메뉴 건너뛰기




Volumn 9, Issue 8, 2010, Pages 1689-1702

Integrative structure modeling of macromolecular assemblies from proteomics data

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE II; MULTIPROTEIN COMPLEX;

EID: 77955388349     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.R110.000067     Document Type: Review
Times cited : (63)

References (149)
  • 1
    • 0032489015 scopus 로고    scopus 로고
    • The cell as a collection of protein machines: Preparing the next generation of molecular biologists
    • Alberts, B. (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291-294
    • (1998) Cell , vol.92 , pp. 291-294
    • Alberts, B.1
  • 2
    • 0037182924 scopus 로고    scopus 로고
    • Proteomics: The society of proteins
    • Abbott, A. (2002) Proteomics: the society of proteins. Nature 417, 894-896
    • (2002) Nature , vol.417 , pp. 894-896
    • Abbott, A.1
  • 3
    • 70350654363 scopus 로고    scopus 로고
    • What recent ribosome structures have revealed about the mechanism of translation
    • Schmeing, T. M., and Ramakrishnan, V. (2009) What recent ribosome structures have revealed about the mechanism of translation. Nature 461, 1234-1242
    • (2009) Nature , vol.461 , pp. 1234-1242
    • Schmeing, T.M.1    Ramakrishnan, V.2
  • 4
    • 33846625924 scopus 로고    scopus 로고
    • Structural insights on the translation initiation complex: Ghosts of a universal initiation complex
    • Allen, G. S., and Frank, J. (2007) Structural insights on the translation initiation complex: ghosts of a universal initiation complex. Mol. Microbiol. 63, 941-950
    • (2007) Mol. Microbiol. , vol.63 , pp. 941-950
    • Allen, G.S.1    Frank, J.2
  • 5
    • 70350020881 scopus 로고    scopus 로고
    • Chaperonin-mediated protein folding: Using a central cavity to kinetically assist polypeptide chain folding
    • Horwich, A. L., and Fenton, W. A. (2009) Chaperonin-mediated protein folding: using a central cavity to kinetically assist polypeptide chain folding. Q. Rev. Biophys. 42, 83-116
    • (2009) Q. Rev. Biophys. , vol.42 , pp. 83-116
    • Horwich, A.L.1    Fenton, W.A.2
  • 6
    • 7444231693 scopus 로고    scopus 로고
    • Mechanism of the eukaryotic chaperonin: Protein folding in the chamber of secrets
    • Spiess, C., Meyer, A. S., Reissmann, S., and Frydman, J. (2004) Mechanism of the eukaryotic chaperonin: protein folding in the chamber of secrets. Trends Cell Biol. 14, 598-604
    • (2004) Trends Cell Biol. , vol.14 , pp. 598-604
    • Spiess, C.1    Meyer, A.S.2    Reissmann, S.3    Frydman, J.4
  • 8
    • 64549115746 scopus 로고    scopus 로고
    • Toward an atomic model of the 26S proteasome
    • Cheng, Y. (2009) Toward an atomic model of the 26S proteasome. Curr. Opin. Struct. Biol. 19, 203-208
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 203-208
    • Cheng, Y.1
  • 12
    • 33646495214 scopus 로고    scopus 로고
    • Ribosome dynamics: Insights from atomic structure modeling into cryo-electron microscopy maps
    • Mitra, K., and Frank, J. (2006) Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annu. Rev. Biophys. Biomol. Struct. 35, 299-317
    • (2006) Annu. Rev. Biophys. Biomol. Struct. , vol.35 , pp. 299-317
    • Mitra, K.1    Frank, J.2
  • 14
    • 37249065351 scopus 로고    scopus 로고
    • The molecular sociology of the cell
    • Robinson, C. V., Sali, A., and Baumeister, W. (2007) The molecular sociology of the cell. Nature 450, 973-982
    • (2007) Nature , vol.450 , pp. 973-982
    • Robinson, C.V.1    Sali, A.2    Baumeister, W.3
  • 18
    • 66149129565 scopus 로고    scopus 로고
    • Relaxation dispersion NMR spectroscopy as a tool for detailed studies of protein folding
    • Neudecker, P., Lundström, P., and Kay, L. E. (2009) Relaxation dispersion NMR spectroscopy as a tool for detailed studies of protein folding. Biophys. J. 96, 2045-2054
    • (2009) Biophys. J. , vol.96 , pp. 2045-2054
    • Neudecker, P.1    Lundström, P.2    Kay, L.E.3
  • 19
    • 44649130753 scopus 로고    scopus 로고
    • Molecular electron microscopy: State of the art and current challenges
    • Stahlberg, H., and Walz, T. (2008) Molecular electron microscopy: state of the art and current challenges. ACS Chem. Biol. 3, 268-281
    • (2008) ACS Chem. Biol. , vol.3 , pp. 268-281
    • Stahlberg, H.1    Walz, T.2
  • 20
    • 14844325731 scopus 로고    scopus 로고
    • Electron cryomicroscopy of biological machines at subnanometer resolution
    • DOI 10.1016/j.str.2004.12.016
    • Chiu, W., Baker, M. L., Jiang, W., Dougherty, M., and Schmid, M. F. (2005) Electron cryomicroscopy of biological machines at subnanometer resolution. Structure 13, 363-372 (Pubitemid 40342875)
    • (2005) Structure , vol.13 , Issue.3 , pp. 363-372
    • Chiu, W.1    Baker, M.L.2    Jiang, W.3    Dougherty, M.4    Schmid, M.F.5
  • 21
    • 48749089692 scopus 로고    scopus 로고
    • Cryo-electron tomography of cells: Connecting structure and function
    • Lucic, V., Leis, A., and Baumeister, W. (2008) Cryo-electron tomography of cells: connecting structure and function. Histochem. Cell Biol. 130, 185-196
    • (2008) Histochem. Cell Biol. , vol.130 , pp. 185-196
    • Lucic, V.1    Leis, A.2    Baumeister, W.3
  • 23
    • 34548418142 scopus 로고    scopus 로고
    • Methods for the detection and analysis of protein-protein interactions
    • Berggård, T., Linse, S., and James, P. (2007) Methods for the detection and analysis of protein-protein interactions. Proteomics 7, 2833-2842
    • (2007) Proteomics , vol.7 , pp. 2833-2842
    • Berggård, T.1    Linse, S.2    James, P.3
  • 24
    • 0035010533 scopus 로고    scopus 로고
    • Determination of domain structure of proteins from X-ray solution scattering
    • Svergun, D. I., Petoukhov, M. V., and Koch, M. H. (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys. J. 80, 2946-2953
    • (2001) Biophys. J. , vol.80 , pp. 2946-2953
    • Svergun, D.I.1    Petoukhov, M.V.2    Koch, M.H.3
  • 26
    • 50649121477 scopus 로고    scopus 로고
    • Advances in single-molecule fluorescence methods for molecular biology
    • Joo, C., Balci, H., Ishitsuka, Y., Buranachai, C., and Ha, T. (2008) Advances in single-molecule fluorescence methods for molecular biology. Annu. Rev. Biochem. 77, 51-76
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 51-76
    • Joo, C.1    Balci, H.2    Ishitsuka, Y.3    Buranachai, C.4    Ha, T.5
  • 27
    • 33847744247 scopus 로고    scopus 로고
    • How complete are current yeast and human protein-interaction networks?
    • Hart, G. T., Ramani, A. K., and Marcotte, E. M. (2006) How complete are current yeast and human protein-interaction networks? Genome Biol. 7, 120
    • (2006) Genome Biol. , vol.7 , pp. 120
    • Hart, G.T.1    Ramani, A.K.2    Marcotte, E.M.3
  • 30
    • 38949092920 scopus 로고    scopus 로고
    • Protein structure fitting and refinement guided by cryo-EM density
    • Topf, M., Lasker, K., Webb, B., Wolfson, H., Chiu, W., and Sali, A. (2008) Protein structure fitting and refinement guided by cryo-EM density. Structure 16, 295-307
    • (2008) Structure , vol.16 , pp. 295-307
    • Topf, M.1    Lasker, K.2    Webb, B.3    Wolfson, H.4    Chiu, W.5    Sali, A.6
  • 31
    • 33645075435 scopus 로고    scopus 로고
    • Refinement of protein structures by iterative comparative modeling and CryoEM density fitting
    • Topf, M., Baker, M. L., Marti-Renom, M. A., Chiu, W., and Sali, A. (2006) Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J. Mol. Biol. 357, 1655-1668
    • (2006) J. Mol. Biol. , vol.357 , pp. 1655-1668
    • Topf, M.1    Baker, M.L.2    Marti-Renom, M.A.3    Chiu, W.4    Sali, A.5
  • 32
    • 63449125993 scopus 로고    scopus 로고
    • Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly
    • Lasker, K., Topf, M., Sali, A., and Wolfson, H. J. (2009) Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly. J. Mol. Biol. 388, 180-194
    • (2009) J. Mol. Biol. , vol.388 , pp. 180-194
    • Lasker, K.1    Topf, M.2    Sali, A.3    Wolfson, H.J.4
  • 33
    • 85069255461 scopus 로고    scopus 로고
    • Determining macromolecular assembly structures by molecular docking and fitting into an electron density map
    • in press
    • Lasker, K., Sali, A., and Wolfson, H. J. (in press) Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. Proteins
    • Proteins
    • Lasker, K.1    Sali, A.2    Wolfson, H.J.3
  • 34
    • 64549095890 scopus 로고    scopus 로고
    • Hybrid approaches: Applying computational methods in cryo-electron microscopy
    • Lindert, S., Stewart, P. L., and Meiler, J. (2009) Hybrid approaches: applying computational methods in cryo-electron microscopy. Curr. Opin. Struct. Biol. 19, 218-225
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 218-225
    • Lindert, S.1    Stewart, P.L.2    Meiler, J.3
  • 35
    • 36049029967 scopus 로고    scopus 로고
    • High-resolution structure prediction and the crystallographic phase problem
    • Qian, B., Raman, S., Das, R., Bradley, P., McCoy, A. J., Read, R. J., and Baker, D. (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450, 259-264
    • (2007) Nature , vol.450 , pp. 259-264
    • Qian, B.1    Raman, S.2    Das, R.3    Bradley, P.4    McCoy, A.J.5    Read, R.J.6    Baker, D.7
  • 37
    • 0034501067 scopus 로고    scopus 로고
    • De novo protein structure determination using sparse NMR data
    • Bowers, P. M., Strauss, C. E., and Baker, D. (2000) De novo protein structure determination using sparse NMR data. J. Biomol. NMR 18, 311-318
    • (2000) J. Biomol. NMR , vol.18 , pp. 311-318
    • Bowers, P.M.1    Strauss, C.E.2    Baker, D.3
  • 42
    • 76349117689 scopus 로고    scopus 로고
    • Structure of clathrin coat with bound Hsc70 and auxilin: Mechanism of Hsc70-facilitated disassembly
    • Xing, Y., Böcking, T., Wolf, M., Grigorieff, N., Kirchhausen, T., and Harrison, S. C. (2010) Structure of clathrin coat with bound Hsc70 and auxilin: mechanism of Hsc70-facilitated disassembly. EMBO J. 29, 655-665
    • (2010) EMBO J. , vol.29 , pp. 655-665
    • Xing, Y.1    Böcking, T.2    Wolf, M.3    Grigorieff, N.4    Kirchhausen, T.5    Harrison, S.C.6
  • 44
    • 70350771279 scopus 로고    scopus 로고
    • Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function
    • Byeon, I. J., Meng, X., Jung, J., Zhao, G., Yang, R., Ahn, J., Shi, J., Concel, J., Aiken, C., Zhang, P., and Gronenborn, A. M. (2009) Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function. Cell 139, 780-790
    • (2009) Cell , vol.139 , pp. 780-790
    • Byeon, I.J.1    Meng, X.2    Jung, J.3    Zhao, G.4    Yang, R.5    Ahn, J.6    Shi, J.7    Concel, J.8    Aiken, C.9    Zhang, P.10    Gronenborn, A.M.11
  • 45
    • 48749103296 scopus 로고    scopus 로고
    • Integrating diverse data for structure determination of macromolecular assemblies
    • Alber, F., Förster, F., Korkin, D., Topf, M., and Sali, A. (2008) Integrating diverse data for structure determination of macromolecular assemblies. Annu. Rev. Biochem. 77, 443-477
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 443-477
    • Alber, F.1    Förster, F.2    Korkin, D.3    Topf, M.4    Sali, A.5
  • 48
    • 2542428546 scopus 로고    scopus 로고
    • Structure and mechanism of the RNA polymerase II transcription machinery
    • Hahn, S. (2004) Structure and mechanism of the RNA polymerase II transcription machinery. Nat. Struct. Mol. Biol. 11, 394-403
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 394-403
    • Hahn, S.1
  • 49
    • 0035827346 scopus 로고    scopus 로고
    • Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution
    • Cramer, P., Bushnell, D. A., and Kornberg, R. D. (2001) Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292, 1863-1876
    • (2001) Science , vol.292 , pp. 1863-1876
    • Cramer, P.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 50
    • 33846223946 scopus 로고    scopus 로고
    • Molecular architecture and conformational flexibility of human RNA polymerase II
    • Kostek, S. A., Grob, P., De Carlo, S., Lipscomb, J. S., Garczarek, F., and Nogales, E. (2006) Molecular architecture and conformational flexibility of human RNA polymerase II. Structure 14, 1691-1700
    • (2006) Structure , vol.14 , pp. 1691-1700
    • Kostek, S.A.1    Grob, P.2    De Carlo, S.3    Lipscomb, J.S.4    Garczarek, F.5    Nogales, E.6
  • 51
    • 10944232674 scopus 로고    scopus 로고
    • Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS
    • Kettenberger, H., Armache, K. J., and Cramer, P. (2004) Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell 16, 955-965
    • (2004) Mol. Cell , vol.16 , pp. 955-965
    • Kettenberger, H.1    Armache, K.J.2    Cramer, P.3
  • 53
    • 0034705128 scopus 로고    scopus 로고
    • High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry
    • Young, M. M., Tang, N., Hempel, J. C., Oshiro, C. M., Taylor, E. W., Kuntz, I. D., Gibson, B. W., and Dollinger, G. (2000) High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 97, 5802-5806
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 5802-5806
    • Young, M.M.1    Tang, N.2    Hempel, J.C.3    Oshiro, C.M.4    Taylor, E.W.5    Kuntz, I.D.6    Gibson, B.W.7    Dollinger, G.8
  • 56
    • 0344120702 scopus 로고    scopus 로고
    • EMDep: A web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information
    • Henrick, K., Newman, R., Tagari, M., and Chagoyen, M. (2003) EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information. J. Struct. Biol. 144, 228-237
    • (2003) J. Struct. Biol. , vol.144 , pp. 228-237
    • Henrick, K.1    Newman, R.2    Tagari, M.3    Chagoyen, M.4
  • 61
    • 0037405790 scopus 로고    scopus 로고
    • Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III
    • Tan, Q., Prysak, M. H., and Woychik, N. A. (2003) Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III. Mol. Cell. Biol. 23, 3329-3338
    • (2003) Mol. Cell. Biol. , vol.23 , pp. 3329-3338
    • Tan, Q.1    Prysak, M.H.2    Woychik, N.A.3
  • 62
    • 0034661246 scopus 로고    scopus 로고
    • The Saccharomyces telomere-binding protein Cdc13p interacts with both the catalytic subunit of DNA polymerase alpha and the telomerase-associated est1 protein
    • Qi, H., and Zakian, V. A. (2000) The Saccharomyces telomere-binding protein Cdc13p interacts with both the catalytic subunit of DNA polymerase alpha and the telomerase-associated est1 protein. Genes Dev. 14, 1777-1788
    • (2000) Genes Dev. , vol.14 , pp. 1777-1788
    • Qi, H.1    Zakian, V.A.2
  • 63
    • 0347065340 scopus 로고    scopus 로고
    • The conserved and non-conserved regions of Rpb4 are involved in multiple phenotypes in Saccharomyces cerevisiae
    • Sampath, V., Rekha, N., Srinivasan, N., and Sadhale, P. (2003) The conserved and non-conserved regions of Rpb4 are involved in multiple phenotypes in Saccharomyces cerevisiae. J. Biol. Chem. 278, 51566-51576
    • (2003) J. Biol. Chem. , vol.278 , pp. 51566-51576
    • Sampath, V.1    Rekha, N.2    Srinivasan, N.3    Sadhale, P.4
  • 64
    • 0029074950 scopus 로고
    • Human RNA polymerase II subunit hsRPB7 functions in yeast and influences stress survival and cell morphology
    • Khazak, V., Sadhale, P. P., Woychik, N. A., Brent, R., and Golemis, E. A. (1995) Human RNA polymerase II subunit hsRPB7 functions in yeast and influences stress survival and cell morphology. Mol. Biol. Cell 6, 759-775
    • (1995) Mol. Biol. Cell , vol.6 , pp. 759-775
    • Khazak, V.1    Sadhale, P.P.2    Woychik, N.A.3    Brent, R.4    Golemis, E.A.5
  • 65
    • 19744362303 scopus 로고    scopus 로고
    • Mapping the interaction site of Rpb4 and Rpb7 subunits of RNA polymerase II in Saccharomyces cerevisiae
    • Sareen, A., Choudhry, P., Mehta, S., and Sharma, N. (2005) Mapping the interaction site of Rpb4 and Rpb7 subunits of RNA polymerase II in Saccharomyces cerevisiae. Biochem. Biophys. Res. Commun. 332, 763-770
    • (2005) Biochem. Biophys. Res. Commun. , vol.332 , pp. 763-770
    • Sareen, A.1    Choudhry, P.2    Mehta, S.3    Sharma, N.4
  • 66
    • 33845604554 scopus 로고    scopus 로고
    • Nucleocytoplasmic shuttling of the Rpb4p and Rpb7p subunits of Saccharomyces cerevisiae RNA polymerase II by two pathways
    • Selitrennik, M., Duek, L., Lotan, R., and Choder, M. (2006) Nucleocytoplasmic shuttling of the Rpb4p and Rpb7p subunits of Saccharomyces cerevisiae RNA polymerase II by two pathways. Eukaryot. Cell 5, 2092-2103
    • (2006) Eukaryot. Cell , vol.5 , pp. 2092-2103
    • Selitrennik, M.1    Duek, L.2    Lotan, R.3    Choder, M.4
  • 68
    • 21844434684 scopus 로고    scopus 로고
    • Distinct regions of RPB11 are required for heterodimerization with RPB3 in human and yeast RNA polymerase II
    • Benga, W. J., Grandemange, S., Shpakovski, G. V., Shematorova, E. K., Kedinger, C., and Vigneron, M. (2005) Distinct regions of RPB11 are required for heterodimerization with RPB3 in human and yeast RNA polymerase II. Nucleic Acids Res. 33, 3582-3590
    • (2005) Nucleic Acids Res. , vol.33 , pp. 3582-3590
    • Benga, W.J.1    Grandemange, S.2    Shpakovski, G.V.3    Shematorova, E.K.4    Kedinger, C.5    Vigneron, M.6
  • 69
    • 0035971082 scopus 로고    scopus 로고
    • Dissociable Rpb4-Rpb7 subassembly of RNA polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation
    • Orlicky, S. M., Tran, P. T., Sayre, M. H., and Edwards, A. M. (2001) Dissociable Rpb4-Rpb7 subassembly of RNA polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation. J. Biol. Chem. 276, 10097-10102
    • (2001) J. Biol. Chem. , vol.276 , pp. 10097-10102
    • Orlicky, S.M.1    Tran, P.T.2    Sayre, M.H.3    Edwards, A.M.4
  • 73
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Connolly, M. L. (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221, 709-713
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 74
    • 16244386921 scopus 로고    scopus 로고
    • The optimal size of a globular protein domain: A simple sphere-packing model
    • Shen, M., Davis, F. P., and Sali, A. (2005) The optimal size of a globular protein domain: a simple sphere-packing model. Chem. Phys. Lett. 405, 224-228
    • (2005) Chem. Phys. Lett. , vol.405 , pp. 224-228
    • Shen, M.1    Davis, F.P.2    Sali, A.3
  • 75
    • 0026572775 scopus 로고
    • Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
    • Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A. A., Aflalo, C., and Vakser, I. A. (1992) Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. U.S.A. 89, 2195-2199
    • (1992) Proc. Natl. Acad. Sci. U.S.A. , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.A.4    Aflalo, C.5    Vakser, I.A.6
  • 77
    • 51249118082 scopus 로고    scopus 로고
    • Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies
    • Förster, F., Webb, B., Krukenberg, K. A., Tsuruta, H., Agard, D. A., and Sali, A. (2008) Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies. J. Mol. Biol. 382, 1089-1106
    • (2008) J. Mol. Biol. , vol.382 , pp. 1089-1106
    • Förster, F.1    Webb, B.2    Krukenberg, K.A.3    Tsuruta, H.4    Agard, D.A.5    Sali, A.6
  • 78
    • 42949147146 scopus 로고    scopus 로고
    • Multiple conformations of E. coli Hsp90 in solution: Insights into the conformational dynamics of Hsp90
    • Krukenberg, K. A., Förster, F., Rice, L. M., Sali, A., and Agard, D. A. (2008) Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90. Structure 16, 755-765
    • (2008) Structure , vol.16 , pp. 755-765
    • Krukenberg, K.A.1    Förster, F.2    Rice, L.M.3    Sali, A.4    Agard, D.A.5
  • 80
    • 33745024278 scopus 로고    scopus 로고
    • Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines
    • Tama, F., and Brooks, C. L. (2006) Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu. Rev. Biophys. Biomol. Struct. 35, 115-133
    • (2006) Annu. Rev. Biophys. Biomol. Struct. , vol.35 , pp. 115-133
    • Tama, F.1    Brooks, C.L.2
  • 81
    • 46249083761 scopus 로고    scopus 로고
    • Assembly reflects evolution of protein complexes
    • Levy, E. D., Boeri Erba, E., Robinson, C. V., and Teichmann, S. A. (2008) Assembly reflects evolution of protein complexes. Nature 453, 1262-1265
    • (2008) Nature , vol.453 , pp. 1262-1265
    • Levy, E.D.1    Boeri Erba, E.2    Robinson, C.V.3    Teichmann, S.A.4
  • 82
    • 14844307627 scopus 로고    scopus 로고
    • Structural characterization of assemblies from overall shape and subcomplex compositions
    • Alber, F., Kim, M. F., and Sali, A. (2005) Structural characterization of assemblies from overall shape and subcomplex compositions. Structure 13, 435-445
    • (2005) Structure , vol.13 , pp. 435-445
    • Alber, F.1    Kim, M.F.2    Sali, A.3
  • 84
    • 0029633186 scopus 로고
    • AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
    • Pearlman, D. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 91, 1-41
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 1-41
    • Pearlman, D.1
  • 86
    • 33645941402 scopus 로고
    • The OPLS Potential Functions for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin
    • Jorgensen, W. L., and Tirado-Rives, J. (1988) The OPLS Potential Functions for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin. J. Am. Chem. Soc. 110, 657-666
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 657-666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 87
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • Shen, M. Y., and Sali, A. (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci. 15, 2507-2524
    • (2006) Protein Sci. , vol.15 , pp. 2507-2524
    • Shen, M.Y.1    Sali, A.2
  • 88
    • 1642575364 scopus 로고    scopus 로고
    • Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential
    • Zhang, C., Liu, S., and Zhou, Y. (2004) Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. Protein Sci. 13, 391-399
    • (2004) Protein Sci. , vol.13 , pp. 391-399
    • Zhang, C.1    Liu, S.2    Zhou, Y.3
  • 89
    • 0036145846 scopus 로고    scopus 로고
    • Statistical potentials for fold assessment
    • Melo, F., Sánchez, R., and Sali, A. (2002) Statistical potentials for fold assessment. Protein Sci. 11, 430-448
    • (2002) Protein Sci. , vol.11 , pp. 430-448
    • Melo, F.1    Sánchez, R.2    Sali, A.3
  • 90
    • 33645792604 scopus 로고    scopus 로고
    • Physically realistic homology models built with ROSETTA can be more accurate than their templates
    • Misura, K. M., Chivian, D., Rohl, C. A., Kim, D. E., and Baker, D. (2006) Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc. Natl. Acad. Sci. U.S.A. 103, 5361-5366
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 5361-5366
    • Misura, K.M.1    Chivian, D.2    Rohl, C.A.3    Kim, D.E.4    Baker, D.5
  • 91
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons, K. T., Kooperberg, C., Huang, E., and Baker, D. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268, 209-225
    • (1997) J. Mol. Biol. , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 92
    • 0032929780 scopus 로고    scopus 로고
    • Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    • Simons, K. T., Ruczinski, I., Kooperberg, C., Fox, B. A., Bystroff, C., and Baker, D. (1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34, 82-95
    • (1999) Proteins , vol.34 , pp. 82-95
    • Simons, K.T.1    Ruczinski, I.2    Kooperberg, C.3    Fox, B.A.4    Bystroff, C.5    Baker, D.6
  • 93
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl, M. J. (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213, 859-883
    • (1990) J. Mol. Biol. , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 94
    • 18744382508 scopus 로고    scopus 로고
    • PIBASE: A comprehensive database of structurally defined protein interfaces
    • Davis, F. P., and Sali, A. (2005) PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 21, 1901-1907
    • (2005) Bioinformatics , vol.21 , pp. 1901-1907
    • Davis, F.P.1    Sali, A.2
  • 97
    • 84976806770 scopus 로고
    • Minimization of unrestrained multivariate functions
    • Shanno, D. F., and Phua, K. H. (1980) Minimization of unrestrained multivariate functions. ACM Trans. Math. Soft. 6, 618-622
    • (1980) ACM Trans. Math. Soft. , vol.6 , pp. 618-622
    • Shanno, D.F.1    Phua, K.H.2
  • 98
    • 84988112508 scopus 로고
    • An efficient newton-like method for molecular mechanics energy minimization of large molecules
    • Ponder, J. W., and Richards, F. M. (1987) An efficient newton-like method for molecular mechanics energy minimization of large molecules. J. Comput. Chem. 8, 1016-1024
    • (1987) J. Comput. Chem. , vol.8 , pp. 1016-1024
    • Ponder, J.W.1    Richards, F.M.2
  • 99
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus, M., and McCammon, J. A. (2002) Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9, 646-652
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 100
    • 0242509772 scopus 로고    scopus 로고
    • Self-guided Langevin dynamics simulation method
    • Wu, X., and Brooks, B. R. (2003) Self-guided Langevin dynamics simulation method. Chem. Phys. Lett. 381, 512-518
    • (2003) Chem. Phys. Lett. , vol.381 , pp. 512-518
    • Wu, X.1    Brooks, B.R.2
  • 101
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita, Y., and Okamoto, Y. (1999) Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314, 141-151
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 102
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • Canutescu, A. A., Shelenkov, A. A., and Dunbrack, R. L., Jr. (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 12, 2001-2014
    • (2003) Protein Sci. , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack Jr., R.L.3
  • 104
    • 51349094337 scopus 로고    scopus 로고
    • Minimizing and learning energy functions for side-chain prediction
    • Yanover, C., Schueler-Furman, O., and Weiss, Y. (2008) Minimizing and learning energy functions for side-chain prediction. J. Comput. Biol. 15, 899-911
    • (2008) J. Comput. Biol. , vol.15 , pp. 899-911
    • Yanover, C.1    Schueler-Furman, O.2    Weiss, Y.3
  • 105
    • 36448972368 scopus 로고    scopus 로고
    • Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition
    • Zhao, J., Malmberg, R. L., and Cai, L. (2008) Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition. J. Math. Biol. 56, 145-159
    • (2008) J. Math. Biol. , vol.56 , pp. 145-159
    • Zhao, J.1    Malmberg, R.L.2    Cai, L.3
  • 106
    • 18844453949 scopus 로고    scopus 로고
    • Prediction of multimolecular assemblies by multiple docking
    • DOI 10.1016/j.jmb.2005.03.039, PII S0022283605003177
    • Inbar, Y., Benyamini, H., Nussinov, R., and Wolfson, H. J. (2005) Prediction of multimolecular assemblies by multiple docking. J. Mol. Biol. 349, 435-447 (Pubitemid 40693761)
    • (2005) Journal of Molecular Biology , vol.349 , Issue.2 , pp. 435-447
    • Inbar, Y.1    Benyamini, H.2    Nussinov, R.3    Wolfson, H.J.4    Honig, B.5
  • 109
    • 36749048724 scopus 로고    scopus 로고
    • Prediction of the structure of symmetrical protein assemblies
    • André, I., Bradley, P., Wang, C., and Baker, D. (2007) Prediction of the structure of symmetrical protein assemblies. Proc. Natl. Acad. Sci. U.S.A. 104, 17656-17661
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 17656-17661
    • André, I.1    Bradley, P.2    Wang, C.3    Baker, D.4
  • 110
    • 0026597444 scopus 로고
    • Free R value: A novel statistical quantity for assessing the accuracy of crystal structures
    • Brünger, A. T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475
    • (1992) Nature , vol.355 , pp. 472-475
    • Brünger, A.T.1
  • 117
    • 0036789265 scopus 로고    scopus 로고
    • Analyzing yeast protein-protein interaction data obtained from different sources
    • Bader, G. D., and Hogue, C. W. (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol. 20, 991-997
    • (2002) Nat. Biotechnol. , vol.20 , pp. 991-997
    • Bader, G.D.1    Hogue, C.W.2
  • 118
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S., and Bork, P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399-403
    • (2002) Nature , vol.417 , pp. 399-403
    • Von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 119
    • 57449099068 scopus 로고    scopus 로고
    • Precision proteomics: The case for high resolution and high mass accuracy
    • Mann, M., and Kelleher, N. L. (2008) Precision proteomics: the case for high resolution and high mass accuracy. Proc. Natl. Acad. Sci. U.S.A. 105, 18132-18138
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 18132-18138
    • Mann, M.1    Kelleher, N.L.2
  • 121
    • 0027172878 scopus 로고
    • Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy
    • Clore, G. M., Robien, M. A., and Gronenborn, A. M. (1993) Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy. J. Mol. Biol. 231, 82-102
    • (1993) J. Mol. Biol. , vol.231 , pp. 82-102
    • Clore, G.M.1    Robien, M.A.2    Gronenborn, A.M.3
  • 122
    • 0032568556 scopus 로고    scopus 로고
    • New methods of structure refinement for macromolecular structure determination by NMR
    • Clore, G. M., and Gronenborn, A. M. (1998) New methods of structure refinement for macromolecular structure determination by NMR. Proc. Natl. Acad. Sci. U.S.A. 95, 5891-5898
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 5891-5898
    • Clore, G.M.1    Gronenborn, A.M.2
  • 123
    • 0027918891 scopus 로고
    • Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation
    • Brünger, A. T., Clore, G. M., Gronenborn, A. M., Saffrich, R., and Nilges, M. (1993) Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation. Science 261, 328-331
    • (1993) Science , vol.261 , pp. 328-331
    • Brünger, A.T.1    Clore, G.M.2    Gronenborn, A.M.3    Saffrich, R.4    Nilges, M.5
  • 126
    • 70349876855 scopus 로고    scopus 로고
    • Mass spectrometry of large complexes
    • Bich, C., and Zenobi, R. (2009) Mass spectrometry of large complexes. Curr. Opin. Struct. Biol. 19, 632-639
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 632-639
    • Bich, C.1    Zenobi, R.2
  • 127
    • 0009482260 scopus 로고
    • Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: Procedure and some applications
    • Towbin, H., Staehelin, T., and Gordon, J. (1979) Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc. Natl. Acad. Sci. U.S.A. 76, 4350-4354
    • (1979) Proc. Natl. Acad. Sci. U.S.A. , vol.76 , pp. 4350-4354
    • Towbin, H.1    Staehelin, T.2    Gordon, J.3
  • 129
    • 54149088214 scopus 로고    scopus 로고
    • Epistasis - The essential role of gene interactions in the structure and evolution of genetic systems
    • Phillips, P. C. (2008) Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems. Nat. Rev. Genet. 9, 855-867
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 855-867
    • Phillips, P.C.1
  • 131
    • 45749101309 scopus 로고    scopus 로고
    • Surface plasmon resonance mass spectrometry in proteomics
    • Visser, N. F., and Heck, A. J. (2008) Surface plasmon resonance mass spectrometry in proteomics. Expert Rev. Proteomics 5, 425-433
    • (2008) Expert Rev. Proteomics , vol.5 , pp. 425-433
    • Visser, N.F.1    Heck, A.J.2
  • 132
    • 66849089268 scopus 로고    scopus 로고
    • Protein microarrays: High-throughput tools for proteomics
    • Stoevesandt, O., Taussig, M. J., and He, M. (2009) Protein microarrays: high-throughput tools for proteomics. Expert Rev. Proteomics 6, 145-157
    • (2009) Expert Rev. Proteomics , vol.6 , pp. 145-157
    • Stoevesandt, O.1    Taussig, M.J.2    He, M.3
  • 133
    • 70349156763 scopus 로고    scopus 로고
    • Dissecting protein function and signaling using protein microarrays
    • Wolf-Yadlin, A., Sevecka, M., and MacBeath, G. (2009) Dissecting protein function and signaling using protein microarrays. Curr. Opin. Chem. Biol. 13, 398-405
    • (2009) Curr. Opin. Chem. Biol. , vol.13 , pp. 398-405
    • Wolf-Yadlin, A.1    Sevecka, M.2    MacBeath, G.3
  • 134
    • 14344252577 scopus 로고    scopus 로고
    • Protein microarrays as a discovery tool for studying protein-protein interactions
    • Korf, U., and Wiemann, S. (2005) Protein microarrays as a discovery tool for studying protein-protein interactions. Expert Rev. Proteomics 2, 13-26
    • (2005) Expert Rev. Proteomics , vol.2 , pp. 13-26
    • Korf, U.1    Wiemann, S.2
  • 135
    • 33745785300 scopus 로고    scopus 로고
    • Visualization of molecular interactions by fluorescence complementation
    • Kerppola, T. K. (2006) Visualization of molecular interactions by fluorescence complementation. Nat. Rev. Mol. Cell Biol. 7, 449-456
    • (2006) Nat. Rev. Mol. Cell Biol. , vol.7 , pp. 449-456
    • Kerppola, T.K.1
  • 136
    • 34247629593 scopus 로고    scopus 로고
    • Application of protein-fragment complementation assays in cell biology
    • Remy, I., and Michnick, S. W. (2007) Application of protein-fragment complementation assays in cell biology. BioTechniques 42, 137-145
    • (2007) BioTechniques , vol.42 , pp. 137-145
    • Remy, I.1    Michnick, S.W.2
  • 137
    • 35448962899 scopus 로고    scopus 로고
    • Isothermal titration calorimetry: Experimental design, data analysis, and probing macromolecule/ligand binding and kinetic interactions
    • Freyer, M. W., and Lewis, E. A. (2008) Isothermal titration calorimetry: experimental design, data analysis, and probing macromolecule/ligand binding and kinetic interactions. Methods Cell Biol. 84, 79-113
    • (2008) Methods Cell Biol. , vol.84 , pp. 79-113
    • Freyer, M.W.1    Lewis, E.A.2
  • 138
    • 3242726206 scopus 로고    scopus 로고
    • Characterization of protein-protein interactions by isothermal titration calorimetry
    • Velazquez-Campoy, A., Leavitt, S. A., and Freire, E. (2004) Characterization of protein-protein interactions by isothermal titration calorimetry. Methods Mol. Biol. 261, 35-54
    • (2004) Methods Mol. Biol. , vol.261 , pp. 35-54
    • Velazquez-Campoy, A.1    Leavitt, S.A.2    Freire, E.3
  • 139
    • 34548417621 scopus 로고    scopus 로고
    • Fluorescent protein FRET: The good, the bad and the ugly
    • Piston, D. W., and Kremers, G. J. (2007) Fluorescent protein FRET: the good, the bad and the ugly. Trends Biochem. Sci. 32, 407-414
    • (2007) Trends Biochem. Sci. , vol.32 , pp. 407-414
    • Piston, D.W.1    Kremers, G.J.2
  • 140
    • 33646343978 scopus 로고    scopus 로고
    • Illuminating insights into proteinprotein interactions using bioluminescence resonance energy transfer (BRET)
    • Pfleger, K. D., and Eidne, K. A. (2006) Illuminating insights into proteinprotein interactions using bioluminescence resonance energy transfer (BRET). Nat. Methods 3, 165-174
    • (2006) Nat. Methods , vol.3 , pp. 165-174
    • Pfleger, K.D.1    Eidne, K.A.2
  • 141
    • 46349104643 scopus 로고    scopus 로고
    • Quantification of structures and gold labeling in transmission electron microscopy
    • Lucocq, J. (2008) Quantification of structures and gold labeling in transmission electron microscopy. Methods Cell Biol. 88, 59-82
    • (2008) Methods Cell Biol. , vol.88 , pp. 59-82
    • Lucocq, J.1
  • 143
    • 46249087610 scopus 로고    scopus 로고
    • From live-cell imaging to scanning electron microscopy (SEM): The use of green fluorescent protein (GFP) as a common label
    • Drummond, S. P., and Allen, T. D. (2008) From live-cell imaging to scanning electron microscopy (SEM): the use of green fluorescent protein (GFP) as a common label. Methods Cell Biol. 88, 97-108
    • (2008) Methods Cell Biol. , vol.88 , pp. 97-108
    • Drummond, S.P.1    Allen, T.D.2
  • 144
    • 64549106038 scopus 로고    scopus 로고
    • Convergence and combination of methods in protein-protein docking
    • Vajda, S., and Kozakov, D. (2009) Convergence and combination of methods in protein-protein docking. Curr. Opin. Struct. Biol. 19, 164-170
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 164-170
    • Vajda, S.1    Kozakov, D.2
  • 145
    • 33745742438 scopus 로고    scopus 로고
    • Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions
    • Sinz, A. (2006) Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom. Rev. 25, 663-682
    • (2006) Mass Spectrom. Rev. , vol.25 , pp. 663-682
    • Sinz, A.1
  • 147
    • 35448956141 scopus 로고    scopus 로고
    • Hydrogen/deuterium exchangemass spectrometry: A powerful tool for probing protein structure, dynamics and interactions
    • Tsutsui, Y., and Wintrode, P. L. (2007) Hydrogen/deuterium exchangemass spectrometry: a powerful tool for probing protein structure, dynamics and interactions. Curr. Med. Chem. 14, 2344-2358
    • (2007) Curr. Med. Chem. , vol.14 , pp. 2344-2358
    • Tsutsui, Y.1    Wintrode, P.L.2
  • 148
    • 33646351295 scopus 로고    scopus 로고
    • Protease accessibility laddering: A proteomic tool for probing protein structure
    • Dokudovskaya, S., Williams, R., Devos, D., Sali, A., Chait, B. T., and Rout, M. P. (2006) Protease accessibility laddering: a proteomic tool for probing protein structure. Structure 14, 653-660
    • (2006) Structure , vol.14 , pp. 653-660
    • Dokudovskaya, S.1    Williams, R.2    Devos, D.3    Sali, A.4    Chait, B.T.5    Rout, M.P.6
  • 149
    • 25144445202 scopus 로고    scopus 로고
    • Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry
    • Guan, J. Q., and Chance, M. R. (2005) Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry. Trends Biochem. Sci. 30, 583-592
    • (2005) Trends Biochem. Sci. , vol.30 , pp. 583-592
    • Guan, J.Q.1    Chance, M.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.