA, Opella, SJ, Stubbs, G, Caspar, DL. 31P nuclear magnetic resonance of the RNA in tobacco mosaic virus. J Mol Biol, 170(4), 1037-43, 1983.

Fish, SR, Hartman, KA, Stubbs, GJ, Thomas, GJ. Structural studies of tobacco mosaic virus and its components by laser Raman spectroscopy. Biochemistry, 20(26), 7449-57, 1981.

Mandelkow, E, Stubbs, G, Warren, S. Structures of the helical aggregates of tobacco mosaic virus protein. J Mol Biol, 152(2), 375-86, 1981.

Stubbs, G, Stauffacher, C. Structure of the RNA in tobacco mosaic virus. J Mol Biol, 152(2), 387-96, 1981.

Stubbs, G, Warren, S, Mandelkow, E. Structural comparisons of the aggregates of tobacco mosaic virus protein. J Supramol Struct, 12(2), 177-83, 1979.

Stubbs, G, Warren, S, Holmes, K. Structure of RNA and RNA binding site in tobacco mosaic virus from 4-A map calculated from X-ray fibre diagrams. Nature, 267(5608), 216-21, 1977.

Holmes, KC, Stubbs, GJ, Mandelkow, E, Gallwitz, U. Structure of tobacco mosaic virus at 6.7 ?Y resolution. Nature, 254(5497), 192-6, 1975.

North, AC, Stubbs, GJ. Crystallography of hemerythrin. J Mol Biol, 88(1), 125-31, 1974.

Bradbury, JH, Stubbs, GJ. Relations between line widths of proton magnetic resonance spectra and molecular weight of poly-gamma-benzyl-l-glutamate. Nature, 218(5146), 1049-50, 1968.

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