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Volumn 173, Issue 3, 2011, Pages 436-444

Modeling pilus structures from sparse data

Author keywords

Cysteine cross linking; Molecular modeling; Pilus assembly; Protein secretion

Indexed keywords

CYSTEINE;

EID: 79851515749     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2010.11.015     Document Type: Article
Times cited : (33)

References (48)
  • 2
    • 4744344737 scopus 로고    scopus 로고
    • Automation of NMR structure determination of proteins
    • Altieri A.S., Byrd R.A. Automation of NMR structure determination of proteins. Curr. Opin. Struct. Biol. 2004, 14:547-553.
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 547-553
    • Altieri, A.S.1    Byrd, R.A.2
  • 3
    • 4444325332 scopus 로고    scopus 로고
    • Crystallographic analysis of the Pseudomonas aeruginosa strain K122-4 monomeric pilin reveals a conserved receptor-binding architecture
    • Audette G.F., Irvin R.T., Hazes B. Crystallographic analysis of the Pseudomonas aeruginosa strain K122-4 monomeric pilin reveals a conserved receptor-binding architecture. Biochemistry 2004, 43:11427-11435.
    • (2004) Biochemistry , vol.43 , pp. 11427-11435
    • Audette, G.F.1    Irvin, R.T.2    Hazes, B.3
  • 4
    • 66149097825 scopus 로고    scopus 로고
    • Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA
    • Bardiaux B., Bernard A., Rieping W., Habeck M., Malliavin T.E., Nilges M. Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA. Proteins 2009, 75:569-585.
    • (2009) Proteins , vol.75 , pp. 569-585
    • Bardiaux, B.1    Bernard, A.2    Rieping, W.3    Habeck, M.4    Malliavin, T.E.5    Nilges, M.6
  • 5
    • 33644793339 scopus 로고    scopus 로고
    • Structural interpretation of hydrogen exchange protection factors in proteins: characterization of the native state fluctuations of CI2
    • Best R.B., Vendruscolo M. Structural interpretation of hydrogen exchange protection factors in proteins: characterization of the native state fluctuations of CI2. Structure 2006, 14:97-106.
    • (2006) Structure , vol.14 , pp. 97-106
    • Best, R.B.1    Vendruscolo, M.2
  • 6
    • 0344931796 scopus 로고    scopus 로고
    • Retinoic acid receptor: a simulation analysis of retinoic acid binding and the resulting conformational changes
    • Blondel A., Renaud J.P., Fischer S., Moras D., Karplus M. Retinoic acid receptor: a simulation analysis of retinoic acid binding and the resulting conformational changes. J. Mol. Biol. 1999, 291:101-115.
    • (1999) J. Mol. Biol. , vol.291 , pp. 101-115
    • Blondel, A.1    Renaud, J.P.2    Fischer, S.3    Moras, D.4    Karplus, M.5
  • 9
    • 0035501755 scopus 로고    scopus 로고
    • Protein molecular dynamics with the Generalized Born/ACE solvent model
    • Calimet N., Schaefer M., Simonson T. Protein molecular dynamics with the Generalized Born/ACE solvent model. Proteins 2001, 45:144-158.
    • (2001) Proteins , vol.45 , pp. 144-158
    • Calimet, N.1    Schaefer, M.2    Simonson, T.3
  • 10
    • 77955628595 scopus 로고    scopus 로고
    • Detailed structural and assembly model of the type II secretion pilus from sparse data
    • Campos M., Nilges M., Cisneros D.A., Francetic O. Detailed structural and assembly model of the type II secretion pilus from sparse data. Proc. Natl. Acad. Sci. USA 2010, 107:13081-13086.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 13081-13086
    • Campos, M.1    Nilges, M.2    Cisneros, D.A.3    Francetic, O.4
  • 12
    • 33747872707 scopus 로고    scopus 로고
    • Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions
    • Craig L., Volkmann N., Arvai A.S., Pique M.E., Yeager M., Egelman E.H., Tainer J.A. Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions. Mol. Cell 2006, 23:651-662.
    • (2006) Mol. Cell , vol.23 , pp. 651-662
    • Craig, L.1    Volkmann, N.2    Arvai, A.S.3    Pique, M.E.4    Yeager, M.5    Egelman, E.H.6    Tainer, J.A.7
  • 13
    • 50649095790 scopus 로고    scopus 로고
    • Macromolecular modeling with Rosetta
    • Das R., Baker D. Macromolecular modeling with Rosetta. Annu. Rev. Biochem. 2008, 77:363-382.
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 363-382
    • Das, R.1    Baker, D.2
  • 15
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
    • Dominguez C., Boelens R., Bonvin A.M.J.J. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 2003, 125:1731-1737.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.J.J.3
  • 16
    • 58849162221 scopus 로고    scopus 로고
    • Automated structure determination from NMR spectra
    • Güntert P. Automated structure determination from NMR spectra. Eur. Biophys. J. 2009, 38:129-143.
    • (2009) Eur. Biophys. J. , vol.38 , pp. 129-143
    • Güntert, P.1
  • 17
    • 33748773323 scopus 로고    scopus 로고
    • Type IV pilin structures: insights on shared architecture, fiber assembly, receptor binding and type II secretion
    • Hansen J.K., Forest K.T. Type IV pilin structures: insights on shared architecture, fiber assembly, receptor binding and type II secretion. J. Mol. Microbiol. Biotechnol. 2006, 11:192-207.
    • (2006) J. Mol. Microbiol. Biotechnol. , vol.11 , pp. 192-207
    • Hansen, J.K.1    Forest, K.T.2
  • 18
    • 0024046835 scopus 로고
    • Model building of disulfide bonds in proteins with known threedimensional structure
    • Hazes B., Dijkstra B.W. Model building of disulfide bonds in proteins with known threedimensional structure. Protein Eng. 1988, 2:119-225.
    • (1988) Protein Eng. , vol.2 , pp. 119-225
    • Hazes, B.1    Dijkstra, B.W.2
  • 19
    • 0034674160 scopus 로고    scopus 로고
    • Crystal structure of Pseudomonas aeruginosa PAK pilin suggests a main-chain-dominated mode of receptor binding
    • Hazes B., Sastry P.A., Hayakawa K., Read R.J., Irvin R.T. Crystal structure of Pseudomonas aeruginosa PAK pilin suggests a main-chain-dominated mode of receptor binding. J. Mol. Biol. 2000, 299:1005-1017.
    • (2000) J. Mol. Biol. , vol.299 , pp. 1005-1017
    • Hazes, B.1    Sastry, P.A.2    Hayakawa, K.3    Read, R.J.4    Irvin, R.T.5
  • 20
    • 0036308102 scopus 로고    scopus 로고
    • Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA
    • Herrmann T., Güntert P., Wüthrich K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 2002, 319:209-227.
    • (2002) J. Mol. Biol. , vol.319 , pp. 209-227
    • Herrmann, T.1    Güntert, P.2    Wüthrich, K.3
  • 27
    • 37549005981 scopus 로고    scopus 로고
    • Vibrio cholerae toxin-coregulated pilus structure analyzed by hydrogen/deuterium exchange mass spectrometry
    • Li J., Lim M.S., Li S., Brock M., Pique M.E., Woods V.L., Craig L. Vibrio cholerae toxin-coregulated pilus structure analyzed by hydrogen/deuterium exchange mass spectrometry. Structure 2008, 16:137-148.
    • (2008) Structure , vol.16 , pp. 137-148
    • Li, J.1    Lim, M.S.2    Li, S.3    Brock, M.4    Pique, M.E.5    Woods, V.L.6    Craig, L.7
  • 28
    • 0034919240 scopus 로고    scopus 로고
    • Automated assignment of ambiguous nuclear Overhauser effects with ARIA
    • Linge J., O'Donoghue S.I., Nilges M. Automated assignment of ambiguous nuclear Overhauser effects with ARIA. Meth. Enzymol. 2001, 339:71-90.
    • (2001) Meth. Enzymol. , vol.339 , pp. 71-90
    • Linge, J.1    O'Donoghue, S.I.2    Nilges, M.3
  • 30
    • 0347062349 scopus 로고    scopus 로고
    • Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum
    • Moulinier L., Case D.A., Simonson T. Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum. Acta Crystallogr. D: Biol. Crystallogr. 2003, 59:2094-2103.
    • (2003) Acta Crystallogr. D: Biol. Crystallogr. , vol.59 , pp. 2094-2103
    • Moulinier, L.1    Case, D.A.2    Simonson, T.3
  • 31
    • 33748757929 scopus 로고    scopus 로고
    • Bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications
    • Ng S.Y.M., Chaban B., Jarrell K.F., flagella Archaeal bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications. J. Mol. Microbiol. Biotechnol. 2006, 11:167-191.
    • (2006) J. Mol. Microbiol. Biotechnol. , vol.11 , pp. 167-191
    • Ng, S.Y.M.1    Chaban, B.2    Jarrell, K.F.3    flagella, A.4
  • 32
    • 0027383637 scopus 로고
    • A calculation strategy for the structure determination of symmetric dimers by 1H NMR
    • Nilges M. A calculation strategy for the structure determination of symmetric dimers by 1H NMR. Proteins 1993, 17:297-309.
    • (1993) Proteins , vol.17 , pp. 297-309
    • Nilges, M.1
  • 33
    • 0028907436 scopus 로고
    • Calculation of protein structures with ambiguous distance restraints: automated assignment of ambiguous NOE crosspeaks and disulphide connectivities
    • Nilges M. Calculation of protein structures with ambiguous distance restraints: automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. J. Mol. Biol. 1995, 245:645-660.
    • (1995) J. Mol. Biol. , vol.245 , pp. 645-660
    • Nilges, M.1
  • 36
    • 84962662718 scopus 로고    scopus 로고
    • Protein structure calculation using ambiguous restraints
    • In: Encyclopedia of Magnetic Resonance. John Wiley & Sons, Ltd.
    • Nilges, M., Malliavin, T., Bardiaux, B., 2010. Protein structure calculation using ambiguous restraints. In: Encyclopedia of Magnetic Resonance. John Wiley & Sons, Ltd. doi:10.1002/9780470034590.emrstm1156.
    • (2010)
    • Nilges, M.1    Malliavin, T.2    Bardiaux, B.3
  • 38
    • 42649085698 scopus 로고    scopus 로고
    • Type IV pili: e pluribus unum?
    • Pelicic V. Type IV pili: e pluribus unum?. Mol. Microbiol. 2008, 68:827-837.
    • (2008) Mol. Microbiol. , vol.68 , pp. 827-837
    • Pelicic, V.1
  • 40
    • 28044443150 scopus 로고    scopus 로고
    • Modeling errors in noe data with a lognormal distribution improves the quality of NMR structures
    • Rieping W., Habeck M., Nilges M. Modeling errors in noe data with a lognormal distribution improves the quality of NMR structures. J. Am. Chem. Soc. 2005, 127:16026-16027.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 16026-16027
    • Rieping, W.1    Habeck, M.2    Nilges, M.3
  • 41
    • 14844338484 scopus 로고    scopus 로고
    • Combining X-ray crystallography and electron microscopy
    • Rossmann M.G., Morais M.C., Leiman P.G., Zhang W. Combining X-ray crystallography and electron microscopy. Structure 2005, 13:355-362.
    • (2005) Structure , vol.13 , pp. 355-362
    • Rossmann, M.G.1    Morais, M.C.2    Leiman, P.G.3    Zhang, W.4
  • 42
    • 0034657719 scopus 로고    scopus 로고
    • Pilus formation and protein secretion by the same machinery in Escherichia coli
    • Sauvonnet N., Vignon G., Pugsley A.P., Gounon P. Pilus formation and protein secretion by the same machinery in Escherichia coli. EMBO J. 2000, 19:2221-2228.
    • (2000) EMBO J. , vol.19 , pp. 2221-2228
    • Sauvonnet, N.1    Vignon, G.2    Pugsley, A.P.3    Gounon, P.4
  • 43
    • 36749078686 scopus 로고    scopus 로고
    • Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution
    • Schröder G.F., Brunger A.T., Levitt M. Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure 2007, 15:1630-1641.
    • (2007) Structure , vol.15 , pp. 1630-1641
    • Schröder, G.F.1    Brunger, A.T.2    Levitt, M.3
  • 44
    • 77951623055 scopus 로고    scopus 로고
    • Super-resolution biomolecular crystallography with low-resolution data
    • Schröder G.F., Levitt M., Brunger A.T. Super-resolution biomolecular crystallography with low-resolution data. Nature 2010, 464:1218-1222.
    • (2010) Nature , vol.464 , pp. 1218-1222
    • Schröder, G.F.1    Levitt, M.2    Brunger, A.T.3
  • 45
    • 84986534166 scopus 로고
    • New spherical cutoff methods for long-range forces in macromolecular simulation
    • Steinbach P., Brooks B. New spherical cutoff methods for long-range forces in macromolecular simulation. J. Comput. Chem. 1994, 15:667-683.
    • (1994) J. Comput. Chem. , vol.15 , pp. 667-683
    • Steinbach, P.1    Brooks, B.2
  • 46
    • 0025978598 scopus 로고
    • Amino acid substitutions in pilin of Pseudomonas aeruginosa: effect on leader peptide cleavage, amino-terminal methylation, and pilus assembly
    • Strom M.S., Lory S. Amino acid substitutions in pilin of Pseudomonas aeruginosa: effect on leader peptide cleavage, amino-terminal methylation, and pilus assembly. J. Biol. Chem. 1991, 266:1656-1664.
    • (1991) J. Biol. Chem. , vol.266 , pp. 1656-1664
    • Strom, M.S.1    Lory, S.2
  • 47
    • 0347380212 scopus 로고    scopus 로고
    • Docking of atomic models into reconstructions from electron microscopy
    • Volkmann N., Hanein D. Docking of atomic models into reconstructions from electron microscopy. Meth. Enzymol. 2003, 374:204-225.
    • (2003) Meth. Enzymol. , vol.374 , pp. 204-225
    • Volkmann, N.1    Hanein, D.2
  • 48
    • 3843129685 scopus 로고    scopus 로고
    • NMR structure of a type IVb pilin from Salmonella typhi and its assembly into pilus
    • Xu X.-F., Tan Y.-W., Lam L., Hackett J., Zhang M., Mok Y.-K. NMR structure of a type IVb pilin from Salmonella typhi and its assembly into pilus. J. Biol. Chem. 2004, 279:31599-31605.
    • (2004) J. Biol. Chem. , vol.279 , pp. 31599-31605
    • Xu, X.-F.1    Tan, Y.-W.2    Lam, L.3    Hackett, J.4    Zhang, M.5    Mok, Y.-K.6


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