SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions

Structure

Volumn 19, Issue 1, 2011, Pages 109-116

  Róycki, Bartosz ^a   Kim, Young C ^b   Hummer, Gerhard ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b NAVAL RESEARCH LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESCRT PROTEIN; PROTEIN CHMP3; PROTEIN ESCRT 3; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; CRYSTAL STRUCTURE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN LOCALIZATION; X RAY CRYSTALLOGRAPHY;

CLUSTER ANALYSIS; COMPUTER SIMULATION; ENDOSOMAL SORTING COMPLEXES REQUIRED FOR TRANSPORT; ENTROPY; HUMANS; MODELS, MOLECULAR; MONTE CARLO METHOD; OSMOLAR CONCENTRATION; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SCATTERING, SMALL ANGLE; X-RAY DIFFRACTION;

EID: 78650948314     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2010.10.006     Document Type: Article

References (47)

1. M. Bajorek, H.L. Schubert, J. McCullough, C. Langelier, D.M. Eckert, W.M.B. Stubblefield, N.T. Uter, D.G. Myszka, C.P. Hill, and W.I. Sundquist Structural basis for ESCRT-III protein autoinhibition Nat. Struct. Mol. Biol. 16 2009 754 762
2. P. Bassereau Division of labour in ESCRT complexes Nat. Cell Biol. 12 2010 422 423
3. P. Bernadó, E. Mylonas, M.V. Petoukhov, M. Blackledge, and D.I. Svergun Structural characterization of flexible proteins using small-angle X-ray scattering J. Am. Chem. Soc. 129 2007 5656 5664 (Pubitemid 46697655)
4. R.B. Best, Y.G. Chen, and G. Hummer Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor Structure 13 2005 1755 1763
5. P. Chacon, F. Moran, J.F. Diaz, E. Pantos, and J.M. Andreu Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm Biophys. J. 74 1998 2760 2775
6. A.B. Datta, G.L. Hura, and C. Wolberger The structure and conformation of Lys63-linked tetraubiquitin J. Mol. Biol. 392 2009 1117 1124
7. F. Förster, B. Webb, K.A. Krukenberg, H. Tsuruta, D.A. Agard, and A. Sali Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies J. Mol. Biol. 382 2008 1089 1106
8. A. Grishaev, J. Wu, J. Trewhella, and A. Bax Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data J. Am. Chem. Soc. 127 2005 16621 16628
9. A. Grishaev, V. Tugarinov, L.E. Kay, J. Trewhella, and A. Bax Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints J. Biomol. NMR 40 2008 95 106
10. P.I. Hanson, R. Roth, Y. Lin, and J.E. Heuser Plasma membrane deformation by circular arrays of ESCRT-III protein filaments J. Cell Biol. 180 2008 389 402
11. D.B. Heidorn, and J. Trewhella Comparison of the crystal and solution structures of calmodulin and troponin-C Biochemistry 27 1988 909 915
12. L.J. Heyer, S. Kruglyak, and S. Yooseph Exploring expression data: identification and analysis of coexpressed genes Genome Res. 9 1999 1106 1115
13. G.L. Hura, A.L. Menon, M. Hammel, R.P. Rambo, F.L. Poole II, S.E. Tsutakawa, F.E. Jenney Jr., S. Classen, K.A. Frankel, and R.C. Hopkins Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS) Nat. Methods 6 2009 606 612
14. J.H. Hurley The ESCRT complexes Crit. Rev. Biochem. Mol. Biol. 45 2010 463 487
15. J.H. Hurley, and P.I. Hanson Membrane budding and scission by the ESCRT machinery: it's all in the neck Nat. Rev. Mol. Cell Biol. 11 2010 556 566
16. D.A. Jacques, and J. Trewhella Small-angle scattering for structural biology - expanding the frontier while avoiding the pitfalls Protein Sci. 19 2010 642 657
17. E.T. Jaynes Information theory and statistical mechanics Phys. Rev. 106 1957 620 630
18. Y.C. Kim, and G. Hummer Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding J. Mol. Biol. 375 2008 1416 1433
19. Y.C. Kim, C. Tang, G.M. Clore, and G. Hummer Replica exchange simulations of transient encounter complexes in protein-protein association Proc. Natl. Acad. Sci. USA 105 2008 12855 12860
20. S. Lata, M. Roessle, J. Solomons, M. Jamin, H.G. Göttlinger, D.I. Svergun, and W. Weissenhorn Structural basis for autoinhibition of ESCRT-III CHMP3 J. Mol. Biol. 378 2008 818 827
21. S. Lee, A. Joshi, K. Nagashima, E.O. Freed, and J.H. Hurley Structural basis for viral late-domain binding to Alix Nat. Struct. Mol. Biol. 14 2007 194 199
22. T. Mittag, J. Marsh, A. Grishaev, S. Orlicky, H. Lin, F. Sicheri, M. Tyers, and J.D. Forman-Kay Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase Structure 18 2010 494 506
23. T. Muziol, E. Pineda-Molina, R.B. Ravelli, A. Zamborlini, Y. Usami, H. Göttlinger, and W. Weissenhorn Structural basis for budding by the ESCRT-III factor CHMP3 Dev. Cell 10 2006 821 830
24. T. Obita, S. Saksena, S. Ghazi-Tabatabai, D.J. Gill, O. Perisic, S.D. Emr, and R.L. Williams Structural basis for selective recognition of ESCRT-III by the AAA ATPase vps4 Nature 449 2007 735 740
25. M. Pelikan, G.L. Hura, and M. Hammel Structure and flexibility within proteins as identified through small angle X-ray scattering Gen. Physiol. Biophys. 28 2009 174 189
26. G. Prag, H. Watson, Y.C. Kim, B.M. Beach, R. Ghirlando, G. Hummer, J.S. Bonifacino, and J.H. Hurley The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting Dev. Cell 12 2007 973 986
27. R.P. Rambo, and J.A. Tainer Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering Curr. Opin. Struct. Biol. 20 2010 128 137
28. X. Ren, D.P. Kloer, Y.C. Kim, R. Ghirlando, L.F. Saidi, G. Hummer, and J.H. Hurley Hybrid structural model of the complete human ESCRT-0 complex Structure 17 2009 406 416
29. S. Saksena, J. Wahlman, D. Teis, A.E. Johnson, and S.D. Emr Functional reconstitution of ESCRT-III assembly and disassembly Cell 136 2009 97 109
30. G.F. Schröder, M. Levitt, and A.T. Brunger Super-resolution biomolecular crystallography with low-resolution data Nature 464 2010 1218 1222
31. Y. Shen, O. Lange, F. Delaglio, P. Rossi, J.M. Aramini, G.H. Liu, A. Eletsky, Y.B. Wu, K.K. Singarapu, and A. Lemak Consistent blind protein structure generation from NMR chemical shift data Proc. Natl. Acad. Sci. USA 105 2008 4685 4690
32. S. Shim, L.A. Kimpler, and P.I. Hanson Structure/function analysis of four core ESCRT-III proteins reveals common regulatory role for extreme C-terminal domain Traffic 8 2007 1068 1079
33. M.D. Stuchell-Brereton, J.J. Skalicky, C. Kieffer, M.A. Karren, S. Ghaffarian, and W.I. Sundquist ESCRT-III recognition by vps4 ATPases Nature 449 2007 740 744
34. K. Sugase, H.J. Dyson, and P.E. Wright Mechanism of coupled folding and binding of an intrinsically disordered protein Nature 447 2007 1021 1025
35. D.I. Svergun Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing Biophys. J. 76 1999 2879 2886
36. D. Svergun, C. Barberato, and M.H.J. Koch CRYSOL - a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates J. Appl. Crystallogr. 28 1995 768 773
37. D.I. Svergun, S. Richard, M.H.J. Koch, Z. Sayers, S. Kuprin, and G. Zaccai Protein hydration in solution: Experimental observation by X-ray and neutron scattering Proc. Natl. Acad. Sci. USA 95 1998 2267 2272
38. D.I. Svergun, M.V. Petoukhov, and M.H.J. Koch Determination of domain structure of proteins from X-ray solution scattering Biophys. J. 80 2001 2946 2953
39. H.T.H. Tsang, J.W. Connell, S.E. Brown, A. Thompson, E. Reid, and C.M. Sanderson A systematic analysis of human CHMP protein interactions: Additional MIT domain-containing proteins bind to multiple components of the human ESCRT III complex Genomics 88 2006 333 346
40. A.G. Turjanski, J.S. Gutkind, R.B. Best, and G. Hummer Binding-induced folding of a natively unstructured transcription factor PLoS Comp. Biol. 4 2008 e1000060
41. J. VanOudenhove, E. Anderson, S. Krueger, and J.L. Cole Analysis of PKR structure by small-angle scattering J. Mol. Biol. 387 2009 910 920
42. R.L. Williams, and S. Urbe The emerging shape of the ESCRT machinery Nat. Rev. Mol. Cell Biol. 8 2007 355 368
43. T. Wollert, and J.H. Hurley Molecular mechanism of multivesicular body biogenesis by ESCRT complexes Nature 464 2010 864 870
44. T. Wollert, C. Wunder, J. Lippincott-Schwartz, and J.H. Hurley Membrane scission by the ESCRT-III complex Nature 458 2009 172 178
45. S. Yang, S. Park, L. Makowski, and B. Roux A rapid coarse residue-based computational method for X-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes Biophys. J. 96 2009 4449 4463
46. S. Yang, L. Blachowicz, L. Makowski, and B. Roux Multidomain assembled states of Hck tyrosine kinase in solution Proc. Natl. Acad. Sci. USA 107 2010 15757 15762
47. A. Zamborlini, Y. Usami, S.R. Radoshitzky, E. Popova, G. Palu, and H. Göttlinger Release of autoinhibition converts ESCRT-III components into potent inhibitors of HIV-1 budding Proc. Natl. Acad. Sci. USA 103 2006 19140 19145