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Fushman, D., & Walker, O. (2010). Exploring the Linkage Dependence of Polyubiquitin Conformations Using Molecular Modeling. Journal of Molecular Biology, 395(4), 803–814.

Authors 2
  1. David Fushman (first)
  2. Olivier Walker (additional)
References 44 Referenced 56
  1. 10.1016/j.cell.2004.12.001 / Cell / Ubiquitin: a Nobel protein by Wilkinson (2004)
  2. 10.1146/annurev.biochem.67.1.425 / Annu. Rev. Biochem. / The ubiquitin system by Hershko (1998)
  3. 10.1016/j.cbpa.2004.09.009 / Curr. Opin. Chem. Biol. / Polyubiquitin chains: polymeric protein signals by Pickart (2004)
  4. 10.1073/pnas.93.2.861 / Proc. Natl Acad. Sci. USA / Surface hydrophobic residues of multiubiquitin chains essential for proteolytic targeting by Beal (1996)
  5. 10.1016/S0021-9258(18)42026-1 / J. Biol. Chem. / Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme (E2) by Cook (1992)
  6. 10.1016/S0022-2836(02)01198-1 / J. Mol. Biol. / Structural properties of polyubiquitin chains in solution by Varadan (2002)
  7. 10.1016/j.jmb.2006.12.065 / J. Mol. Biol. / Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH by Eddins (2007)
  8. 10.1002/prot.20476 / Proteins / Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data by Dijk (2005)
  9. 10.1074/jbc.M309184200 / J. Biol. Chem. / Solution conformation of Lys63-linked di-ubiquitin chain provides clues to functional diversity of polyubiquitin signaling by Varadan (2004)
  10. 10.1111/j.1365-2443.2004.00780.x / Genes Cells / Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chains by Tenno (2004)
  11. 10.1038/embor.2009.55 / EMBO Rep. / Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains by Komander (2009)
  12. 10.1016/j.jmb.2009.07.090 / J. Mol. Biol. / The structure and conformation of Lys63-linked tetraubiquitin by Datta (2009)
  13. 10.1016/j.molcel.2005.05.013 / Mol. Cell / Structural determinants for selective recognition of a Lys48-linked polyubiquitin chain by a UBA domain by Varadan (2005)
  14. 10.1016/j.molcel.2009.02.011 / Mol. Cell / Linkage-specific avidity defines the lysine 63-linked polyubiquitin-binding preference of rap80 by Sims (2009)
  15. 10.1038/nsmb.1637 / Nat. Struct. Mol. Biol. / Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains by Sims (2009)
  16. 10.1038/nbt849 / Nat. Biotechnol. / A proteomics approach to understanding protein ubiquitination by Peng (2003)
  17. 10.1016/j.bbapap.2006.09.004 / Biochim. Biophys. Acta / Dissecting the ubiquitin pathway by mass spectrometry by Xu (2006)
  18. 10.1074/jbc.M609659200 / J. Biol. Chem. / Certain pairs of ubiquitin-conjugating enzymes (E2s) and ubiquitin–protein ligases (E3s) synthesize nondegradable forked ubiquitin chains containing all possible isopeptide linkages by Kim (2007)
  19. 10.1007/s00018-008-8090-6 / Cell. Mol. Life Sci. / Polyubiquitin chains: functions, structures, and mechanisms by Li (2008)
  20. 10.1038/embor.2008.93 / EMBO Rep. / Atypical ubiquitin chains: new molecular signals. ‘Protein Modifications: Beyond the Usual Suspects’ review series by Ikeda (2008)
  21. 10.1006/jmbi.1994.1169 / J. Mol. Biol. / Structure of tetraubiquitin shows how multiubiquitin chains can be formed by Cook (1994)
  22. 10.1107/S090744490001800X / Acta Crystallogr. Sect. D / Structure of a new crystal form of tetraubiquitin by Phillips (2001)
  23. 10.1016/S0022-2836(02)01198-1 / J. Mol. Biol. / Structural properties of polyubiquitin chains in solution by Varadan (2002)
  24. 10.1021/ja026939x / J. Am. Chem. Soc. / HADDOCK: a protein–protein docking approach based on biochemical or biophysical information by Dominguez (2003)
  25. 10.1038/nrm1701 / Nat. Rev. Mol. Cell Biol. / Ubiquitin-binding domains by Hicke (2005)
  26. 10.1042/BJ20061138 / Biochem. J. / Ubiquitin-binding domains by Hurley (2006)
  27. 10.1016/j.pbiomolbio.2004.07.010 / Prog. Biophys. Mol. Biol. / Morphological aspects of oligomeric protein structures by Ponstingl (2005)
  28. 10.1002/prot.20019 / Proteins / A physical reference state unifies the structure-derived potential of mean force for protein folding and binding by Liu (2004)
  29. 10.1016/j.pnmrs.2004.02.001 / Prog. NMR Spectrosc. / Determining domain orientation in macromolecules by using spin-relaxation and residual dipolar coupling measurements by Fushman (2004)
  30. 10.1006/jmbi.1998.2439 / J. Mol. Biol. / The atomic structure of protein–protein recognition sites by Lo Conte (1999)
  31. 10.1016/j.jmb.2003.12.073 / J. Mol. Biol. / A dissection of specific and non-specific protein–protein interfaces by Bahadur (2004)
  32. 10.1002/prot.10461 / Proteins / Dissecting subunit interfaces in homodimeric proteins by Bahadur (2003)
  33. 10.1016/S0959-440X(00)00065-8 / Curr. Opin. Struct. Biol. / Electrostatic aspects of protein–protein interactions by Sheinerman (2000)
  34. 10.1110/ps.12901 / Protein Sci. / Electrostatic contributions to protein–protein interactions: fast energetic filters for docking and their physical basis by Norel (2001)
  35. {'key': '10.1016/j.jmb.2009.10.039_bib35', 'series-title': 'Frontiers in Molecular Biology', 'article-title': 'Protein–protein recognition', 'author': 'Kleanthous', 'year': '2000'} / Frontiers in Molecular Biology / Protein–protein recognition by Kleanthous (2000)
  36. 10.1038/nbt0308-303 / Nat. Biotechnol. / What is principal component analysis? by Ringnér (2008)
  37. {'key': '10.1016/j.jmb.2009.10.039_bib37', 'series-title': "A User's Guide to Principal Components", 'author': 'Jackson', 'year': '1991'} / A User's Guide to Principal Components by Jackson (1991)
  38. {'key': '10.1016/j.jmb.2009.10.039_bib38', 'series-title': 'Chemometrics: Data Analysis for the Laboratory and Chemical Plant', 'author': 'Brereton', 'year': '2003'} / Chemometrics: Data Analysis for the Laboratory and Chemical Plant by Brereton (2003)
  39. 10.1110/ps.062508007 / Protein Sci. / Effects of cyclization on conformational dynamics and binding properties of Lys48-linked di-ubiquitin by Dickinson (2007)
  40. 10.1002/prot.20917 / Proteins / Interdomain mobility in di-ubiquitin revealed by NMR by Ryabov (2006)
  41. 10.1021/ja067667r / J. Am. Chem. Soc. / A model of interdomain mobility in a multidomain protein by Ryabov (2007)
  42. 10.1002/prot.21723 / Proteins / HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets by Vries (2007)
  43. 10.1021/ja00214a001 / J. Am. Chem. Soc. / The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin by Jorgensen (1988)
  44. 10.1093/protein/8.2.127 / Protein Eng. / LIGPLOT: a program to generate schematic diagrams of protein–ligand interactions by Wallace (1995)
Dates
Type When
Created 15 years, 10 months ago (Oct. 23, 2009, 4:37 a.m.)
Deposited 2 years, 6 months ago (Feb. 22, 2023, 2:23 p.m.)
Indexed 1 year, 2 months ago (July 1, 2024, 12:36 p.m.)
Issued 15 years, 8 months ago (Jan. 1, 2010)
Published 15 years, 8 months ago (Jan. 1, 2010)
Published Print 15 years, 8 months ago (Jan. 1, 2010)
Funders 0

None

@article{Fushman_2010, title={Exploring the Linkage Dependence of Polyubiquitin Conformations Using Molecular Modeling}, volume={395}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/j.jmb.2009.10.039}, DOI={10.1016/j.jmb.2009.10.039}, number={4}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Fushman, David and Walker, Olivier}, year={2010}, month=jan, pages={803–814} }