Erratum to "Standard Conformations of β-Arches in β-Solenoid Proteins" [J. Mol. Biol. (2006) 358, 1094-1105] (DOI:10.1016/j.jmb.2006.02.039);Standard Conformations of β-Arches in β-Solenoid Proteins

Journal of Molecular Biology

Volumn 358, Issue 4, 2006, Pages 1094-1105

  Hennetin, Jérôme ^a   Jullian, Bérangère ^a   Steven, Alasdair C ^b   Kajava, Andrey V ^a  

^a Centre National de la Recherche Scientifique   (France)

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

Author keywords

amyloid; arc; helix; structure; turn

Indexed keywords

AMYLOID; AMYLOID PROTEIN; GLOBULAR PROTEIN; POLYPEPTIDE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN STRUCTURE; ROTATION; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

EID: 33646076466     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.05.028     Document Type: Erratum

References (41)

1. Efimov A.V. Patterns of loop regions in proteins. Curr. Opin. Struct. Biol. 3 (1993) 379-384
2. Oliva B., Bates P.A., Querol E., Aviles F.X., and Sternberg M.J. An automated classification of the structure of protein loops. J. Mol. Biol. 266 (1997) 814-830
3. Kwasigroch J.M., Chomilier J., and Mornon J.P. A global taxonomy of loops in globular proteins. J. Mol. Biol. 259 (1996) 855-872
4. Burke D.F., Deane C.M., and Blundell T.L. Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure. Bioinformatics 16 (2000) 513-519
5. Venkatachalam C.M. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 6 (1968) 1425-1436
6. Sibanda B.L., and Thornton J.M. Beta-hairpin families in globular proteins. Nature 316 (1985) 170-174
7. Sibanda B.L., Blundell T.L., and Thornton J.M. Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J. Mol. Biol. 206 (1989) 759-777
8. Efimov A.V. Pseudo-homology of protein standard structures formed by two consecutive beta-strands. FEBS Letters 224 (1987) 372-376
9. Milner-White E.J., and Poet R. Four classes of beta-hairpins in proteins. Biochem. J. 240 (1986) 289-292
10. Efimov A.V. Standard conformations of a polypeptide chain in irregular protein regions. Mol. Biol. (Moskow) 20 (1986) 250-260
11. Kobe B., and Kajava A.V. When protein folding is simplified to protein coiling: the continuum of solenoid protein structures. Trends Biochem. Sci. 25 (2000) 509-515
12. Groves M.R., and Barford D. Topological characteristics of helical repeat proteins. Curr. Opin. Struct. Biol. 9 (1999) 383-389
13. Yoder M.D., and Jurnak F. Protein motifs. 3. The parallel beta helix and other coiled folds. FASEB J. 9 (1995) 335-342
14. Jenkins J., and Pickersgill R. The architecture of parallel beta-helices and related folds. Prog. Biophys. Mol. Biol. 77 (2001) 111-175
15. Yoder M.D., Keen N.T., and Jurnak F. New domain motif: the structure of pectate lyase C, a secreted plant virulence factor. Science 260 (1993) 1503-1507
16. Baumann U., Wu S., Flaherty K.M., and McKay D.B. Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif. EMBO J. 12 (1993) 3357-3364
17. Margittai M., and Langen R. Template-assisted filament growth by parallel stacking of tau. Proc. Natl Acad. Sci. USA 101 (2004) 10278-10283
18. Kajava A.V., Baxa U., Wickner R.B., and Steven A.C. A model for Ure2p prion filaments and other amyloids: the parallel superpleated beta-structure. Proc. Natl Acad. Sci. USA 101 (2004) 7885-7890
19. Govaerts C., Wille H., Prusiner S.B., and Cohen F.E. Evidence for assembly of prions with left-handed beta-helices into trimers. Proc. Natl Acad. Sci. USA 101 (2004) 8342-8347
20. Ritter C., Maddelein M.L., Siemer A.B., Luhrs T., Ernst M., Meier B.H., et al. Correlation of structural elements and infectivity of the HET-s prion. Nature 435 (2005) 844-848
21. Chothia C., and Murzin A.G. New folds for all-beta proteins. Structure 1 (1993) 217-222
22. Emsley P., Charles I.G., Fairweather N.F., and Isaacs N.W. Structure of Bordetella pertussis virulence factor P.69 pertactin. Nature 381 (1996) 90-92
23. Kajava A.V., Cheng N., Cleaver R., Kessel M., Simon M.N., Willery E., et al. Beta-helix model for the filamentous haemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteins. Mol. Microbiol. 42 (2001) 279-292
24. Nummelin H., Merckel M.C., Leo J.C., Lankinen H., Skurnik M., and Goldman A. The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll. EMBO J. 23 (2004) 701-711
25. Raetz C.R., and Roderick S.L. A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase. Science 270 (1995) 997-1000
26. Thomas L.M., Doan C.N., Oliver R.L., and Yoder M.D. Structure of pectate lyase A: comparison to other isoforms. Acta Crystallog. sect. D 58 (2002) 1008-1015
27. Jenkins J., Shevchik V.E., Hugouvieux-Cotte-Pattat N., and Pickersgill R.W. The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi. J. Biol. Chem. 279 (2004) 9139-9145
28. Liou Y.C., Tocilj A., Davies P.L., and Jia Z. Mimicry of ice structure by surface hydroxyls and water of a beta-helix antifreeze protein. Nature 406 (2000) 322-324
29. Pickersgill R.W. A primordial structure underlying amyloid. Structure (Camb) 11 (2003) 137-138
30. Petkova A.T., Ishii Y., Balbach J.J., Antzutkin O.N., Leapman R.D., Delaglio F., and Tycko R. A structural model for Alzheimer's beta -amyloid fibrils based on experimental constraints from solid state NMR. Proc. Natl Acad. Sci. USA 99 (2002) 16742-16747
31. Diaz-Avalos R., King C.Y., Wall J., Simon M., and Caspar D.L. Strain-specific morphologies of yeast prion amyloid fibrils. Proc. Natl Acad. Sci. USA 102 (2005) 10165-10170
32. DePace A.H., and Weissman J.S. Origins and kinetic consequences of diversity in Sup35 yeast prion fibers. Nature Struct. Biol. 9 (2002) 389-396
33. Uptain S.M., Sawicki G.J., Caughey B., and Lindquist S. Strains of [PSI(+)] are distinguished by their efficiencies of prion-mediated conformational conversion. EMBO J. 20 (2001) 6236-6245
34. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucl. Acids Res. 28 (2000) 235-242
35. Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
36. Holm L., and Sander C. Dali: a network tool for protein structure comparison. Trends Biochem. Sci. 20 (1995) 478-480
37. Efimov A.V. Standard structures in proteins. Prog. Biophys. Mol. Biol. 60 (1993) 201-239
38. Dayringer H.E., Tramontano A., Sprang S.R., and Fletterick R.J. Interactive program for visualization and modelling of proteins, nucleic acids and small molecules. J. Mol. Graph. 4 (1986) 82-87
39. Lovell S.C., Davis I.W., Arendall III W.B., de Bakker P.I., Word J.M., Prisant M.G., et al. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins: Struct. Funct. Genet. 50 (2003) 437-450
40. Lietzke S.E., Scavetta R.D., Yoder M.D., and Jurnak F. The refined three-dimensional structure of pectate lyase E from Erwinia chrysanthemi at 2.2 Å Resolution. Plant Physiol. 111 (1996) 73-92
41. Michel G., Chantalat L., Fanchon E., Henrissat B., Kloareg B., and Dideberg O. The iota-carrageenase of Alteromonas fortis. A beta-helix fold-containing enzyme for the degradation of a highly polyanionic polysaccharide. J. Biol. Chem. 276 (2001) 40202-40209