Summary
Expansion of a homomeric stretch of glutamine residues beyond a critical threshold can produce neurodegenerative disease. This observation led to the idea that abnormal polyglutamine stretches can alter protein structure in ways that contribute to disease. Because they are prone to aggregation, proteins with abnormal polyglutamine expansions have been difficult to study with conventional biophysical approaches. Some of these proteins are also very large, complicating efforts to generate them in vitro or to purify them for biochemical studies. An alternative approach has been to use antibodies with known binding specificity as probes of protein folding and protein structure. Antibodies can often bind to specific protein epitopes in situ and are, therefore, one of the few tools that can be used to probe protein structure in a physiological context and in the presence of that protein’s normal binding partners. However, antibodies are complex reagents, and an understanding of their binding properties, methods of use, and limitations is needed to interpret results properly. We have developed monoclonal antibodies that specifically recognize expanded polyglutamine stretches in mutant huntingtin. Here, we describe several methods for using one of these antibodies to explore the structure of abnormal polyglutamine expansions and the proteins that contain them.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Gusella, J. F. and MacDonald, M. E. (1996) Trinucleotide instability: a repeating theme in human inherited disorders. Annu. Rev. Med. 47, 201–209.
Zoghbi, H. Y. and Orr, H. T. (2000) Glutamine repeats and neurodegeneration. Annu. Rev. Neurosci. 23, 217–247.
Gusella, J. F. and MacDonald, M. E. (1995) Huntington’s disease: CAG genetics expands neurobiology. Curr. Opin. Neurobiol. 5, 656–662.
Paulson, H. L. and Fishbeck, K. H. (1996) Trinucleotide repeats in neurogenetics disorders. Annu. Rev. Neurosci. 19, 79–107.
Andrew, S. E., Goldberg, Y. P., and Hayden, M. R. (1997) Rethinking genotype and phenotype correlations in polyglutamine expansion disorders. Hum. Mol. Genet. 6, 2005–2010.
Zeron, M. M., Hansson, O., Chen, N., et al. (2002) Increased sensitivity to N-methyl-D-aspartate receptor-mediated excitotoxicity in a mouse model of Huntington’s disease. Neuron 33, 849–860.
Ambrose, C., Duyao, M. P., Barnes, G., et al. (1994) Structure and expression of the Huntington’s disease gene: evidence against simple inactivation due to an expanded CAG repeat. Somat. Cell Mol. Genet. 20, 27–38.
Dragatsis, I., Levine, M. S., and Zeitlin, S. (2000) Inactivation of Hdh in the brain and testis results in progressive neurodegeneration and sterility in mice. Nature Genet. 26, 300–306.
Chamberlain, N. L., Driver, E. D., and Miesfeld, R. L. (1994) The length and location of CAG trinucleotide repeats in the androgen receptor N-terminal domain affect transactivation function. Nucleic Acids Res. 22, 3181–3186.
Mhatre, A. N., Trifiro, M. A., Kaufman, M., et al. (1993) Reduced transcriptional regulatory competence of the androgen receptor in X-linked spinal and bulbar muscular atrophy. Nature 5, 184–187.
Rigamonti, D., Bauer, H. J., De-Fraja, C., et al. (2000) Wild-type huntingtin protects from apoptosis upstream of caspase-3. J. Neurosci. 20, 3705–3713.
Leavitt, B. R., Guttman, J. A., Hodgson, J. G., et al. (2001) Wild-type huntingtin reduces the cellular toxicity of mutant huntingtin in vivo. Am. J. Hum. Genet. 68, 313–324.
Zuccato, C., Ciammola, A., Rigamonti, D., et al. (2001) Loss of huntingtin-mediated BDNF gene transcription in Huntington’s disease. Science 293, 493–498.
Scherzinger, E., Lurz, R., Turmaine, M., et al. (1997) Huntingtin-encoded polyglutamine expansions form amyloid-like protein aggregates in vitro and in vivo. Cell 90, 549–558.
Georalis, Y., Starikov, E. B., Hollenbach, B., et al. (1998) Huntingtin aggregation monitored by dynamic light scattering. Proc. Natl. Acad. Sci. USA 95, 6118–6121.
Martindale, D., Hackam, A., Wieczorek, A., et al. (1998) Length of huntingtin and its polyglutamine tract influences localization and frequency of intracellular aggregates. Nature Genet. 18, 150–154.
Rajan, R. S., Illing, M. E., Bence, N. F., et al. (2001) Specificity in intracellular protein aggregation and inclusion body formation. Proc. Natl. Acad. Sci. USA 98, 13,060–13,065.
Nucifora, F. C., Jr., Sasaki, M., Peters, M. F., et al. (2001) Interference by huntingtin and atrophin-1 with CBP-mediated transcription leading to cellular toxicity. Science 291, 2423–2428.
Preisinger, E., Jordan, B. M., Kazantsev, A., et al. (1999) Evidence for a recruitment and sequestration mechanism in Huntington’s disease. Phil. Trans. R. Soc. (Lond.) B: Biol. Sci. 354, 1029–1034.
Kazantsev, A., Preisinger, E., Dranovsky, A., et al. (1999) Insoluble detergent-resistant aggregates form between pathological and nonpathological lengths of polyglutamine in mammalian cells. Proc. Natl. Acad. Sci. USA 96, 11,404–11,409.
Stott, K., Blackburn, J. M., Butler, P. J. G., et al. (1995) Incorporation of glutamine repeats makes protein oligomerize: implications for neurodegenerative disease. Proc. Natl. Acad. Sci. USA 92, 6509–6513.
Perutz, M. F. (1995) Glutamine repeats as polar zippers: their role in inherited neurogenerative disease. Mol. Med. 1, 718–721.
DiFiglia, M., Sapp, E., Chase, K. O., et al. (1997) Aggregation of huntingtin in neuronal intranuclear inclusions and dystrophic neurites in brain. Science 277, 1990–1993.
Davies, S. W., Turmaine, M., Cozens, B. A., et al. (1997) Formation of neuronal intranuclear inclusions underlies the neurological dysfunction in mice transgenic for the HD mutation. Cell 90, 537–548.
Ross, C. A. (1997) Intranuclear neuronal inclusions: a common pathogenic mechanism for glutamine-repeat neurodegenerative diseases. Neuron 19, 1147–1150.
Becher, M. W., Kotzuk, J. A., Sharp, A. H., et al. (1998) Intranuclear neuronal inclusions in Huntington’s disease and dentatorubral and pallidoluysian atrophy—correlation between the density of inclusions and IT-15 CAG triplet repeat length. Neurobiol. Dis. 4, 387–397.
Davies, S. W., Beardsall, K., Turmaine, M., et al. (1998) Are neuronal intranuclear inclusions the common neuropathology of triplet-repeat disorders with polyglutamine-repeat expansions? Lancet 351, 131–133.
Davies, S. W., Turmaine, M., Cozens, B. A., et al. (1999) From neuronal inclusions to neurodegeneration: neuropathological investigation of a transgenic mouse model of Huntington’s disease. Phil. Trans. R. Soc. (Lond.) B: Biol. Sci. 354, 971–979.
Perutz, M. F. and Windle, A. H. (2001) Cause of neural death in neurodegenerative disease attributable to expansion of glutamine repeats. Nature 412, 143–144.
Li, H., Li, S. H., Yu, Z. X., et al. (2001) Huntingtin aggregate-associated axonal degeneration is an early pathological event in Huntington’s disease mice. J. Neurosci. 21, 8473–8481.
Chen, S., Berthelier, V., Yang, W., et al. (2001) Polyglutamine aggregation behavior in vitro supports a recruitment mechanism of cytotoxicity. J. Mol. Biol. 311, 173–182.
Stenoinen, D. L., Cummings, C. J., Adams, H. P., et al. (1999) Polyglutamine-expanded androgen receptors form aggregates that sequester heat shock proteins, proteasome components and SRC-1, and are suppressed by the HDJ-2 chaperone. Hum. Mol. Genet. 8, 731–741.
Suh, S., Senut, M., Whitelegge, J., et al. (2001) Identities of sequestered proteins in aggregates from cells with induced polyglutamine expression. J. Cell Biol. 153, 283–294.
La Spada, A. R., Fu, Y.-H., Sopher, B. L., et al. (2001) Polyglutamine-expanded ataxin-7 antagonizes CRX function and induces cone-rod dystrophy in amouse model of SCA7. Neuron 31, 913–927.
Kouroku, Y., Fujita, E., Jimbo, A., et al. (2002) Polyglutamine aggregates stimulate ER stress signals and caspase-12 activation. Hum. Mol. Genet. 11, 1505–1515.
Bence, N. F., Sampat, R. M., and Kopito, R. R. (2001) Impairment of the ubiquitin-proteasome system by protein aggregation. Science 292, 1552–1555.
Hodgson, J. G., Agopyan, N., Gutekunst, C. A., et al. (1999) A YAC mouse model for Huntington’s disease with full-length mutant huntingtin, cytoplasmic toxicity, and selective striatal neurodegeneration. Neuron 23, 181–192.
Heintz, N. and Zoghbi, H. Y. (2000) Insights from mouse models into the molecular basis of neurodegeneration. Annu. Rev. Physiol. 62, 779–802.
Huynh, D. P., Figueroa, K., Hoang, N., et al. (2000) Nuclear localization or inclusion body formation of ataxin-2 are not necessary for SCA2 pathogenesis in mouse or human. Nature Genet. 26, 44–50.
Kuemmerle, S., Gutekunst, C. A., Klein, A. M., et al. (1999) Huntingtin aggregates may not predict neuronal death in Huntington’s disease. Ann. Neurol. 46, 842–849.
Saudou, F., Finkbeiner, S., Devys, D., et al. (1998) Huntingtin acts in the nucleus to induce apoptosis, but death does not correlate with the formation of intranuclear inclusions. Cell 95, 55–66.
Kim, M., Lee, H.-S., LaForet, G., et al. (1999) Mutant huntingtin expression in clonal stratial cells: dissociation of inclusion formation and neuronal survival by caspase inhibition. J. Neurosci. 19, 964–973.
Cummings, C. J., Reinstein, E., Sun, Y., et al. (1999) Mutation of the E6-AP ubiquitin ligase reduces nuclear inclusion frequency while accelerating polyglutamine-induced pathology in SCA1 mice. Neuron 24, 879–892.
Yu, Z.-X., Li, S.-H., Nguyen, H.-P., et al. (2002) Huntingtin inclusions do not deplete polyglutamine-containing transcription factors in HD mice. Hum. Mol. Genet. 11, 905–914.
Sisodia, S. S. (1998) Nuclear inclusions in glutamine repeat disorders: are they pernicious, coincidental or beneficial? Cell 95, 1–4.
Rich, T., Assier, E., Skepper, J., et al. (1999) Disassembly of nuclear inclusions in the dividing cell—a novel insight into neurodegeneration. Hum. Mol. Genet. 8, 2451–2459.
Floyd, J. A. and Hamilton, B. A. (1999) Intranuclear inclusions and the ubiquitin-proteasome pathway: digestion of a red herring? Neuron 24, 765–766.
Scherzinger, E., Sittler, A., Schweiger, K., et al. (1999) Self-assembly of polyglutamine-containing huntingtin fragments into amyloid-like fibrils: implications for Huntington’s disease pathology. Proc. Natl. Acad. Sci. USA 96, 4604–4609.
Walsh, D. M., Klyubin, I., Fadeeva, J. V., et al. (2002) Naturally secreted oligomers of amyloid b protein potently inhibit hippocampal long-term potentiation in vivo. Nature 416, 535–539.
Lambert, M. P., Barlow, A. K., Chromy, B. A., et al. (1998) Diffusible, nonfibrillar ligands derived from Abeta 1–42 are potent central nervous system toxins. Proc. Natl. Acad. Sci. USA 95, 6448–6453.
Conway, K. A., Lee, S.-J., Rochet, J.-C., et al. (2000) Acceleration of oligomerization, not fibrillization, is a shared property of both a-synuclein mutations linked to early-onset Parkinson’s disease: implications for pathogenesis and therapy. Proc. Natl. Acad. Sci. USA 97, 571–576.
DePace, A. H., Santoso, A., Hillner, P., et al. (1998) A critical role for amino-terminal glutamine/asparagine repeats in the formation and propagation of yeast prion. Cell 93, 1241–1252.
Osherovich, L. Z. and Weissman, J. S. (2001) Multiple Gln/Asn-rich prion domains confer susceptibility to induction of the yeast [PSI +] prion. Cell 106, 183–194.
Lindquist, S., Krobitsch, S., Li, L., et al. (2001) Investigating protein conformation-based inheritance and disease in yeast. Phil. Trans. R. Soc. (Lond.) B: Biol. Sci. 356, 169–176.
Scheibel, T. and Lindquist, S. L. (2001) The role of conformational flexibility in prion propagation and maintenance for Sup35p. Nature Struct. Biol. 8, 958–962.
Serio, T. R., Cashikar, A. G., Kowal, A. S., et al. (2000) Nucleated conformational conversion and the replication of conformational information by a prion determinant. Science 289, 1317–1321.
Altschuler, E. L., Hud, N. V., Mazrimas, J. A., et al. (1997) Random coil conformation for extended polyglutamine stretches in aqueous soluble monomeric peptides. J. Pept. Res. 50, 73–75.
Minor, D. L., Jr. and Kim, P. S. (1994) Context is a major determinant of b-sheet propensity. Nature 371, 264–267.
Minor, D. L., Jr. and Kim, P. S. (1996) Context-dependent secondary structure formation of a designed protein sequence. Nature 380, 730–734.
Lathrop, R. H., Casale, M., Tobias, D. J., et al. (1998) Modeling protein homopolymeric repeats: possible polyglutamine structural motifs for Huntington’s Disease. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6, 105–114.
Peretz, D., Williamson, R. A., Legname, G., et al. (2002) A change in the conformation of prions accompanies the emergence of a new prion strain. Neuron 34, 921–932.
Peretz, D., Williamson, R. A., Kaneko, K., et al. (2001) Antibodies inhibit prion propagation and clear cell cultures of prion infectivity. Nature 412, 739–743.
Li, L. and Lindquist, S. (2000) Creating a protein-based element of inheritance. Science 287, 661–664.
Laver, W. G., Air, G. M., Webster, R. G., et al. (1990) Epitopes on protein antigens: misconceptions and realities. Cell 61, 553–556.
Sachs, D. H., Schechter, A. N., Eastlake, A., et al. (1972) An immunologic approach to the conformational equilibria of polypeptides. Proc. Natl. Acad. Sci. USA 69, 3790–3794.
Sela, M. (1969) Antigenicity: some molecular aspects. Science 166, 1365–1374.
Chen, G., Dubrawsky, I., Mendez, P., et al. (1999) In vitro scanning saturation mutagenesis of all the specificity determining residues in an antibody binding site. Protein Eng. 12, 349–356.
Chothia, C. and Lesk, A. M. (1987) Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196, 901–917.
Chothia, C., Lesk, A. M., Tramontano, A., et al. (1989) Conformations of immunoglobulin hypervariable regions. Nature 342, 877–883.
Zou, W., Mackenzie, R., Therien, L., et al. (1999) Conformational epitope of the type III group B Streptococcus capsular polysaccharide. J. Immunol. 163, 820–825.
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., et al. (1977) The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542.
Graille, M., Stura, E. A., Corper, A. L., et al. (2000) Crystal structure of a Staphylococcus aureus protein. A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity. Proc. Natl. Acad. Sci. USA 97, 5399–5404.
Kistler, J., Aebi, U., Onorato, L., et al. (1978) Structural changes during the transformation of bacteriophage T4 polyheads: characterization of the initial and final states by freeze-drying and shadowing Fab-fragment-labelled preparations. J. Mol. Biol. 126, 571–589.
Fairclough, R. H., Twaddle, G. M., Gudipati, E., et al. (1998) Mapping the mAb 383C epitope to a2 (187–199) of the Torpedo acetylcholine receptor on the three-dimensional model. J. Mol. Biol. 282, 301–315.
Sun, W., Barchi, R. L., and Cohen, S. A. (1995) Probing sodium channel cytoplasmic domain structure. Evidence for the interaction of the rSkM1 amino and carboxyl termini. J. Biol. Chem. 270, 22,271–22,276.
Tzartos, S. J., Barkas, T., Cung, M. T., et al. (1998) Anatomy of the antigenic structure of a large membrane autoantigen, the muscle-type nicotinic acetylcholine receptor. Immunol. Rev. 163, 89–120.
Harlow, E. and Lane, D. (1988) Antibodies: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
Berzofsky, J. A., Berkower, I. J., and Epstein, S. L. (1999) Antigen antibody interactions and monoclonal antibodies, Fundamental Immunology, 4th ed. (W. E. Paul, ed.), Lippincott-Raven, Philadelphia, pp. 75–110.
Ways, J. P. and Parham, P. (1983) The binding of monoclonal antibodies to cell-surface molecules. A quantitative analysis with immunoglobulin G against two alloantigenic determinants of the human transplantation antigen HLA-A2. Biochem. J. 216, 423–432.
Parham, P. (1984) The binding of monoclonal antibodies to cell surface molecules. Quantitative analysis of the reactions and cross-reactions of an antibody (MB40.3) with four HLA-B molecules. J. Biol. Chem. 259, 13,077–13,083.
MacKenzie, R. and To, R. (1998) The role of valency in the selection of anti-carbohydrate single-chain Fvs from phage display libraries. J. Immunol. Methods 220, 39–49.
Stevanin, G., Trottier, Y., Cancel, G., et al. (1996) Screening for proteins with polyglutamine expansions in autosomal dominant cerebellar ataxias. Hum. Mol. Genet. 5, 1887–1892.
DeLano, W. L., Ultsch, M. H., de Vos, A. M., et al. (2000) Convergent solutions to binding at as protein-protein interface. Science 287, 1279–1283.
Lescar, J., Stouracova, R., Riottot, M.-M., et al. (1997) Three-dimensional structure of an Fab-peptide complex: structural basis of HIV-1 protease inhibition by amonoclonal antibody. J. Mol. Biol. 267, 1207–1222.
Persichetti, F., Trettel, F., Huang, C. C., et al. (1999) Mutant huntingtin forms in vivo complexes with distinct context-dependent conformations of the polyglutamine segment. Neurobiol. Dis. 6, 364–375.
Ko, J., Ou, S., and Patterson, P. H. (2001) New anti-huntingtin monoclonal antibodies: implications for huntingtin conformation and its binding proteins. Brain Res. Bull. 56, 319–329.
Mende-Mueller, L. M., Toneff, T., Hwang, S. R., et al. (2001) Tissue-specific proteolysis of huntingtin (htt) in human brain: evidence of enhanced levels of N-and C-terminal htt fragments in Huntinton’s disease striatum. J. Neurosci. 21, 1830–1837.
Kim, Y. J., Yi, Y., Sapp, E., et al. (2001) Caspase 3-cleaved N-terminal fragments of wild-type and mutant huntingtin are present in normal and Huntington’s disease brains, associate with membranes, and undergo calpain-dependent proteolysis. Proc. Natl. Acad. Sci. USA 98, 12,784–12,789.
Humbert, S., Bryson, E. A., Cordelières, F. P., et al. (2002) The IGF-1/Akt pathway is neuroprotective in Huntington’s disease and involves huntingtin phosphorylation by Akt. Dev. Cell. 3, 1–20.
Das, T. K., Mazumdar, S., and Mitra, S. (1998) Characterization of a partially unfolded structure of cytochrome C induced by sodium dodecyl sulphate and the kinetics of its refolding. Eur. J. Biochem. 254, 662–670.
Mitraki, A., Barge, A., Chroboczek, J., et al. (1999) Unfolding studies of human adenovirus type 2 fibre trimers. Eur. J. Biochem. 264, 599–606.
Dunn, S. D. (1986) Effects of the modification of transfer buffer composition and the renaturation of proteins in gels on the recognition of proteins on Western blots by monoclonal antibodies. Anal. Biochem. 157, 144–153.
Hubbard, M. J. and Klee, C. B. (1987) Calmodulin binding by calcineurin. Ligand-induced renaturation of protein immoblized on nitrocellulose. J. Biol. Chem. 262, 15,062–15,070.
Birk, H. W. and Koepsell, H. (1987) Reaction of monoclonal antibodies with plasmamembrane proteins after binding on nitrocellulose: renaturation of antigenic sites and reduction of nonspecific antibody binding. Anal. Biochem. 164, 12–22.
Celenza, J. L. and Carlson, M. (1991) Renaturation of protein kinase activity of protein blots. Methods Enzymol. 200, 423–430.
Fischer, R., Wei, Y., and Berchtold, M. (1996) Detection of calmodulin-binding proteins using a 32P-labeled GST-calmodulin fusion protein and a novel renaturation protocol. Biotechniques 21, 292–296.
Klinz, F. J. (1994) GTP-blot analysis of small GTP-binding proteins. The C-terminus is involved in renaturation of blotted proteins. Eur. J. Biochem. 225, 99–105.
Shackelford, D. A. and Zivin, J. A. (1993) Renaturation of calcium/calmodulin-dependent protein kinase activity after electrophoretic transfer from sodium dodecyl sulfate-polyacrylamide gels to membranes. Anal. Biochem. 211, 131–138.
Zeng, F. Y., Oka, J. A., and Weigel, P. H. (1996) Renaturation and ligand blotting of the major subunit of the rat asialoglycoprotein receptor after denaturing polyacrylamide gel electrophoresis. Glycobiology 6, 247–255.
Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory, Plainview, NY, p. 16.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Humana Press Inc.
About this protocol
Cite this protocol
Brooks, E., Arrasate, M., Cheung, K., Finkbeiner, S.M. (2004). Using Antibodies to Analyze Polyglutamine Stretches. In: Kohwi, Y. (eds) Trinucleotide Repeat Protocols. Methods in Molecular Biology™, vol 277. Humana Press. https://doi.org/10.1385/1-59259-804-8:103
Download citation
DOI: https://doi.org/10.1385/1-59259-804-8:103
Publisher Name: Humana Press
Print ISBN: 978-1-58829-243-8
Online ISBN: 978-1-59259-804-5
eBook Packages: Springer Protocols