Protein-protein interactions in clathrin vesicular assembly: Radial distribution of evolutionary constraints in interfaces

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Gadkari, Rupali A ^a   Srinivasan, Narayanaswamy ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTOR PROTEIN; CLATHRIN; BIOLOGICAL MARKER; VESICULAR TRANSPORT ADAPTOR PROTEIN;

ARTICLE; CELL VACUOLE; COATED VESICLE; CONTROLLED STUDY; COW; CRYOELECTRON MICROSCOPY; EUKARYOTE; GENETIC CONSERVATION; HUMAN; MOUSE; NONHUMAN; PHYLOGENY; PREDICTION; PROTEIN ASSEMBLY; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TRANSPORT; RAT; ANIMAL; CATTLE; CHEMICAL STRUCTURE; CHEMISTRY; ENDOCYTOSIS; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION;

EUKARYOTA;

ADAPTOR PROTEINS, VESICULAR TRANSPORT; ANIMALS; BIOLOGICAL MARKERS; CATTLE; CLATHRIN; CLATHRIN-COATED VESICLES; ENDOCYTOSIS; EVOLUTION, MOLECULAR; HUMANS; MICE; MODELS, MOLECULAR; PHYLOGENY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; RATS;

EID: 84857475182     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031445     Document Type: Article

References (53)

1. Schwartz A, (1990) Cell biology of intracellular protein trafficking. Annu Rev Immunol 8: 195-229.
2. Young A, (2007) Structural insights into the clathrin coat. Semin Cell Dev Biol 18: 448-458.
3. Mills IG, (2007) The interplay between clathrin-coated vesicles and cell signalling. Semin Cell Dev Biol 18: 459-470.
4. Liu Z, Zheng Y, (2009) A requirement for epsin in mitotic membrane and spindle organization. J Cell Biol 186: 473-480.
5. Hölzenspies J, Roelen BA, Colenbrander B, Romijn RA, Hemrika W, et al. (2010) Clathrin is essential for meiotic spindle function in oocytes. Reproduction Jun 3.
6. Roth T, Porter KR, (1964) YOLK PROTEIN UPTAKE IN THE OOCYTE OF THE MOSQUITO AEDES AEGYPTI. L. J Cell Biol 20: 313-332.
7. Pearse BM, (1976) Clathrin: a unique protein associated with intracellular transfer of membrane by coated vesicles. Proc Natl Acad Sci U S A 73: 1255-1259.
8. Keen JH, Willingham MC, Pastan IH, (1979) Clathrin-coated vesicles: isolation, dissociation and factor-dependent reassociation of clathrin baskets. Cell 16: 303-312.
9. Conibear E, (2010) Converging views of endocytosis in yeast and mammals. Curr Opin Cell Biol.
10. Pearse BM, Crowther RA, (1987) Structure and assembly of coated vesicles. Annu Rev Biophys Biophys Chem 16: 49-68.
11. Pearse BM, (1987) Clathrin and coated vesicles. Embo J 6: 2507-2512.
12. Heuser J, (1989) Effects of cytoplasmic acidification on clathrin lattice morphology. J Cell Biol 108: 401-411.
13. Heuser JE, Anderson RG, (1989) Hypertonic media inhibit receptor-mediated endocytosis by blocking clathrin-coated pit formation. J Cell Biol 108: 389-400.
14. Keyel PA, Mishra SK, Roth R, Heuser JE, Watkins SC, et al. (2006) A single common portal for clathrin-mediated endocytosis of distinct cargo governed by cargo-selective adaptors. Mol Biol Cell 17: 4300-4317.
15. Brodsky FM, Chen CY, Knuehl C, Towler MC, Wakeham DE, (2001) Biological basket weaving: formation and function of clathrin-coated vesicles. Annu Rev Cell Dev Biol 17: 517-568.
16. Stagg SM, LaPointe P, Balch WE, (2007) Structural design of cage and coat scaffolds that direct membrane traffic. Curr Opin Struct Biol 17: 221-228.
17. Edeling MA, Smith C, Owen D, (2006) Life of a clathrin coat: insights from clathrin and AP structures. Nat Rev Mol Cell Biol 7: 32-44.
18. Szymkiewicz I, Shupliakov O, Dikic I, (2004) Cargo- and compartment-selective endocytic scaffold proteins. Biochem J 383: 1-11.
19. Lewin DA, Mellman I, (1998) Sorting out adaptors. Biochim Biophys Acta 1401: 129-145.
20. Schmid EM, McMahon HT, (2007) Integrating molecular and network biology to decode endocytosis. Nature 448: 883-888.
21. Heldwein EE, Macia E, Wang J, Yin HL, Kirchhausen T, et al. (2004) Crystal structure of the clathrin adaptor protein 1 core. Proc Natl Acad Sci U S A 101: 14108-14113.
22. Owen DJ, Vallis Y, Pearse BM, McMahon HT, Evans PR, (2000) The structure and function of the beta 2-adaptin appendage domain. Embo J 19: 4216-4227.
23. Owen DJ, Collins BM, Evans PR, (2004) Adaptors for clathrin coats: structure and function. Annu Rev Cell Dev Biol 20: 153-191.
24. Owen DJ, Wigge P, Vallis Y, Moore JD, Evans PR, et al. (1998) Crystal structure of the amphiphysin-2 SH3 domain and its role in the prevention of dynamin ring formation. Embo J 17: 5273-5285.
25. Miele AE, Watson PJ, Evans PR, Traub LM, Owen DJ, (2004) Two distinct interaction motifs in amphiphysin bind two independent sites on the clathrin terminal domain beta-propeller. Nat Struct Mol Biol 11: 242-248.
26. Fotin A, Cheng Y, Sliz P, Grigorieff N, Harrison SC, et al. (2004) Molecular model for a complete clathrin lattice from electron cryomicroscopy. Nature 432: 573-579.
27. Fotin A, Cheng Y, Grigorieff N, Walz T, Harrison SC, et al. (2004) Structure of an auxilin-bound clathrin coat and its implications for the mechanism of uncoating. Nature 432: 649-653.
28. Gadkari RA, Varughese D, Srinivasan N, (2009) Recognition of interaction interface residues in low-resolution structures of protein assemblies solely from the positions of C(alpha) atoms. PLoS ONE 4: e4476.
29. Gadkari RA, Srinivasan N, (2010) Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures. BMC Struct Biol 10: 17.
30. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
31. Hubbard SJ, Thornton JM, (1993) NACCESS, Department of Biochemistry and Molecular Biology, University College, London.
32. Rekha N, Machado SM, Narayanan C, Krupa A, Srinivasan N, (2005) Interaction interfaces of protein domains are not topologically equivalent across families within superfamilies: Implications for metabolic and signaling pathways. Proteins 58: 339-353.
33. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
34. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, et al. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497-3500.
35. Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N, (2005) The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins 58: 610-617.
36. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, et al. (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33: W299-302.
37. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
38. Guindon S, Lethiec F, Duroux P, Gascuel O, (2005) PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33: W557-559.
39. Moeller HB, Knepper MA, Fenton RA, (2008) Serine 269 phosphorylated aquaporin-2 is targeted to the apical membrane of collecting duct principal cells. Kidney Int.
40. Schmidt HA, Strimmer K, Vingron M, von Haeseler A, (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
41. ter Haar E, Musacchio A, Harrison SC, Kirchhausen T, (1998) Atomic structure of clathrin: a beta propeller terminal domain joins an alpha zigzag linker. Cell 95: 563-573.
42. Ybe JA, Brodsky FM, Hofmann K, Lin K, Liu SH, et al. (1999) Clathrin self-assembly is mediated by a tandemly repeated superhelix. Nature 399: 371-375.
43. Collins BM, McCoy AJ, Kent HM, Evans PR, Owen DJ, (2002) Molecular architecture and functional model of the endocytic AP2 complex. Cell 109: 523-535.
44. ter Haar E, Harrison SC, Kirchhausen T, (2000) Peptide-in-groove interactions link target proteins to the beta-propeller of clathrin. Proc Natl Acad Sci U S A 97: 1096-1100.
45. Brett TJ, Traub LM, Fremont DH, (2002) Accessory protein recruitment motifs in clathrin-mediated endocytosis. Structure 10: 797-809.
46. Jackson LP, Kelly BT, McCoy AJ, Gaffry T, James LC, et al. (2010) A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex. Cell 141: 1220-1229.
47. Schmid EM, Ford MG, Burtey A, Praefcke GJ, Peak-Chew SY, et al. (2006) Role of the AP2 beta-appendage hub in recruiting partners for clathrin-coated vesicle assembly. PLoS Biol 4: e262.
48. Bonazzi M, Vasudevan L, Mallet A, Sachse M, Sartori A, et al. (2011) Clathrin phosphorylation is required for actin recruitment at sites of bacterial adhesion and internalization. J Cell Biol 195: 525-536.
49. Saffarian S, Kirchhausen T, (2008) Differential evanescence nanometry: live-cell fluorescence measurements with 10-nm axial resolution on the plasma membrane. Biophys J 94: 2333-2342.
50. Saffarian S, Cocucci E, Kirchhausen T, (2009) Distinct dynamics of endocytic clathrin-coated pits and coated plaques. PLoS Biol 7: e1000191.
51. Boucrot E, Saffarian S, Zhang R, Kirchhausen T, (2010) Roles of AP-2 in clathrin-mediated endocytosis. PLoS One 5: e10597.
52. Schmid SL, (1997) Clathrin-coated vesicle formation and protein sorting: an integrated process. Annu Rev Biochem 66: 511-548.
53. DeLlano W, (2002) The PyMOL molecular graphics system (http://www.pymol.org/).