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Volumn 109, Issue 25, 2012, Pages 9875-9880

Accurate protein structure modeling using sparse NMR data and homologous structure information

Author keywords

Biochemistry; Biophysics; Computational biology; Nuclear magnetic resonance; Structural genomics

Indexed keywords

ARTICLE; CRYSTAL STRUCTURE; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE;

EID: 84862545655     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1202485109     Document Type: Article
Times cited : (35)

References (37)
  • 1
    • 0024988099 scopus 로고
    • 4-Dimensional heteronuclear triple-resonance NMR-spectroscopy of interleukin-1-beta in solution
    • Kay LE, Clore GM, Bax A, Gronenborn AM (1990) 4-Dimensional heteronuclear triple-resonance NMR-spectroscopy of interleukin-1-beta in solution. Science 249:411-414.
    • (1990) Science , vol.249 , pp. 411-414
    • Kay, L.E.1    Clore, G.M.2    Bax, A.3    Gronenborn, A.M.4
  • 2
    • 0033582287 scopus 로고    scopus 로고
    • Chemical ligation of folded recombinant proteins: Segmental isotopic labeling of domains for NMR studies
    • Xu R, Ayers B, Cowburn D, Muir TW (1999) Chemical ligation of folded recombinant proteins: segmental isotopic labeling of domains for NMR studies. Proc Natl Acad Sci USA 96:388-393.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 388-393
    • Xu, R.1    Ayers, B.2    Cowburn, D.3    Muir, T.W.4
  • 3
    • 0030735988 scopus 로고    scopus 로고
    • Solution NMR spectroscopy beyond 25 kDa
    • Kay LE, Gardner KH (1997) Solution NMR spectroscopy beyond 25 kDa. Curr Opin Struct Biol 7:722-731.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 722-731
    • Kay, L.E.1    Gardner, K.H.2
  • 4
    • 0032898682 scopus 로고    scopus 로고
    • A robust and cost-effective method for the production of Val, Leu, Ile (delta 1) methyl-protonated N-15-, C-13-, H-2-labeled proteins
    • Goto NK, Gardner KH, Mueller GA, Willis RC, Kay LE (1999) A robust and cost-effective method for the production of Val, Leu, Ile (delta 1) methyl-protonated N-15-, C-13-, H-2-labeled proteins. J Biomol NMR 13:369-374.
    • (1999) J Biomol NMR , vol.13 , pp. 369-374
    • Goto, N.K.1    Gardner, K.H.2    Mueller, G.A.3    Willis, R.C.4    Kay, L.E.5
  • 5
    • 33644774471 scopus 로고    scopus 로고
    • Optimal isotope labelling for NMR protein structure determinations
    • Kainosho M, et al. (2006) Optimal isotope labelling for NMR protein structure determinations. Nature 440:52-57.
    • (2006) Nature , vol.440 , pp. 52-57
    • Kainosho, M.1
  • 6
    • 79960607694 scopus 로고    scopus 로고
    • Solid-state NMR of proteins sedimented by ultracentrifugation
    • Bertini I, et al. (2011) Solid-state NMR of proteins sedimented by ultracentrifugation. Proc Natl Acad Sci USA 108:10396-10399.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 10396-10399
    • Bertini, I.1
  • 7
    • 0030612833 scopus 로고    scopus 로고
    • Attenuated T-2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution
    • Pervushin K, Riek R, Wider G, Wuthrich K (1997) Attenuated T-2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Natl Acad Sci USA 94:12366-12371.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 12366-12371
    • Pervushin, K.1    Riek, R.2    Wider, G.3    Wuthrich, K.4
  • 9
    • 33846928691 scopus 로고    scopus 로고
    • Quantitative dynamics and binding studies of the 20 S proteasome by NMR
    • Sprangers R, Kay LE (2007) Quantitative dynamics and binding studies of the 20 S proteasome by NMR. Nature 445:618-622.
    • (2007) Nature , vol.445 , pp. 618-622
    • Sprangers, R.1    Kay, L.E.2
  • 10
    • 33745863903 scopus 로고    scopus 로고
    • Disorder-order folding transitions underlie catalysis in the helicase motor of SecA
    • Keramisanou D, et al. (2006) Disorder-order folding transitions underlie catalysis in the helicase motor of SecA. Nat Struct Mol Biol 13:594-602.
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 594-602
    • Keramisanou, D.1
  • 11
    • 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, Guntert P, Wuthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209-227.
    • (2002) J Mol Biol , vol.319 , pp. 209-227
    • Herrmann, T.1    Guntert, P.2    Wuthrich, K.3
  • 12
    • 80051691505 scopus 로고    scopus 로고
    • Exclusively NOESY-based automated NMR assignment and structure determination of proteins
    • Ikeya T, et al. (2011) Exclusively NOESY-based automated NMR assignment and structure determination of proteins. J Biomol NMR 50:137-146.
    • (2011) J Biomol NMR , vol.50 , pp. 137-146
    • Ikeya, T.1
  • 13
    • 31944451135 scopus 로고    scopus 로고
    • A topology-constrained distance network algorithm for protein structure determination from NOESY data
    • Huang YJ, Tejero R, Powers R, Montelione GT (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins 62:587-603.
    • (2006) Proteins , vol.62 , pp. 587-603
    • Huang, Y.J.1    Tejero, R.2    Powers, R.3    Montelione, G.T.4
  • 14
    • 84863011912 scopus 로고    scopus 로고
    • Blind testing of routine, fully automated determination of protein structures from NMR data
    • Rosato A, et al. (2012) Blind testing of routine, fully automated determination of protein structures from NMR data. Structure 20:227-236.
    • (2012) Structure , vol.20 , pp. 227-236
    • Rosato, A.1
  • 15
    • 42449146665 scopus 로고    scopus 로고
    • Consistent blind protein structure generation from NMR chemical shift data
    • Shen Y, et al. (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105:4685-4690.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 4685-4690
    • Shen, Y.1
  • 17
    • 77149179401 scopus 로고    scopus 로고
    • NMR structure determination for larger proteins using backbone-only data
    • Raman S, et al. (2010) NMR structure determination for larger proteins using backbone-only data. Science 327:1014-1018.
    • (2010) Science , vol.327 , pp. 1014-1018
    • Raman, S.1
  • 18
    • 79954990720 scopus 로고    scopus 로고
    • Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings
    • Sgourakis NG, et al. (2011) Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings. J Am Chem Soc 133:6288-6298.
    • (2011) J Am Chem Soc , vol.133 , pp. 6288-6298
    • Sgourakis, N.G.1
  • 19
    • 0037076277 scopus 로고    scopus 로고
    • CLOUDS, a protocol for deriving a molecular proton density via NMR
    • Grishaev A, Llinas M (2002) CLOUDS, a protocol for deriving a molecular proton density via NMR. Proc Natl Acad Sci USA 99:6707-6712.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 6707-6712
    • Grishaev, A.1    Llinas, M.2
  • 20
    • 0346103679 scopus 로고    scopus 로고
    • Rapid protein fold determination using unassigned NMR data
    • Meiler J, Baker D (2003) Rapid protein fold determination using unassigned NMR data. Proc Natl Acad Sci USA 100:15404-15409.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 15404-15409
    • Meiler, J.1    Baker, D.2
  • 21
    • 18844433630 scopus 로고    scopus 로고
    • Assessing precision and accuracy of protein structures derived from NMR data
    • Snyder DA, Bhattacharya A, Huang YJ, Montelione GT (2005) Assessing precision and accuracy of protein structures derived from NMR data. Proteins 59:655-661.
    • (2005) Proteins , vol.59 , pp. 655-661
    • Snyder, D.A.1    Bhattacharya, A.2    Huang, Y.J.3    Montelione, G.T.4
  • 23
    • 22144489530 scopus 로고    scopus 로고
    • Inferential structure determination
    • Rieping W, Habeck M, Nilges M (2005) Inferential structure determination. Science 309:303-306.
    • (2005) Science , vol.309 , pp. 303-306
    • Rieping, W.1    Habeck, M.2    Nilges, M.3
  • 24
    • 0025367860 scopus 로고
    • Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat
    • Torda AE, Scheek RM, van Gunsteren WF (1990) Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat. J Mol Biol 214:223-235.
    • (1990) J Mol Biol , vol.214 , pp. 223-235
    • Torda, A.E.1    Scheek, R.M.2    Van Gunsteren, W.F.3
  • 25
    • 33846532929 scopus 로고    scopus 로고
    • The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins
    • Richter B, Gsponer J, Varnai P, Salvatella X, Vendruscolo M (2007) The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins. J Biomol NMR 37:117-135.
    • (2007) J Biomol NMR , vol.37 , pp. 117-135
    • Richter, B.1    Gsponer, J.2    Varnai, P.3    Salvatella, X.4    Vendruscolo, M.5
  • 26
    • 0029022355 scopus 로고
    • Conformational variability of solution nuclear magnetic resonance structures
    • Bonvin AM, Brunger AT (1995) Conformational variability of solution nuclear magnetic resonance structures. J Mol Biol 250:80-93.
    • (1995) J Mol Biol , vol.250 , pp. 80-93
    • Bonvin, A.M.1    Brunger, A.T.2
  • 27
    • 79960078022 scopus 로고    scopus 로고
    • Incorporation of evolutionary information into Rosetta comparative modeling
    • Thompson J, Baker D (2011) Incorporation of evolutionary information into Rosetta comparative modeling. Proteins 79:2380-2388.
    • (2011) Proteins , vol.79 , pp. 2380-2388
    • Thompson, J.1    Baker, D.2
  • 28
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 29
    • 33748441391 scopus 로고    scopus 로고
    • A general method for the unbiased improvement of solution NMR structures by the use of related X-ray data, the AUREMOL-ISIC algorithm
    • Brunner K, Gronwald W, Trenner JM, Neidig KP, Kalbitzer HR (2006) A general method for the unbiased improvement of solution NMR structures by the use of related X-ray data, the AUREMOL-ISIC algorithm. BMC Struct Biol 6:14.
    • (2006) BMC Struct Biol , vol.6 , pp. 14
    • Brunner, K.1    Gronwald, W.2    Trenner, J.M.3    Neidig, K.P.4    Kalbitzer, H.R.5
  • 30
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • Bradley P, Misura KM, Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309:1868-1871.
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.2    Baker, D.3
  • 31
    • 0032396395 scopus 로고    scopus 로고
    • Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments
    • Sahasrabudhe PV, Tejero R, Kitao S, Furuichi Y, Montelione GT (1998) Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments. Proteins 33:558-566.
    • (1998) Proteins , vol.33 , pp. 558-566
    • Sahasrabudhe, P.V.1    Tejero, R.2    Kitao, S.3    Furuichi, Y.4    Montelione, G.T.5
  • 32
    • 34447508216 scopus 로고    scopus 로고
    • Phaser crystallographic software
    • McCoy AJ, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40:658-674.
    • (2007) J Appl Crystallogr , vol.40 , pp. 658-674
    • McCoy, A.J.1
  • 33
    • 35448929112 scopus 로고    scopus 로고
    • A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing
    • Andrec M, et al. (2007) A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins 69:449-465.
    • (2007) Proteins , vol.69 , pp. 449-465
    • Andrec, M.1
  • 34
    • 13644252170 scopus 로고    scopus 로고
    • Protein NMR recall, precision, and F-measure scores (RPF scores): Structure quality assessment measures based on information retrieval statistics
    • Huang YJ, Powers R, Montelione GT (2005) Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127:1665-1674.
    • (2005) J Am Chem Soc , vol.127 , pp. 1665-1674
    • Huang, Y.J.1    Powers, R.2    Montelione, G.T.3
  • 35
    • 48849113878 scopus 로고    scopus 로고
    • Comparative protein structure modeling using MODELLER
    • Chap 2:Unit 2 9; 10.1002/0471140864.ps0209s50
    • Eswar N, et al. (2007) Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci, Chap 2:Unit 2 9; 10.1002/0471140864. ps0209s50.
    • (2007) Curr Protoc Protein Sci
    • Eswar, N.1
  • 36
    • 19444387760 scopus 로고    scopus 로고
    • The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions
    • Forster A, Masters EI, Whitby FG, Robinson H, Hill CP (2005) The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions. Mol Cell 18:589-599.
    • (2005) Mol Cell , vol.18 , pp. 589-599
    • Forster, A.1    Masters, E.I.2    Whitby, F.G.3    Robinson, H.4    Hill, C.P.5
  • 37
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33:2302-2309.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2


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