Integrating molecular and network biology to decode endocytosis (original) (raw)

• Kirchhausen, T. Clathrin. Annu. Rev. Biochem. 69, 699–727 (2000)
  Article CAS Google Scholar
• Marsh, M. & McMahon, H. T. The structural era of endocytosis. Science 285, 215–220 (1999)
  Article CAS Google Scholar
• Perry, M. M. & Gilbert, A. B. Yolk transport in the ovarian follicle of the hen (Gallus domesticus): lipoprotein-like particles at the periphery of the oocyte in the rapid growth phase. J. Cell Sci. 39, 257–272 (1979)
  CAS PubMed Google Scholar
• Marsh, M. & Helenius, A. Virus entry: open sesame. Cell 124, 729–740 (2006)
  Article CAS Google Scholar
• Brodin, L., Low, P. & Shupliakov, O. Sequential steps in clathrin-mediated synaptic vesicle endocytosis. Curr. Opin. Neurobiol. 10, 312–320 (2000)
  Article CAS Google Scholar
• Schmid, E. M. et al. Role of the AP2 β-appendage hub in recruiting partners for CCV assembly. PLoS Biol. 4, e262 (2006)
  Article Google Scholar
• Owen, D. J. et al. A structural explanation for the binding of multiple ligands by the α-adaptin appendage domain. Cell 97, 805–815 (1999)
  Article CAS Google Scholar
• Owen, D. J., Vallis, Y., Pearse, B. M., McMahon, H. T. & Evans, P. R. The structure and function of the β2-adaptin appendage domain. EMBO J. 19, 4216–4227 (2000)
  Article CAS Google Scholar
• Blondeau, F. et al. Tandem MS analysis of brain CCVs reveals their critical involvement in synaptic vesicle recycling. Proc. Natl Acad. Sci. USA 101, 3833–3838 (2004)
  Article ADS CAS Google Scholar
• Praefcke, G. J. et al. Evolving nature of the AP2 α-appendage hub during CCV endocytosis. EMBO J. 23, 4371–4383 (2004)
  Article CAS Google Scholar
• Mishra, S. K. et al. Dual engagement regulation of protein interactions with the AP-2 adaptor α appendage. J. Biol. Chem. 279, 46191–46203 (2004)
  Article CAS Google Scholar
• Edeling, M. A. et al. Molecular switches involving the AP-2 β2 appendage regulate endocytic cargo selection and clathrin coat assembly. Dev. Cell 10, 329–342 (2006)
  Article CAS Google Scholar
• Barabasi, A. L. & Oltvai, Z. N. Network biology: understanding the cell's functional organization. Nature Rev. Genet. 5, 101–113 (2004)
  Article CAS Google Scholar
• Alon, U. Biological networks: the tinkerer as an engineer. Science 301, 1866–1867 (2003)
  Article ADS CAS Google Scholar
• Albert, R. Scale-free networks in cell biology. J. Cell Sci. 118, 4947–4957 (2005)
  Article CAS Google Scholar
• Gavin, A. C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636 (2006)
  Article ADS CAS Google Scholar
• Hartwell, L. H., Hopfield, J. J., Leibler, S. & Murray, A. W. From molecular to modular cell biology. Nature 402, (suppl.)C47–C52 (1999)
  Article CAS Google Scholar
• Yarar, D., Waterman-Storer, C. M. & Schmid, S. L. A dynamic actin cytoskeleton functions at multiple stages of clathrin-mediated endocytosis. Mol. Biol. Cell 16, 964–975 (2005)
  Article CAS Google Scholar
• Merrifield, C. J., Feldman, M. E., Wan, L. & Almers, W. Imaging actin and dynamin recruitment during invagination of single clathrin-coated pits. Nature Cell Biol. 4, 691–698 (2002)
  Article CAS Google Scholar
• Kaksonen, M., Toret, C. P. & Drubin, D. G. A modular design for the clathrin- and actin-mediated endocytosis machinery. Cell 123, 305–320 (2005)
  Article CAS Google Scholar
• Ekman, D., Light, S., Bjorklund, A. K. & Elofsson, A. What properties characterize the hub proteins of the protein–protein interaction network of Saccharomyces cerevisiae?. Genome Biol. 7, R45 (2006)
  Article Google Scholar
• Han, J. D. et al. Evidence for dynamically organized modularity in the yeast protein–protein interaction network. Nature 430, 88–93 (2004)
  Article ADS CAS Google Scholar
• McMahon, H. T. & Mills, I. G. COP and CCV budding: different pathways, common approaches. Curr. Opin. Cell Biol. 16, 379–391 (2004)
  Article CAS Google Scholar
• Brett, T. J. & Traub, L. M. Molecular structures of coat and coat-associated proteins: function follows form. Curr. Opin. Cell Biol. 18, 395–406 (2006)
  Article CAS Google Scholar
• Niethammer, P. et al. Discrete states of a protein interaction network govern interphase and mitotic microtubule dynamics. PLoS Biol. 5, e29 (2007)
  Article Google Scholar
• Slepnev, V. I. & De Camilli, P. Accessory factors in clathrin-dependent synaptic vesicle endocytosis. Nature Rev. Neurosci. 1, 161–172 (2000)
  Article CAS Google Scholar
• Honing, S. et al. Phosphatidylinositol-(4,5)-bisphosphate regulates sorting signal recognition by the clathrin-associated adaptor complex AP2. Mol. Cell 18, 519–531 (2005)
  Article Google Scholar
• Jeong, H., Mason, S. P., Barabasi, A. L. & Oltvai, Z. N. Lethality and centrality in protein networks. Nature 411, 41–42 (2001)
  Article ADS CAS Google Scholar
• Motley, A., Bright, N. A., Seaman, M. N. & Robinson, M. S. Clathrin-mediated endocytosis in AP-2-depleted cells. J. Cell Biol. 162, 909–918 (2003)
  Article CAS Google Scholar
• Kruchten, A. E. & McNiven, M. A. Dynamin as a mover and pincher during cell migration and invasion. J. Cell Sci. 119, 1683–1690 (2006)
  Article CAS Google Scholar
• Wienke, D. C., Knetsch, M. L., Neuhaus, E. M., Reedy, M. C. & Manstein, D. J. Disruption of a dynamin homologue affects endocytosis, organelle morphology, and cytokinesis in Dictyostelium discoideum. Mol. Biol. Cell 10, 225–243 (1999)
  Article CAS Google Scholar
• Praefcke, G. J. & McMahon, H. T. The dynamin superfamily: universal membrane tubulation and fission molecules? Nature Rev. Mol. Cell Biol. 5, 133–147 (2004)
  Article CAS Google Scholar
• Hinrichsen, L., Harborth, J., Andrees, L., Weber, K. & Ungewickell, E. J. Effect of clathrin heavy chain- and α-adaptin-specific small inhibitory RNAs on endocytic accessory proteins and receptor trafficking in HeLa cells. J. Biol. Chem. 278, 45160–45170 (2003)
  Article CAS Google Scholar
• Maslov, S. & Sneppen, K. Specificity and stability in topology of protein networks. Science 296, 910–913 (2002)
  Article ADS CAS Google Scholar
• Shenoy, S. K. & Lefkowitz, R. J. Seven-transmembrane receptor signaling through β-arrestin. Sci. STKE 2005, cm10 (2005)
  PubMed Google Scholar
• Puthenveedu, M. A. & von Zastrow, M. Cargo regulates clathrin-coated pit dynamics. Cell 127, 113–124 (2006)
  Article CAS Google Scholar
• Marks, B. & McMahon, H. T. Calcium triggers calcineurin-dependent synaptic vesicle recycling in mammalian nerve terminals. Curr. Biol. 8, 740–749 (1998)
  Article CAS Google Scholar
• Slepnev, V. I., Ochoa, G. C., Butler, M. H., Grabs, D. & De Camilli, P. Role of phosphorylation in regulation of the assembly of endocytic coat complexes. Science 281, 821–824 (1998)
  Article ADS CAS Google Scholar
• Prachumwat, A. & Li, W. H. Protein function, connectivity, and duplicability in yeast. Mol. Biol. Evol. 23, 30–39 (2006)
  Article CAS Google Scholar
• Mills, I. G. et al. EpsinR: an AP1/clathrin interacting protein involved in vesicle trafficking. J. Cell Biol. 160, 213–222 (2003)
  Article Google Scholar
• Schubert, W. et al. Analyzing proteome topology and function by automated multidimensional fluorescence microscopy. Nature Biotechnol. 24, 1270–1278 (2006)
  Article CAS Google Scholar
• Smith, C. J., Grigorieff, N. & Pearse, B. M. Clathrin coats at 21 Å resolution: a cellular assembly designed to recycle multiple membrane receptors. EMBO J. 17, 4943–4953 (1998)
  Article CAS Google Scholar