Beyond BLASTing: Tertiary and quaternary structure analysis helps identify major vault proteins

Genome Biology and Evolution

Volumn 5, Issue 1, 2013, Pages 217-232

  Daly, Toni K ^a   Sutherland Smith, Andrew J ^a   Penny, David ^a  

^a MASSEY UNIVERSITY   (New Zealand)

Author keywords

BLAST; Homology modeling; I TASSER; Naegleria gruberi; RosettaDock

Indexed keywords

EUKARYOTA; NAEGLERIA GRUBERI; RATTUS; RATTUS NORVEGICUS; RODENTIA; RUMEX; STRONGYLOCENTROTUS PURPURATUS;

EID: 84876518729     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs135     Document Type: Article

References (59)

1. Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Berger W, Steiner E, Grusch M, Elbling L, Micksche M. 2009. Vaults and the major vault protein: novel roles in signal pathway regulation and immunity. Cell Mol Life Sci. 66:43-61.
3. Burkhard P, Stetefeld J, Strelkov SV. 2001. Coiled coils: a highly versatile protein folding motif. Trends Cell Biol. 11:82-88.
4. Clark AR, Sawyer GM, Robertson SP, Sutherland-Smith AJ. 2009. Skeletal dysplasias due to filamin A mutations result from a gain-of-function mechanism distinct from allelic neurological disorders. Hum Mol Genet. 18:4791-4800.
5. Collins L, Penny D. 2005. Complex spliceosomal organization ancestral to extant eukaryotes. Mol Biol Evol. 22:1053-1066.
6. Deschamps P, et al. 2011. Phylogenomic analysis of kinetoplastids supports that trypanosomatids arose from within bodonids.Mol Biol Evol. 28:53-58.
7. Finn RD, et al. 2010. The Pfam protein families database. Nucleic Acids Res. 38:D211-D222.
8. Finnigan GC, Hanson-Smith V, Stevens TH, Thornton JW. 2012. Evolution of increased complexity in a molecularmachine. Nature 481:360-364.
9. Fritz-Laylin LK, et al. 2010. The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell 140:631-642.
10. Gray JJ, et al. 2003. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol. 331:281-299.
11. Gronenborn AM, et al. 1991. A novel highly stable fold of the immunoglobulin binding domain of streptococcal protein-G. Science 253: 657-661.
12. Hamill DR, Suprenant KA. 1997. Characterization of the sea urchin major vault protein: a possible role for vault ribonucleoprotein particles in nucleocytoplasmic transport. Dev Biol. 190:117-128.
13. Herrmann C, Zimmermann H, Volknandt W. 1997. Analysis of a cDNA encoding the major vault protein from the electric ray Discopyge ommata. Gene 188:85-90.
14. Holm L, Sander C. 1997. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins 28:72-82.
15. Kedersha NL, Heuser JE, Chugani DC, Rome LH. 1991. Vaults. III. Vault ribonucleoprotein particles open into flower-like structures with octagonal symmetry. J Cell Biol. 112:225-235.
16. Kedersha NL, Rome LH. 1986. Isolation and characterization of a novel ribonucleoprotein particle-large structures contain a single species of small RNA. J Cell Biol. 103:699-709.
17. Kelley LA, Sternberg MJ. 2009. Protein structure prediction on the web: a case study using the Phyre server. Nat Protoc. 4:363-371.
18. Kickhoefer VA, Rome LH. 1994. The sequence of a cDNA encoding the major vault protein from Rattus norvegicus. Gene 151:257-260.
19. Kickhoefer VA, et al. 2009. Targeting vault nanoparticles to specific cell surface receptors. ACS Nano 3:27-36.
20. Koonin EV. 2010. The incredible expanding ancestor of eukaryotes. Cell 140:606-608.
21. Kozakov D, Brenke R, Comeau SR, Vajda S. 2006. PIPER: an FFT-based protein docking program with pairwise potentials. Proteins 65: 392-406.
22. Kozlov G, et al. 2006. Solution structure of a two-repeat fragment of major vault protein. J Mol Biol. 356:444-452.
23. Kurland CG, Collins LJ, Penny D. 2006. Genomics and the irreducible nature of eukaryote cells. Science 312:1011-1014.
24. Kuwahara Y, et al. 2009. Unusual thermal disassembly of the SPFH domain oligomer from Pyrococcus horikoshii. Biophys J. 97:2034-2043.
25. Lara PC, Pruschy M, Zimmermann M, Henriquez-Hernandez LA. 2011. MVP and vaults: a role in the radiation response. Radiat Oncol. 6: 148.
26. Liu B, et al. 2011. Up-regulation ofmajor vault protein in the frontal cortex of patients with intractable frontal lobe epilepsy. J Neurol Sci. 308: 88-93.
27. Lyskov S, Gray JJ. 2008. The RosettaDock server for local protein-protein docking. Nucleic Acids Res. 36:233-238.
28. Matsumoto T, et al. 2011. Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol. 156:20-28.
29. Mossel E, Steel M. 2004. A phase transition for a random clustermodel on phylogenetic trees. Math Biosci. 187:189-203.
30. Moult J, Pedersen JT, Judson R, Fidelis K. 1995. A large-scale experiment to assess protein structure prediction methods. Proteins 23:ii-iv.
31. Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP-a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 247:536-540.
32. Neumann N, Lundin D, Poole AM. 2010. Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor. PloS One 5:e13241.
33. Orengo CA, et al. 1997. CATH-a hierarchic classification of protein domain structures. Structure 5:1093-1108.
34. Pan KM, et al. 1993. Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins. Proc Natl Acad Sci U S A. 90:10962-10966.
35. Paspalas CD, et al. 2009. Major vault protein is expressed along the nucleus-neurite axis and associates with mRNAs in cortical neurons. Cereb Cortex. 19:1666-1677.
36. Qian W, He X, Chan E, Xu H, Zhang J. 2011. Measuring the evolutionary rate of protein-protein interaction. Proc Natl Acad Sci U S A. 108: 8725-8730.
37. Querol-Audi J, et al. 2009. The mechanism of vault opening from the high resolution structure of the N-terminal repeats of MVP. EMBO J. 28: 3450-3457.
38. Roy A, Kucukural A, Zhang Y. 2010. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 5: 725-738.
39. Roy A, Xu D, Poisson J, Zhang Y. 2011. A protocol for computer-based protein structure and function prediction. J Vis Exp. 57:e3259.
40. Sali A, Blundell TL. 1993. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 234:779-815.
41. Sawyer GM, Clark AR, Robertson SP, Sutherland-Smith AJ. 2009. Diseaseassociated substitutions in the filamin B actin binding domain confer enhanced actin binding affinity in the absence of major structural disturbance: insights from the crystal structures of filamin B actin binding domains. J Mol Biol. 390:1030-1047.
42. Schäffer AA, et al. 2001. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29:2994-3005.
43. Stadler PF, et al. 2009. Evolution of vault RNAs. Mol Biol Evol. 26: 1975-1991.
44. Steitz TA, Moore PB. 2003. RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Trends Biochem Sci. 28:411-418.
45. Stephen AG, et al. 2001. Assembly of vault-like particles in insect cells expressing only the major vault protein. J Biol Chem. 276: 23217-23220.
46. Stevens MI, Hunger SA, Hills SFK, Gemmill CEC. 2007. Phantom hitch-hikers mislead estimates of genetic variation in Antarctic mosses. Plant Systematics Evol. 263:191-201.
47. Stewart PL, et al. 2005. Sea urchin vault structure, composition, and differential localization during development. BMC Dev Biol. 5:3.
48. Tanaka H, et al. 2009. The structure of rat liver vault at 3.5 Angstrom resolution. Science 323:384-388.
49. Tovchigrechko A, Vakser IA. 2006. GRAMM-X public web server for protein-protein docking. Nucleic Acids Res. 34:W310-W314.
50. van Zon A, et al. 2002. Structural domains of vault proteins: a role for the coiled coil domain in vault assembly. Biochem Biophys Res Commun. 291:535-541.
51. Vasu SK, Kedersha NL, Rome LH. 1993. cDNA cloning and disruption of the major vault protein alpha gene (mvpA) in Dictyostelium discoideum. J Biol Chem. 268:15356-15360.
52. Vasu SK, Rome LH. 1995. Dictyostelium vaults: disruption of the major proteins reveals growth and morphological defects and uncovers a new associated protein. J Biol Chem. 270:16588-16594.
53. Vollmar F, et al. 2009. Assembly of nuclear pore complexes mediated by major vault protein. J Cell Sci. 122:780-786.
54. Watson JD, Laskowski RA, Thornton JM. 2005. Predicting protein function from sequence and structural data. Curr Opin Struct Biol. 15:275-284.
55. WuS, Zhang Y. 2008.MUSTER: improving protein sequence profile-profile alignments by usingmultiple sources of structure information. Proteins 72:547-556.
56. Xu D, Zhang J, Roy A, Zhang Y. 2011. Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. Proteins 79: 147-160.
57. Yang J, et al. 2010. Vaults are dynamically unconstrained cytoplasmic nanoparticles capable of half vault exchange. ACS Nano 4: 7229-7240.
58. Ye Y, Godzik A. 2003. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19:ii246-ii255.
59. Zhang Y. 2008. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:409.