Using NMR spectroscopy to monitor ubiquitin chain conformation and interactions with ubiquitin-binding domains

Methods in Enzymology

Volumn 399, Issue , 2005, Pages 177-192

  Ranjani Varadan, ^a   Assfalg, Michael ^a   Fushman, David ^a  

^a University of Maryland   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING AFFINITY; COMPLEX FORMATION; LABELING INDEX; MEASUREMENT; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; REVIEW; SIGNAL TRANSDUCTION; STOICHIOMETRY;

MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; UBIQUITIN;

EID: 28844440078     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)99012-5     Document Type: Review

References (29)

1. Aguilar R.C., and Wendland B. Ubiquitin: Not just for proteasomes anymore Curr. Opin. Cell Biol. 15 2003 184 190
2. Berliner L.J., Grunwald J., Hankovszky H.O., and Hideg K. A novel reversible thiol-specific spin label: Papain active site labeling and inhibition Anal. Biochem. 119 1982 450 455
3. Clore G.M., and Schwieters C.D. Docking of protein-protein complexes on the basis of highly ambiguous intermolecular distance restraints derived from 1H/15N chemical shift mapping and backbone 15N-1H residual dipolar couplings using conjoined rigid body/torsion angle dynamics J. Am. Chem. Soc. 125 2003 2902 2912
4. Cook W.J., Jeffrey L.C., Kasperek E., and Pickart C.M. Structure of tetraubiquitin shows how multiubiquitin chains can be formed J. Mol. Biol. 236 1994 601 609
5. Dominguez C., Boelens R., and Bonvin A.M. HADDOCK: A protein-protein docking approach based on biochemical or biophysical information J. Am. Chem. Soc. 125 2003 1731 1737
6. Donaldson L.W., Skrynnikov N.R., Choy W.Y., Muhandiram D.R., Sarkar B., Forman-Kay J.D., and Kay L.E. Structural characterization of proteins with an attached ATCUN motif by paramagnetic relaxation enhancement NMR spectroscopy J. Am. Chem. Soc. 123 2001 9843 9847
7. Fushman D., Cahill S., and Cowburn D. The main-chain dynamics of the dynamin pleckstrin homology (PH) domain in solution: Analysis of 15N relaxation with monomer/dimer equilibration J. Mol. Biol. 266 1997 173 194
8. Fushman D., Varadan R., Assfalg M., and Walker O. Determining domain orientation in macromolecules by using spin-relaxation and residual dipolar coupling measurements Progr. NMR Spectrosc. 44 2004 189 214
9. Hershko A., and Ciechanover A. The ubiquitin system Annu. Rev. Biochem. 67 1998 425 480
10. Ikegami T., Verdier L., Sakhaii P., Grimme S., Pescatore B., Saxena K., Fiebig K.M., and Griesinger C. Novel techniques for weak alignment of proteins in solution using chemical tags coordinating lanthanide ions J. Biomol. NMR. 29 2004 339 349
11. Jain N.U., Venot A., Umemoto K., Leffler H., and Prestegard J.H. Distance mapping of protein-binding sites using spin-labeled oligosaccharide ligands Protein Sci. 10 2001 2393 2400
12. Kang R.S., Daniels C.M., Francis S.A., Shih S.C., Salerno W.J., Hicke L., and Radhakrishnan I. Solution structure of a CUE-ubiquitin complex reveals a conserved mode of ubiquitin binding Cell 113 2003 621 630
13. Kosen P.A. Spin labeling of proteins Methods Enzymol. 177 1989 86 121
14. McCracken A.A., and Brodsky J.L. Evolving questions and paradigm shifts in endoplasmic-reticulum-associated degradation (ERAD) Bioessays 25 2003 868 877
15. Mueller T.D., Kamionka M., and Feigon J. Specificity of the interaction between ubiquitin-associated domains and ubiquitin J. Biol. Chem. 279 2004 11926 11936
16. Muratani M., and Tansey W.P. How the ubiquitin-proteasome system controls transcription Nat. Rev. Mol. Cell. Biol. 4 2003 192 201
17. Osley M.A. H2B ubiquitylation: The end is in sight Biochim. Biophys. Acta 1677 2004 74 78
18. Phillips C.L., Thrower J., Pickart C.M., and Hill C.P. Structure of a new crystal form of tetraubiquitin Acta Cryst. D. 57 2000 341 344
19. Pickart C.M. Ubiquitin enters the new millennium Mol. Cell. 8 2001 499 504
20. Pickart C.M., and Fushman D. Polyubiquitin chains: Polymeric protein signals Curr. Opin. Chem. Biol. 8 2004 610 616
21. Piotrowski J., Beal R., Hoffmann L., Wilkinson K.D., Cohen R.E., and Pickart C.M. Inhibition of the 26S proteasome by polyubiquitin chains synthesized to have defined lengths J. Biol. Chem. 272 1997 23712 23721
22. Ryu K.S., Lee K.J., Bae S.H., Kim B.K., Kim K.A., and Choi B.S. Binding surface mapping of intra and inter domain interactions among hHR23B, ubiquitin and poly ubiquitin binding site 2 of S5a J. Biol. Chem. 278 2003 36621 36627
23. 15N-relaxation data Proteins 60 2005 367 381
24. Varadan R., Assfalg M., Haririnia A., Raasi S., Pickart C., and Fushman D. Solution conformation of Lys63-linked di-ubiqutin chain provides clues to functional diversity of polyubiquitin signaling J. Biol. Chem. 279 2004 7055 7063
25. Varadan R., Walker O., Pickart C., and Fushman D. Structural properties of polyubiquitin chains in solution J. Mol. Biol. 324 2002 637 647
26. Walker O., Varadan R., and Fushman D. Efficient and accurate determination of the overall rotational diffusion tensor of a molecule from 15N relaxation data using computer program ROTDIF J. Magn. Reson. 168 2004 336 345
27. Wang Q., Goh A.M., Howley P.M., and Walters K.J. Ubiquitin recognition by the DNA repair protein hHR23a Biochemistry 42 2003 13529 13535
28. Wohnert J., Franz K.J., Nitz M., Imperiali B., and Schwalbe H. Protein alignment by a coexpressed lanthanide-binding tag for the measurement of residual dipolar couplings J. Am. Chem. Soc. 125 2003 13338-1339.
29. Zuiderweg E.R. Mapping protein-protein interactions in solution by NMR spectroscopy Biochemistry 41 2002 1 7