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Volumn 52, Issue 4, 2012, Pages 351-364

Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space

Author keywords

CYANA; CYRANGE; NMR structure; REGMEAN; Regularization

Indexed keywords

DIMER; HALORHODOPSIN; PROTEIN; PROTEIN COPZ; PROTEIN CPRP; PROTEIN ENTH; PROTEIN FSH2; PROTEIN FSPO; PROTEIN PBPA; PROTEIN SCAM; PROTEIN SMBP; PROTEIN WMKT; PROTEIN WW2D; RIBONUCLEASE A; UNCLASSIFIED DRUG;

EID: 84863110091     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-012-9615-8     Document Type: Article
Times cited : (21)

References (52)
  • 1
    • 0029767015 scopus 로고    scopus 로고
    • Ancestral βγ-crystallin precursor structure in a yeast killer toxin
    • DOI 10.1038/nsb0896-662
    • Antuch W, Güntert P, Wüthrich K (1996) Ancestral bc-crystallin precursor structure in a yeast killer toxin. Nat Struct Biol 3:662-665 (Pubitemid 26260053)
    • (1996) Nature Structural Biology , vol.3 , Issue.8 , pp. 662-665
    • Antuch, W.1    Guntert, P.2    Wuthrich, K.3
  • 3
    • 0000467663 scopus 로고    scopus 로고
    • Finding the Needle in a Haystack: Educing Native Folds from Ambiguous Ab Initio Protein Structure Predictions
    • DOI 10.1002/1096-987X(20 0102)22:3<339::AID-JC C1006>3.0.CO;2-R
    • Betancourt MR, Skolnick J (2001) Finding the needle in a haystack: educing native folds from ambiguous ab initio protein structure predictions. J Comput Chem 22:339-353 (Pubitemid 33645663)
    • (2001) Journal of Computational Chemistry , vol.22 , Issue.3 , pp. 339-353
    • Betancourt, M.R.1    Skolnick, J.2
  • 4
    • 77949319406 scopus 로고    scopus 로고
    • The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus at 1g79260.1
    • Bianchetti CM, Blouin GC, Bitto E, Olson JS, Phillips GN (2010) The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At 1g79260.1. Proteins 78:917-931
    • (2010) Proteins , vol.78 , pp. 917-931
    • Bianchetti, C.M.1    Blouin, G.C.2    Bitto, E.3    Olson, J.S.4    Phillips, G.N.5
  • 5
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie JU, Lüthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known 3-dimensional structure. Science 253:164-170 (Pubitemid 21917131)
    • (1991) Science , vol.253 , Issue.5016 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 8
    • 3242886389 scopus 로고    scopus 로고
    • MolProbity: Structure validation and all-atom contact analysis for nucleic acids and their complexes
    • DOI 10.1093/nar/gkh398
    • Davis IW, Murray LW, Richardson JS, Richardson DC (2004) MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 32:W615-W619 (Pubitemid 38997409)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS.
    • Davis, I.W.1    Murray, L.W.2    Richardson, J.S.3    Richardson, D.C.4
  • 10
    • 63849199864 scopus 로고    scopus 로고
    • Improving consensus structure by eliminating averaging artifacts
    • Dukka BKC (2009) Improving consensus structure by eliminating averaging artifacts. BMC Struct Biol 9:12
    • (2009) BMC Struct Biol , vol.9 , pp. 12
    • Dukka, B.K.C.1
  • 12
    • 4344698912 scopus 로고    scopus 로고
    • Automated NMR protein structure calculation
    • Güntert P (2003) Automated NMR protein structure calculation. Prog Nucl Magn Reson Spectrosc 43:105-125
    • (2003) Prog Nucl Magn Reson Spectrosc , vol.43 , pp. 105-125
    • Güntert, P.1
  • 13
    • 58849162221 scopus 로고    scopus 로고
    • Automated structure determination from NMR spectra
    • Güntert P (2009) Automated structure determination from NMR spectra. Eur Biophys J 38:129-143
    • (2009) Eur Biophys J , vol.38 , pp. 129-143
    • Güntert, P.1
  • 14
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program DYANA
    • DOI 10.1006/jmbi.1997.1284
    • Güntert P, Mumenthaler C, Wüthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283-298 (Pubitemid 27460230)
    • (1997) Journal of Molecular Biology , vol.273 , Issue.1 , pp. 283-298
    • Guntert, P.1    Mumenthaler, C.2    Wuthrich, K.3
  • 15
    • 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
    • DOI 10.1016/S0022-2836(02)00241-3
    • Herrmann T, Güntert P, Wüthrich 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 (Pubitemid 34729497)
    • (2002) Journal of Molecular Biology , vol.319 , Issue.1 , pp. 209-227
    • Herrmann, T.1    Guntert, P.2    Wuthrich, K.3
  • 18
    • 33644774471 scopus 로고    scopus 로고
    • Optimal isotope labelling for NMR protein structure determinations
    • DOI 10.1038/nature04525, PII N04525
    • Kainosho M, Torizawa T, Iwashita Y, Terauchi T, Ono AM, Güntert P (2006) Optimal isotope labelling for NMR protein structure determinations. Nature 440:52-57 (Pubitemid 43336263)
    • (2006) Nature , vol.440 , Issue.7080 , pp. 52-57
    • Kainosho, M.1    Torizawa, T.2    Iwashita, Y.3    Terauchi, T.4    Mei Ono, A.5    Guntert, P.6
  • 19
    • 0029831680 scopus 로고    scopus 로고
    • An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
    • Kelley LA, Gardner SP, Sutcliffe MJ(1996) An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Protein Eng 9:1063-1065 (Pubitemid 26402310)
    • (1996) Protein Engineering , vol.9 , Issue.11 , pp. 1063-1065
    • Kelley, L.A.1    Gardner, S.P.2    Sutcliffe, M.J.3
  • 20
    • 79955968115 scopus 로고    scopus 로고
    • Objective identification of residue ranges for the superposition of protein structures
    • Kirchner DK, Güntert P (2011) Objective identification of residue ranges for the superposition of protein structures. BMC Bioinform 12:170
    • (2011) BMC Bioinform , vol.12 , pp. 170
    • Kirchner, D.K.1    Güntert, P.2
  • 21
    • 0034717007 scopus 로고    scopus 로고
    • Structure of the light-driven chloride pump halorhodopsin at 1.8 A Resolution
    • DOI 10.1126/science.288.5470.1390
    • Kolbe M, Besir H, Essen LO, Oesterhelt D (2000) Structure of the light-driven chloride pump halorhodopsin at 1.8 A ° resolution. Science 288:1390-1396 (Pubitemid 30366319)
    • (2000) Science , vol.288 , Issue.5470 , pp. 1390-1396
    • Kolbe, M.1    Besir, H.2    Essen, L.-O.3    Oesterhelt, D.4
  • 22
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • DOI 10.1016/0263-7855(96)00009-4
    • Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14:51-55 (Pubitemid 26152976)
    • (1996) Journal of Molecular Graphics , vol.14 , Issue.1 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3
  • 23
    • 0034140558 scopus 로고    scopus 로고
    • Point-centered domain decomposition for parallel molecular dynamics simulation
    • DOI 10.1016/S0010-4655(99)00436-1
    • Koradi R, Billeter M, Güntert P (2000) Point-centered domain decomposition for parallel molecular dynamics simulation. Comput Phys Commun 124:139-147 (Pubitemid 30562273)
    • (2000) Computer Physics Communications , vol.124 , Issue.2-3 , pp. 139-147
    • Koradi, R.1    Billeter, M.2    Guntert, P.3
  • 24
    • 70349321435 scopus 로고    scopus 로고
    • X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: Further insight into protein stability
    • Kurpiewska K, Font J, Ribó M, Vilanova M, Lewiński K (2009) X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability. Proteins 77:658-669
    • (2009) Proteins , vol.77 , pp. 658-669
    • Kurpiewska, K.1    Font, J.2    Ribó, M.3    Vilanova, M.4    Lewiński, K.5
  • 27
    • 33749524593 scopus 로고    scopus 로고
    • Automated protein structure determination from NMR spectra
    • DOI 10.1021/ja061136l
    • López-Méndez B, Güntert P (2006) Automated protein structure determination from NMR spectra. J Am Chem Soc 128: 13112-13122 (Pubitemid 44527681)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.40 , pp. 13112-13122
    • Lopez-Mendez, B.1    Guntert, P.2
  • 29
    • 0026610767 scopus 로고
    • Assessment of protein models with 3-dimensional profiles
    • Lüthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with 3-dimensional profiles. Nature 356:83-85
    • (1992) Nature , vol.356 , pp. 83-85
    • Lüthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 30
    • 0030236215 scopus 로고    scopus 로고
    • The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules
    • Luginbühl P, Güntert P, Billeter M, Wüthrich K (1996) The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules. J Biomol NMR 8:136-146 (Pubitemid 126706783)
    • (1996) Journal of Biomolecular NMR , vol.8 , Issue.2 , pp. 136-146
    • Luginbuhl, P.1    Guntert, P.2    Billeter, M.3    Wuthrich, K.4
  • 32
    • 0024285896 scopus 로고
    • Determination of threedimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations
    • Nilges M, Clore GM, Gronenborn AM (1988) Determination of threedimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett 229:317-324
    • (1988) FEBS Lett , vol.229 , pp. 317-324
    • Nilges, M.1    Clore, G.M.2    Gronenborn, A.M.3
  • 38
    • 0242443693 scopus 로고    scopus 로고
    • Force fields for protein simulations
    • DOI 10.1016/S0065-3233(03)66002-X
    • Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Prot Chem 66:27-85 (Pubitemid 37392314)
    • (2003) Advances in Protein Chemistry , vol.66 , pp. 27-85
    • Ponder, J.W.1    Case, D.A.2
  • 42
    • 44449124693 scopus 로고    scopus 로고
    • Fast procedure for reconstruction of full-atom protein models from reduced representations
    • DOI 10.1002/jcc.20906
    • Rotkiewicz P, Skolnick J (2008) Fast procedure for reconstruction of full-atom protein models from reduced representations. J Comput Chem 29:1460-1465 (Pubitemid 351757769)
    • (2008) Journal of Computational Chemistry , vol.29 , Issue.9 , pp. 1460-1465
    • Rotkiewicz, P.1    Skolnick, J.2
  • 43
    • 0036367763 scopus 로고    scopus 로고
    • Reweighted atomic densities to represent ensembles of NMR structures
    • DOI 10.1023/A:1019875223132
    • Schwieters CD, Clore GM (2002) Reweighted atomic densities to represent ensembles of NMR structures. J Biomol NMR 23: 221-225 (Pubitemid 34982254)
    • (2002) Journal of Biomolecular NMR , vol.23 , Issue.3 , pp. 221-225
    • Schwieters, C.D.1    Clore, G.M.2
  • 46
    • 0027490731 scopus 로고
    • Recognition of errors in three-dimensional structures of proteins
    • DOI 10.1002/prot.340170404
    • Sippl MJ (1993) Recognition of errors in 3-dimensional structures of proteins. Proteins 17:355-362 (Pubitemid 23358545)
    • (1993) Proteins: Structure, Function and Genetics , vol.17 , Issue.4 , pp. 355-362
    • Sippl, M.J.1
  • 47
    • 0027178211 scopus 로고
    • Representing an ensemble of NMR-derived protein structures by a single structure
    • Sutcliffe MJ (1993) Representing an ensemble of NMR-derived protein structures by a single structure. Protein Sci 2:936-944 (Pubitemid 23152086)
    • (1993) Protein Science , vol.2 , Issue.6 , pp. 936-944
    • Sutcliffe, M.J.1
  • 49
    • 0037406141 scopus 로고    scopus 로고
    • Can correct protein models be identified?
    • DOI 10.1110/ps.0236803
    • Wallner B, Elofsson A (2003) Can correct protein models be identified? Protein Sci 12:1073-1086 (Pubitemid 36505441)
    • (2003) Protein Science , vol.12 , Issue.5 , pp. 1073-1086
    • Wallner, B.1    Elofsson, A.2
  • 50
    • 0033529633 scopus 로고    scopus 로고
    • NMR structure and metal interactions of the CopZ copper chaperone
    • Wimmer R, Herrmann T, Solioz M, Wüthrich K (1999) NMR structure and metal interactions of the CopZ copper chaperone. J Biol Chem 274:22597-22603
    • (1999) J Biol Chem , vol.274 , pp. 22597-22603
    • Wimmer, R.1    Herrmann, T.2    Solioz, M.3    Wüthrich, K.4
  • 51
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: A clustering approach to identify near-native protein folds
    • Zhang Y, Skolnick J (2004) SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 25:865-871
    • (2004) J Comput Chem , vol.25 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 52
    • 0028232369 scopus 로고
    • An assessment of the precision and accuracy of protein structures determined by NMR: Dependence on distance errors
    • Zhao DQ, Jardetzky O (1994) An assessment of the precision and accuracy of protein structures determined by NMR: dependence on distance errors. J Mol Biol 239:601-607
    • (1994) J Mol Biol , vol.239 , pp. 601-607
    • Zhao, D.Q.1    Jardetzky, O.2


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