The molecular sociology of the cell (original) (raw)

• Blundell, T. L. & Johnson, L. Protein Crystallography (Academic, New York, 1976).
  Google Scholar
• Wimberley, B. T. et al. Structure of the 30S ribosomal subunit. Nature 407, 327–339 (2000).
  Article ADS Google Scholar
• Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. The complete atomic structure of the large ribosomal subunit at 2.4 Å. Science 289, 905–920 (2000).
  CAS PubMed ADS Google Scholar
• Schluenzen, F. et al. Structure of functionally activated small ribosomal subunit at 3.3 Å resolution. Cell 102, 615–623 (2000).
  Article CAS PubMed Google Scholar
• Malhotra, A. & Harvey, S. C. A quantitative model of the Escherichia coli 16S RNA in the 30S ribosomal subunit. J. Mol. Biol. 240, 308–340 (1994).
  Article CAS PubMed Google Scholar
• Alber, F., Kim, M. F. & Sali, A. Structural characterization of assemblies from overall shape and subcomplex compositions. Structure 13, 435–445 (2005).
  Article CAS PubMed Google Scholar
• Alber, F. et al. Determining the architectures of macromolecular assemblies. Nature 450, 683–694 (2007).
  Article CAS PubMed ADS Google Scholar
• Sali, A., Glaeser, R., Earnest, T. & Baumeister, W. From words to literature in structural proteomics. Nature 422, 216–225 (2003).
  Article CAS PubMed ADS Google Scholar
• Hernandez, H., Dziembowski, A., Taverner, T., Seraphin, B. & Robinson, C. V. Subunit architecture of multimeric complexes isolated directly from cells. EMBO Rep. 7, 605–610 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Davis, F. P. et al. Protein complex compositions predicted by structural similarity. Nucleic Acids Res. 34, 2943–2952 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• van Dijk, A. D. et al. Modeling protein–protein complexes involved in the cytochrome c oxidase copper-delivery pathway. J. Proteome Res. 6, 1530–1539 (2007).
  Article CAS PubMed Google Scholar
• Todd, A. E., Marsden, R. L., Thornton, J. M. & Orengo, C. A. Progress of structural genomics initiatives: an analysis of solved target structures. J. Mol. Biol. 348, 1235–1260 (2005).
  Article CAS PubMed Google Scholar
• Alber, F., Eswar, N. & Sali, A. in Practical Bioinformatics 1950–1954 (Springer, Heidelberg, 2004).
  Google Scholar
• Sivasubramanian, A., Chao, G., Pressler, H. M., Wittrup, K. D. & Gray, J. J. Structural model of the mAb 806–EGFR complex using computational docking followed by computational and experimental mutagenesis. Structure 14, 401–414 (2006).
  Article CAS PubMed Google Scholar
• Rossmann, M. G., Morais, M. C., Leiman, P. G. & Zhang, W. Combining X-ray crystallography and electron microscopy. Structure 13, 355–362 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Fotin, A. et al. Structure of an auxilin-bound clathrin coat and its implications for the mechanism of uncoating. Nature 432, 649–653 (2004).
  Article CAS PubMed ADS Google Scholar
• Mitchell, P., Petfalski, E., Shevchenko, A., Mann, M. & Tollervey, D. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3′→5′ exoribonucleases. Cell 91, 457–466 (1997).
  Article CAS PubMed Google Scholar
• Baumeister, W., Walz, J., Zuhl, F. & Seemuller, E. The proteasome: paradigm of a self-compartmentalizing protease. Cell 92, 367–380 (1998).
  Article CAS PubMed Google Scholar
• Lim, R. Y. & Fahrenkrog, B. The nuclear pore complex up close. Curr. Opin. Cell Biol. 18, 342–347 (2006).
  Article CAS PubMed Google Scholar
• Beck, M., Lucic, V., Forster, F., Baumeister, W. & Medalia, O. Snapshots of nuclear pore complexes in action captured by cryo-electron tomography. Nature 449, 611–615 (2007).
  Article CAS PubMed ADS Google Scholar
• Alber, F. et al. The molecular architecture of the nuclear pore complex. Nature 450, 695–701 (2007).
  Article CAS PubMed ADS Google Scholar
• Meinhart, A. & Cramer, P. Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors. Nature 430, 223–226 (2004).
  Article CAS PubMed ADS Google Scholar
• Liu, Q., Greimann, J. C. & Lima, C. D. Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 127, 1223–1237 (2006).
  Article CAS PubMed Google Scholar
• Egea, P. F. et al. Substrate twinning activates the signal recognition particle and its receptor. Nature 427, 215–221 (2004).
  Article CAS PubMed ADS Google Scholar
• Bonvin, A. M., Boelens, R. & Kaptein, R. NMR analysis of protein interactions. Curr. Opin. Chem. Biol. 9, 501–508 (2005).
  Article CAS PubMed Google Scholar
• Zuiderweg, E. R. Mapping protein–protein interactions in solution by NMR spectroscopy. Biochemistry 41, 1–7 (2002).
  Article CAS PubMed Google Scholar
• McCoy, M. A. & Wyss, D. F. Structures of protein–protein complexes are docked using only NMR restraints from residual dipolar coupling and chemical shift perturbations. J. Am. Chem. Soc. 124, 2104–2105 (2002).
  Article CAS PubMed Google Scholar
• Wuthrich, K. The way to NMR structures of proteins. Nature Struct. Biol. 8, 923–925 (2001).
  Article CAS PubMed Google Scholar
• Rieping, W., Habeck, M. & Nilges, M. Inferential structure determination. Science 309, 303–306 (2005).
  Article CAS PubMed ADS Google Scholar
• Vachette, P., Koch, M. H. & Svergun, D. I. Looking behind the beamstop: X-ray solution scattering studies of structure and conformational changes of biological macromolecules. Methods Enzymol. 374, 584–615 (2003).
  Article CAS PubMed Google Scholar
• Nagar, B. & Kuriyan, J. SAXS and the working protein. Structure 13, 169–170 (2005).
  Article CAS PubMed Google Scholar
• Tidow, H. et al. Quaternary structures of tumor suppressor p53 and a specific p53 DNA complex. Proc. Natl Acad. Sci. USA 104, 12324–12329 (2007).
  Article CAS PubMed ADS PubMed Central Google Scholar
• Grishaev, A., Wu, J., Trewhella, J. & Bax, A. Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data. J. Am. Chem. Soc. 127, 16621–16628 (2005).
  Article CAS PubMed Google Scholar
• Rosenberg, O. S., Deindl, S., Sung, R. J., Nairn, A. C. & Kuriyan, J. Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme. Cell 123, 849–860 (2005).
  Article CAS PubMed Google Scholar
• Sondermann, H., Nagar, B., Bar-Sagi, D. & Kuriyan, J. Computational docking and solution X-ray scattering predict a membrane-interacting role for the histone domain of the Ras activator son of sevenless. Proc. Natl Acad. Sci. USA 102, 16632–16637 (2005).
  Article CAS PubMed ADS PubMed Central Google Scholar
• Yamagata, A. & Tainer, J. A. Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism. EMBO J. 26, 878–890 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Hainfeld, J. F. & Powell, R. D. New frontiers in gold labeling. J. Histochem. Cytochem. 48, 471–480 (2000).
  Article CAS PubMed Google Scholar
• Pye, V. E. et al. Structural insights into the p97–Ufd1–Npl4 complex. Proc. Natl Acad. Sci. USA 104, 467–472 (2007).
  Article CAS PubMed ADS PubMed Central Google Scholar
• Guan, J. Q., Almo, S. C., Reisler, E. & Chance, M. R. Structural reorganization of proteins revealed by radiolysis and mass spectrometry: G-actin solution structure is divalent cation dependent. Biochemistry 42, 11992–12000 (2003).
  Article CAS PubMed Google Scholar
• Anand, G. S. et al. Identification of the protein kinase A regulatory RIα-catalytic subunit interface by amide H/2H exchange and protein docking. Proc. Natl Acad. Sci. USA 100, 13264–13269 (2003).
  Article CAS PubMed ADS PubMed Central Google Scholar
• Lee, T. et al. Docking motif interactions in MAP kinases revealed by hydrogen exchange mass spectrometry. Mol. Cell 14, 43–55 (2004).
  Article CAS PubMed Google Scholar
• Yan, Y. & Marriott, G. Analysis of protein interactions using fluorescence technologies. Curr. Opin. Chem. Biol. 7, 635–640 (2003).
  Article CAS PubMed Google Scholar
• Muller, E. G. et al. The organization of the core proteins of the yeast spindle pole body. Mol. Biol. Cell 16, 3341–3352 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Gavin, A. C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636 (2006).
  Article CAS PubMed ADS Google Scholar
• Sharon, M., Taverner, T., Ambroggio, X. I., Deshaies, R. J. & Robinson, C. V. Structural organization of the 19S proteasome lid: insights from MS of intact complexes. PLoS Biol. 4, e267 (2006).
  Article PubMed PubMed Central CAS Google Scholar
• Parrish, J. R., Gulyas, K. D. & Finley, R. L. Yeast two-hybrid contributions to interactome mapping. Curr. Opin. Biotechnol. 17, 387–393 (2006).
  Article CAS PubMed Google Scholar
• Uetz, P. et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae . Nature 403, 623–627 (2000).
  Article CAS PubMed ADS Google Scholar
• Michnick, S. W., Ear, P. H., Manderson, E. N., Remy, I. & Stefan, E. Universal strategies in research and drug discovery based on protein-fragment complementation assays. Nature Rev. Drug Discov. 6, 569–582 (2007).
  Article CAS Google Scholar
• Landgraf, C. et al. Protein interaction networks by proteome peptide scanning. PLoS Biol. 2, e14 (2004).
  Article PubMed PubMed Central Google Scholar
• MacBeath, G. & Schreiber, S. L. Printing proteins as microarrays for high-throughput function determination. Science 289, 1760–1763 (2000).
  Article CAS PubMed ADS Google Scholar
• Piehler, J. New methodologies for measuring protein interactions in vivo and in vitro . Curr. Opin. Struct. Biol. 15, 4–14 (2005).
  Article CAS PubMed Google Scholar
• Collins, S. R. et al. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446, 806–810 (2007).
  Article CAS PubMed ADS Google Scholar
• Krogan, N. J., Cagney, G., Haiyuan, Y., Zhong, G. & Guo, X. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae . Nature 440, 637–643 (2006).
  Article CAS PubMed ADS Google Scholar
• Collins, S. R. et al. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae . Mol. Cell. Proteomics 6, 439–450 (2007).
  Article CAS PubMed Google Scholar
• Bauer, A. & Kuster, B. Affinity purification — mass spectrometry. Powerful tools for the characterization of protein complexes. Eur. J. Biochem. 270, 570–578 (2003).
  Article CAS PubMed Google Scholar
• Rappas, M. et al. Structural insights into the activity of enhancer-binding proteins. Science 307, 1972–1975 (2005).
  Article CAS PubMed PubMed Central ADS Google Scholar
• Poliakov, A. et al. Macromolecular mass spectrometry and electron microscopy as complementary tools for investigation of the heterogeneity of bacteriophage portal assemblies. J. Struct. Biol. 157, 371–383 (2007).
  Article CAS PubMed Google Scholar
• Hernandez, H. & Robinson, C. V. Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry. Nature Protoc. 2, 715–726 (2007).
  Article CAS Google Scholar
• Lorentzen, E. et al. The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nature Struct. Mol. Biol. 12, 575–581 (2005).
  Article CAS ADS Google Scholar
• Buttner, K., Wenig, K. & Hopfner, K. P. Structural framework for the mechanism of archaeal exosomes in RNA processing. Mol. Cell 20, 461–471 (2005).
  Article PubMed CAS Google Scholar
• Aloy, P. et al. Structure-based assembly of protein complexes in yeast. Science 303, 2026–2029 (2004).
  Article CAS PubMed ADS Google Scholar
• Voges, D., Zwickl, P. & Baumeister, W. The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu. Rev. Biochem. 68, 1015–1068 (1999).
  Article CAS PubMed Google Scholar
• Groll, M. et al. Structure of 20S proteasome from yeast at 2.4 Å resolution. Nature 386, 463–471 (1997).
  Article CAS PubMed ADS Google Scholar
• Sprangers, R. & Kay, L. E. Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature 445, 618–622 (2007).
  Article CAS PubMed Google Scholar
• Hanna, J. & Finley, D. A proteasome for all occasions. FEBS Lett. 581, 2854–2861 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Scheres, S. H. W. et al. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nature Methods 4, 27–29 (2007).
  Article CAS PubMed Google Scholar
• Nickell, S. et al. Automated cryoelectron microscopy of 'single particles' applied to the 26S proteasome. FEBS Lett. 581, 2751–2756 (2007).
  Article CAS PubMed Google Scholar
• Davy, A. et al. A protein–protein interaction map of the Caenorhabditis elegans 26S proteasome. EMBO Rep. 2, 821–828 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Ferrell, K., Wilkinson, C. R., Dubiel, W. & Gordon, C. Regulatory subunit interactions of the 26S proteasome, a complex problem. Trends Biochem. Sci. 25, 83–88 (2000).
  Article CAS PubMed Google Scholar
• Hinshaw, J. E., Carragher, B. O. & Milligan, R. A. Architecture and design of the nuclear pore complex. Cell 69, 1133–1141 (1992).
  Article CAS PubMed Google Scholar
• Rout, M. P. et al. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148, 635–651 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Devos, D. et al. Simple fold composition and modular architecture of the nuclear pore complex. Proc. Natl Acad. Sci. USA 103, 2172–2177 (2006).
  Article CAS PubMed ADS PubMed Central Google Scholar
• Koster, A. J. et al. Perspectives of molecular and cellular electron tomography. J. Struct. Biol. 120, 276–308 (1997).
  Article CAS PubMed Google Scholar
• Nickell, S., Kofler, C., Leis, A. P. & Baumeister, W. A visual approach to proteomics. Nature Rev. Mol. Cell. Biol. 7, 225–230 (2006).
  Article CAS Google Scholar
• Baumeister, W. From proteomic inventory to architecture. FEBS Lett. 579, 933–937 (2005).
  Article CAS PubMed Google Scholar
• Benesch, J. L., Ruotolo, B. T., Simmons, D. A. & Robinson, C. V. Protein complexes in the gas phase: technology for structural genomics and proteomics. Chem. Rev. 107, 3544–3567 (2007).
  Article CAS PubMed Google Scholar
• Lowe, J. et al. Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Å resolution. Science 268, 533–539 (1995).
  Article CAS PubMed ADS Google Scholar
• Unno, M. et al. The structure of the mammalian 20S proteasome at 2.75 Å resolution. Structure 10, 609–618 (2002).
  Article CAS PubMed Google Scholar
• Kwon, Y. D., Nagy, I., Adams, P. D., Baumeister, W. & Jap, B. K. Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly. J. Mol. Biol. 335, 233–245 (2004).
  Article CAS PubMed Google Scholar
• Ortiz, J. O., Forster, F., Kurner, J., Linaroudis, A. A. & Baumeister, W. Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition. J. Struct. Biol. 156, 334–341 (2006).
  Article CAS PubMed Google Scholar
• Gabashvili, I. S. et al. Solution structure of the E. coli 70S ribosome at 11.5 Å resolution. Cell 100, 537–549 (2000).
  Article CAS PubMed Google Scholar
• Sharon, M. & Robinson, C. V. The role of mass spectrometry in structure elucidation of dynamic protein complexes. Annu. Rev. Biochem. 76, 167–193 (2007).
  Article CAS PubMed Google Scholar
• Ilag, L. L. et al. Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem MS of intact ribosomes from thermophilic bacteria. Proc. Natl Acad Sci. USA 102, 8192–8197 (2005).
  Article CAS PubMed ADS PubMed Central Google Scholar
• Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003).
  Article CAS PubMed ADS Google Scholar
• Synowsky, S. A., van den Heuvel, R. H., Mohammed, S., Pijnappel, P. W. & Heck, A. J. Probing genuine strong interactions and post-translational modifications in the heterogeneous yeast exosome protein complex. Mol. Cell. Proteomics 5, 1581–1592 (2006).
  Article CAS PubMed Google Scholar
• Back, J. W., de Jong, L., Muijsers, A. O. & de Koster, C. G. Chemical cross-linking and mass spectrometry for protein structural modeling. J. Mol. Biol. 331, 303–313 (2003).
  Article CAS PubMed Google Scholar
• Vasilescu, J. & Figeys, D. Mapping protein–protein interactions by mass spectrometry. Curr. Opin. Biotechnol. 17, 394–399 (2006).
  Article CAS PubMed Google Scholar
• von Helden, G., Wyttenbach, T. & Bowers, M. T. Conformation of macromolecules in the gas phase: use of matrix-assisted laser desorption methods in ion chromatography. Science 267, 1483–1485 (1995).
  Article CAS PubMed ADS Google Scholar
• Ruotolo, B. T. et al. Evidence for macromolecular protein rings in the absence of bulk water. Science 310, 1658–1661 (2005).
  Article CAS PubMed ADS Google Scholar
• Ruotolo, B. T. et al. Ion mobility–mass spectrometry reveals long-lived, unfolded intermediates in the dissociation of protein complexes. Angew. Chem. Int. Ed. Engl. 46, 8001–8004 (2007).
  Article CAS PubMed Google Scholar
• Henderson, R. Realizing the potential of electron cryo-microscopy. Q. Rev. Biophys. 37, 3–13 (2004).
  Article CAS PubMed Google Scholar
• Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41–60 (2005).
  Article CAS PubMed Google Scholar
• Johnson, J. E. & Chiu, W. DNA packaging and delivery machines in tailed bacteriophages. Curr. Opin. Struct. Biol. 17, 237–243 (2007).
  Article CAS PubMed Google Scholar
• Taylor, D. J. et al. Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation. EMBO J. 26, 2421–2431 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Vaughan, C. K. et al. Structure of an Hsp90–Cdc37–Cdk4 complex. Mol. Cell 23, 697–707 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Woodhead, J. L. et al. Atomic model of a myosin filament in the relaxed state. Nature 436, 1195–1199 (2005).
  Article CAS PubMed ADS Google Scholar
• Wang, H. W. & Nogales, E. Nucleotide-dependent bending flexibility of tubulin regulates microtubule assembly. Nature 435, 911–915 (2005).
  Article CAS PubMed PubMed Central ADS Google Scholar
• Stark, H. & Luhrmann, R. Cryo-electron microscopy of spliceosomal components. Annu. Rev. Biophys. Biomol. Struct. 35, 435–457 (2006).
  Article CAS PubMed Google Scholar
• Fath, S., Mancias, J. D., Bi, X. & Goldberg, J. Structure and organization of coat proteins in the COPII cage. Cell 129, 1325–1336 (2007).
  Article CAS PubMed Google Scholar
• Mitra, K. & Frank, J. Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annu. Rev. Biophys. Biomol. Struct. 35, 299–317 (2006).
  Article CAS PubMed Google Scholar