Coiled-coil networking shapes cell molecular machinery

Molecular Biology of the Cell

Volumn 23, Issue 19, 2012, Pages 3911-3922

  Wang, Yongqiang ^a   Zhang, Xinlei ^a,b   Zhang, Hong ^a   Lu, Yi ^a,b   Huang, Haolong ^a   Dong, Xiaoxi ^a,b   Chen, Jinan ^a,b   Dong, Jiuhong ^a   Yang, Xiao ^a,b   Hang, Haiying ^a   Jiang, Taijiao ^a  

^a INSTITUTE OF BIOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL DISRUPTION; CELL DIVISION; CELL SHAPE; CELL STRUCTURE; CENTROMERE; COILED COIL INTERACTION; COMPUTER ANALYSIS; COMPUTER NETWORK; CONTROLLED STUDY; GENETIC ASSOCIATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE;

GENOME, FUNGAL; KINETOCHORES; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE ANNOTATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPS; PROTEIN STRUCTURE, SECONDARY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TWO-HYBRID SYSTEM TECHNIQUES;

SACCHAROMYCES CEREVISIAE;

EID: 84867161119     PISSN: 10591524     EISSN: 19394586     Source Type: Journal    
DOI: 10.1091/mbc.E12-05-0396     Document Type: Article

References (65)

1. Ashburner M, et al. (2000). Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25, 25-29. (Pubitemid 30257031)
2. Barabasi AL, Oltvai ZN (2004). Network biology: understanding the cell's functional organization. Nat Rev Genet 5, 101-113.
3. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I (2001). Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125, 279-284. (Pubitemid 33000466)
4. Bertin A, McMurray MA, Grob P, Park SS, Garcia G, III, Patanwala I, Ng HL, Alber T, Thorner J, Nogales E (2008). Saccharomyces cerevisiae septins: supramolecular organization of heterooligomers and the mechanism of filament assembly. Proc Natl Acad Sci USA 105, 8274-8279. (Pubitemid 351904746)
5. Bieche I, et al. (2011). Expression analysis of mitotic spindle checkpoint genes in breast carcinoma: role of NDC80/HEC1 in early breast tumorigenicity, and a two-gene signature for aneuploidy. Mol Cancer 10, 23.
6. Boato F, Thomas RM, Ghasparian A, Freund-Renard A, Moehle K, Robinson JA (2007). Synthetic virus-like particles from self-assembling coiled-coil lipopeptides and their use in antigen display to the immune system. Angew Chem Int Ed Engl 46, 9015-9018. (Pubitemid 350232757)
7. Boxem M, et al. (2008). A protein domain-based interactome network for C. elegans early embryogenesis. Cell 134, 534-545.
8. Bromley EH, Channon K, Moutevelis E, Woolfson DN (2008). Peptide and protein building blocks for synthetic biology: from programming biomolecules to self-organized biomolecular systems. ACS Chem Biol 3, 38-50. (Pubitemid 351227984)
9. Burke DJ, Stukenberg PT (2008). Linking kinetochore-microtubule binding to the spindle checkpoint. Dev Cell 14, 474-479. (Pubitemid 351479945)
10. Carr CM, Kim PS (1993). A spring-loaded mechanism for the conformational change of influenza hemagglutinin. Cell 73, 823-832. (Pubitemid 23159019)
11. Cheeseman IM, Chappie JS, Wilson-Kubalek EM, Desai A (2006). The conserved KMN network constitutes the core microtubule-binding site of the kinetochore. Cell 127, 983-997. (Pubitemid 44792248)
12. Cheeseman IM, Niessen S, Anderson S, Hyndman F, Yates JR, III, Oegema K, Desai A (2004). A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tension. Genes Dev 18, 2255-2268. (Pubitemid 39209574)
13. Ciferri C, Musacchio A, Petrovic A (2007). The Ndc80 complex: hub of kinetochore activity. FEBS Lett 581, 2862-2869. (Pubitemid 46881153)
14. Crick FHC (1953). The packing of alpha-helices - simple coiled-coils. Acta Crystallogr 6, 689-697.
15. Cully M, Shiu J, Piekorz RP, Muller WJ, Done SJ, Mak TW (2005). Transforming acidic coiled coil 1 promotes transformation and mammary tumorigenesis. Cancer Res 65, 10363-10370. (Pubitemid 41743729)
16. Diaz-Rodriguez E, Sotillo R, Schvartzman JM, Benezra R (2008). Hec1 overexpression hyperactivates the mitotic checkpoint and induces tumor formation in vivo. Proc Natl Acad Sci USA 105, 16719-16724.
17. Eschli B, Quirin K, Wepf A, Weber J, Zinkernagel R, Hengartner H (2006). Identification of an N-terminal trimeric coiled-coil core within arenavirus glycoprotein 2 permits assignment to class I viral fusion proteins. J Virol 80, 5897-5907. (Pubitemid 43849167)
18. Gavin AC, et al. (2006). Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636.
19. Gillingham AK, Munro S (2003). Long coiled-coil proteins and membrane traffic. Biochim Biophys Acta 1641, 71-85. (Pubitemid 36952588)
20. Grigoryan G, Reinke AW, Keating AE (2009). Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature 458, 859-864.
21. Hart GT, Ramani AK, Marcotte EM (2006). How complete are current yeast and human protein-interaction networks? Genome Biol 7, 120.
22. Hesselberth JR, Miller JP, Golob A, Stajich JE, Michaud GA, Fields S (2006). Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins. Genome Biol 7, R30.
23. Hu CD, Chinenov Y, Kerppola TK (2002). Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol Cell 9, 789-798. (Pubitemid 34454889)
24. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98, 4569-4574. (Pubitemid 32295017)
25. Jahn R, Scheller RH (2006). SNAREs - engines for membrane fusion. Nat Rev Mol Cell Biol 7, 631-643. (Pubitemid 44268209)
26. Kerppola TK (2008). Bimolecular fluorescence complementation (BiFC) analysis as a probe of protein interactions in living cells. Annu Rev Biophys 37, 465-487.
27. Kilby JM, et al. (1998). Potent suppression of HIV-1 replication in humans by T-20, a peptide inhibitor of gp41-mediated virus entry. Nat Med 4, 1302-1307. (Pubitemid 28512112)
28. Kim Y, Heuser JE, Waterman CM, Cleveland DW (2008). CENP-E combines a slow, processive motor and a flexible coiled coil to produce an essential motile kinetochore tether. J Cell Biol 181, 411-419. (Pubitemid 351645031)
29. Kline-Smith SL, Sandall S, Desai A (2005). Kinetochore-spindle microtubule interactions during mitosis. Curr Opin Cell Biol 17, 35-46. (Pubitemid 40138086)
30. Komurov K, White M (2007). Revealing static and dynamic modular architecture of the eukaryotic protein interaction network. Mol Syst Biol 3, 110.
31. Krogan NJ, et al. (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643.
32. Liu J, Rost B (2001). Comparing function and structure between entire proteomes. Protein Sci 10, 1970-1979. (Pubitemid 32911216)
33. Lomander A, Hwang W, Zhang S (2005). Hierarchical self-assembly of a coiled-coil peptide into fractal structure. Nano Lett 5, 1255-1260. (Pubitemid 41084400)
34. Lupas A, Van Dyke M, Stock J (1991). Predicting coiled coils from protein sequences. Science 252, 1162-1164. (Pubitemid 21917026)
35. Lupas AN, Gruber M (2005). The structure of α-helical coiled coils. Adv Protein Chem 70, 37-78.
36. Maere S, Heymans K, Kuiper M (2005). BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448-3449. (Pubitemid 41222459)
37. Mason JM, Schmitz MA, Muller KM, Arndt KM (2006). Semirational design of Jun-Fos coiled coils with increased affinity: universal implications for leucine zipper prediction and design. Proc Natl Acad Sci USA 103, 8989-8994. (Pubitemid 43902521)
38. McAinsh AD, Tytell JD, Sorger PK (2003). Structure, function, and regulation of budding yeast kinetochores. Annu Rev Cell Dev Biol 19, 519-539. (Pubitemid 37487359)
39. McDonnell AV, Jiang T, Keating AE, Berger B (2006). Paircoil2: improved prediction of coiled coils from sequence. Bioinformatics 22, 356-358. (Pubitemid 43205384)
40. McFarlane AA, Orriss GL, Stetefeld J (2009). The use of coiled-coil proteins in drug delivery systems. Eur J Pharmacol 625, 101-107.
41. Newman JR, Wolf E, Kim PS (2000). A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae. Proc Natl Acad Sci USA 97, 13203-13208.
42. O'Shea EK, Klemm JD, Kim PS, Alber T (1991). X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254, 539-544. (Pubitemid 21917367)
43. O'Shea EK, Rutkowski R, Kim PS (1992). Mechanism of specificity in the Fos-Jun oncoprotein heterodimer. Cell 68, 699-708.
44. Obuse C, Iwasaki O, Kiyomitsu T, Goshima G, Toyoda Y, Yanagida M (2004). A conserved Mis12 centromere complex is linked to heterochromatic HP1 and outer kinetochore protein Zwint-1. Nat Cell Biol 6, 1135-1141. (Pubitemid 39468016)
45. Parry DA (1982). Coiled-coils in alpha-helix-containing proteins: analysis of the residue types within the heptad repeat and the use of these data in the prediction of coiled-coils in other proteins. Biosci Rep 2, 1017-1024.
46. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL (2002). Hierarchical organization of modularity in metabolic networks. Science 297, 1551-1555. (Pubitemid 34971002)
47. Robson Marsden H, Kros A (2010). Self-assembly of coiled coils in synthetic biology: inspiration and progress. Angew Chem Int Ed Engl 49, 2988-3005.
48. Rose A, Meier I (2004). Scaffolds, levers, rods and springs: diverse cellular functions of long coiled-coil proteins. Cell Mol Life Sci 61, 1996-2009. (Pubitemid 39149890)
49. Schliwa M, Woehlke G (2003). Molecular motors. Nature 422, 759-765. (Pubitemid 36514119)
50. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498-2504. (Pubitemid 37428274)
51. Shekhawat SS, Porter JR, Sriprasad A, Ghosh I (2009). An autoinhibited coiled-coil design strategy for split-protein protease sensors. J Am Chem Soc 131, 15284-15290.
52. Shlizerman C, Atanassov A, Berkovich I, Ashkenasy G, Ashkenasy N (2010). De novo designed coiled-coil proteins with variable conformations as components of molecular electronic devices. J Am Chem Soc 132, 5070-5076.
53. Stiffler MA, Chen JR, Grantcharova VP, Lei Y, Fuchs D, Allen JE, Zaslavskaia LA, MacBeath G (2007). PDZ domain binding selectivity is optimized across the mouse proteome. Science 317, 364-369.
54. Strauss HM, Keller S (2008). Pharmacological interference with protein-protein interactions mediated by coiled-coil motifs. In: Protein-Protein Interactions as New Drug Targets, ed. E Klussmann and J Scott, Handbook of Experimental Pharmacology, Vol. 186, Berlin: Springer, 461-482.
55. Tarassov K, Messier V, Landry CR, Radinovic S, Serna Molina MM, Shames I, Malitskaya Y, Vogel J, Bussey H, Michnick SW (2008). An in vivo map of the yeast protein interactome. Science 320, 1465-1470. (Pubitemid 351929421)
56. Uetz P et al. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627. (Pubitemid 30103994)
57. Ungar D, Hughson FM (2003). SNARE protein structure and function. Annu Rev Cell Dev Biol 19, 493-517. (Pubitemid 37487358)
58. Wang HW, Long S, Ciferri C, Westermann S, Drubin D, Barnes G, Nogales E (2008). Architecture and flexibility of the yeast Ndc80 kinetochore complex. J Mol Biol 383, 894-903.
59. Westermann S, Cheeseman IM, Anderson S, Yates JR, III, Drubin DG, Barnes G (2003). Architecture of the budding yeast kinetochore reveals a conserved molecular core. J Cell Biol 163, 215-222. (Pubitemid 37363122)
60. Westermann S, Drubin DG, Barnes G (2007). Structures and functions of yeast kinetochore complexes. Annu Rev Biochem 76, 563-591.
61. Wild C, Oas T, McDanal C, Bolognesi D, Matthews T (1992). A synthetic peptide inhibitor of human immunodeficiency virus replication: correlation between solution structure and viral inhibition. Proc Natl Acad Sci USA 89, 10537-10541.
62. Wu K, Liu J, Johnson RN, Yang J, Kopecek J (2009). Drug-free macromolecular therapeutics: induction of apoptosis by coiled-coil-mediated cross-linking of antigens on the cell surface. Angew Chem Int Ed Engl 49, 1451-1455.
63. Yu H et al. (2008). High-quality binary protein interaction map of the yeast interactome network. Science 322, 104-110.
64. Zhang H, Chen J, Wang Y, Peng L, Dong X, Lu Y, Keating AE, Jiang T (2009). A computationally guided protein-interaction screen uncovers coiled-coil interactions involved in vesicular trafficking. J Mol Biol 392, 228-241.
65. Zhang H, Siede W (2004). Analysis of the budding yeast Saccharomyces cerevisiae cell cycle by morphological criteria and flow cytometry. Methods Mol Biol 241, 77-91.