메뉴 건너뛰기




Volumn 105, Issue 38, 2008, Pages 14389-14394

Quantum chemical 13Cα chemical shift calculations for protein NMR structure determination, refinement, and validation

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTON NUCLEAR MAGNETIC RESONANCE; VALIDATION PROCESS; X RAY CRYSTALLOGRAPHY; BACILLUS SUBTILIS; CHEMICAL STRUCTURE; CHEMISTRY; HYDROGEN BOND; MECHANICAL TORSION; NUCLEAR MAGNETIC RESONANCE; PROTEIN TERTIARY STRUCTURE; REPRODUCIBILITY;

EID: 55749100006     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0807105105     Document Type: Article
Times cited : (50)

References (34)
  • 3
    • 41149141810 scopus 로고    scopus 로고
    • α chemical shifts for accurate determination of β-sheet structures in solution
    • α chemical shifts for accurate determination of β-sheet structures in solution. Proc Natl Acad Sci USA 105: 1891-1896.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 1891-1896
    • Vila, J.A.1    Arnautova, Y.A.2    Scheraga, H.A.3
  • 4
    • 41149110741 scopus 로고    scopus 로고
    • α chemical shifts to determine, refine, and validate protein structures
    • α chemical shifts to determine, refine, and validate protein structures. Proteins Struct Funct Bioinf 71:641-654.
    • (2008) Proteins Struct Funct Bioinf , vol.71 , pp. 641-654
    • Vila, J.A.1    Scheraga, H.A.2
  • 5
    • 0347610773 scopus 로고
    • 13C nuclear-magnetic-resonance chemical shifts
    • 13C nuclear-magnetic-resonance chemical shifts. J Am Chem Soc 113:5490-5492.
    • (1991) J Am Chem Soc , vol.113 , pp. 5490-5492
    • Spera, S.1    Bax, A.2
  • 6
    • 0027308278 scopus 로고
    • Secondary and tertiary structural effects on protein NMR chemical shifts: An ab initio approach
    • deDios AC, Pearson JG, Oldfield E (1993) Secondary and tertiary structural effects on protein NMR chemical shifts: An ab initio approach. Science 260:1491-1496.
    • (1993) Science , vol.260 , pp. 1491-1496
    • deDios, A.C.1    Pearson, J.G.2    Oldfield, E.3
  • 8
    • 0031450809 scopus 로고    scopus 로고
    • Predicting chemical shifts in proteins: Structure refinement of valine residues by using ab initio and empirical geometry optimizations
    • Pearson JG, et al. (1997) Predicting chemical shifts in proteins: Structure refinement of valine residues by using ab initio and empirical geometry optimizations. J Am Chem Soc 119:11941-11950.
    • (1997) J Am Chem Soc , vol.119 , pp. 11941-11950
    • Pearson, J.G.1
  • 10
    • 0033064395 scopus 로고    scopus 로고
    • β carbon-13 chemical shifts in protein from an empirical database
    • β carbon-13 chemical shifts in protein from an empirical database. J Biomol NMR 13:199-211.
    • (1999) J Biomol NMR , vol.13 , pp. 199-211
    • Iwadate, M.1    Asakura, T.2    Williamson, M.P.3
  • 11
    • 0035544152 scopus 로고    scopus 로고
    • 13C′ chemical shifts in proteins using a density functional database
    • 13C′ chemical shifts in proteins using a density functional database. J Biomol NMR 21:321-333.
    • (2001) J Biomol NMR , vol.21 , pp. 321-333
    • Xu, X.-P.1    Case, D.A.J.2
  • 12
    • 0037094144 scopus 로고    scopus 로고
    • Carbon-13 NMR shielding in the twenty common amino acids: Comparisons with experimental results in proteins
    • Sun H, Sanders LK, Oldfield E (2002) Carbon-13 NMR shielding in the twenty common amino acids: Comparisons with experimental results in proteins. J Am Chem Soc 124:5486-5495.
    • (2002) J Am Chem Soc , vol.124 , pp. 5486-5495
    • Sun, H.1    Sanders, L.K.2    Oldfield, E.3
  • 14
    • 0037326508 scopus 로고    scopus 로고
    • Identification of a protein, YneA, responsible for cell division suppression during the SOS response in Bacillus subtilis
    • Kawai Y, Moriya S, Ogasawara N (2003) Identification of a protein, YneA, responsible for cell division suppression during the SOS response in Bacillus subtilis. Mol Microbiol 47:1113-1122.
    • (2003) Mol Microbiol , vol.47 , pp. 1113-1122
    • Kawai, Y.1    Moriya, S.2    Ogasawara, N.3
  • 15
    • 44949100344 scopus 로고    scopus 로고
    • Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis
    • Aramini JM, et al. (2008) Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis. Proteins 72:526-530.
    • (2008) Proteins , vol.72 , pp. 526-530
    • Aramini, J.M.1
  • 16
    • 55749104149 scopus 로고    scopus 로고
    • Kuzin AP, et al. (2008) Crystal structure of UPF0291 protein ynzC from Bacillus subtilis at resolution 2.0 A. Northeast Structural Genomics Consortium target SR384. 10.2210/pdb3bhp/pdb.
    • Kuzin AP, et al. (2008) Crystal structure of UPF0291 protein ynzC from Bacillus subtilis at resolution 2.0 A. Northeast Structural Genomics Consortium target SR384. 10.2210/pdb3bhp/pdb.
  • 17
    • 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
  • 18
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Lüthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83-85.
    • (1992) Nature , vol.356 , pp. 83-85
    • Lüthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 19
    • 0027490731 scopus 로고
    • Recognition of errors in three-dimensional structures of proteins
    • Sippl MJ (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17:355-362.
    • (1993) Proteins , vol.17 , pp. 355-362
    • Sippl, M.J.1
  • 20
  • 21
    • 0037441653 scopus 로고    scopus 로고
    • Structure validation by Cα geometry: φ, ψ, and Cβ deviation
    • Lovell SC, et al. (2003) Structure validation by Cα geometry: φ, ψ, and Cβ deviation. Proteins 50:437-450.
    • (2003) Proteins , vol.50 , pp. 437-450
    • Lovell, S.C.1
  • 22
    • 34547592557 scopus 로고    scopus 로고
    • MolProbity: All-atom contacts and structure validation for proteins and nucleic acids
    • Davis IW, et al. (2007) MolProbity: All-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375-W383.
    • (2007) Nucleic Acids Res , vol.35
    • Davis, I.W.1
  • 23
    • 33847079676 scopus 로고    scopus 로고
    • Evaluating protein structures determined by structural genomics consortia
    • Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66:778-795.
    • (2007) Proteins , vol.66 , pp. 778-795
    • Bhattacharya, A.1    Tejero, R.2    Montelione, G.T.3
  • 24
    • 0029181728 scopus 로고
    • 15N random coil NMR chemical-shifts of the common amino-acids. 1. Investigations of nearest-neighbor effects
    • 15N random coil NMR chemical-shifts of the common amino-acids. 1. Investigations of nearest-neighbor effects. J Biomol NMR 5:67-81.
    • (1995) J Biomol NMR , vol.5 , pp. 67-81
    • Wishart, D.S.1    Bigam, C.G.2    Holm, A.3    Hodges, R.S.4    Sykes, B.D.5
  • 25
    • 0023914645 scopus 로고
    • Variable-target-function and buildup procedures for the calculation of protein conformation - Application to bovine pancreatic trypsin-inhibitor using limited simulated nuclear magnetic-resonance data
    • Vásquez M, Scheraga HA (1988) Variable-target-function and buildup procedures for the calculation of protein conformation - Application to bovine pancreatic trypsin-inhibitor using limited simulated nuclear magnetic-resonance data. J Biomol Struct Dyn 5:757-784.
    • (1988) J Biomol Struct Dyn , vol.5 , pp. 757-784
    • Vásquez, M.1    Scheraga, H.A.2
  • 26
    • 0029249555 scopus 로고
    • Combined use of 13C chemical shift and 1Hα-13Cα heteronuclear NOE data in monitoring a protein NMR structure refinement
    • Celda B, Biamonti C, Arnau MJ, Tejero R, Montelione GT (1995) Combined use of 13C chemical shift and 1Hα-13Cα heteronuclear NOE data in monitoring a protein NMR structure refinement. J Biomol NMR 5:161-172.
    • (1995) J Biomol NMR , vol.5 , pp. 161-172
    • Celda, B.1    Biamonti, C.2    Arnau, M.J.3    Tejero, R.4    Montelione, G.T.5
  • 27
    • 0001415022 scopus 로고
    • in Numerical Recipes in Fortran 77. The Art of Scientific Computing (Cambridge Univ Press, Cambridge, UK)
    • Press HW, Teukolsky SA, Vetterling WT, Flannery BP (1992) in Numerical Recipes in Fortran 77. The Art of Scientific Computing (Cambridge Univ Press, Cambridge, UK), Second Ed, pp 630-633.
    • (1992) Second Ed , pp. 630-633
    • Press, H.W.1    Teukolsky, S.A.2    Vetterling, W.T.3    Flannery, B.P.4
  • 28
    • 0032528033 scopus 로고    scopus 로고
    • Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase
    • Cornilescu G, Marquardt JL, Ottiger M, Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc120:6836-6837.
    • (1998) J Am Chem Soc , vol.120 , pp. 6836-6837
    • Cornilescu, G.1    Marquardt, J.L.2    Ottiger, M.3    Bax, A.4
  • 29
    • 0023644679 scopus 로고
    • Structure of ubiquitin refined at 1.8 Å resolution
    • Vijay-Kumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 Å resolution. J Mol Biol 194:531-544.
    • (1987) J Mol Biol , vol.194 , pp. 531-544
    • Vijay-Kumar, S.1    Bugg, C.E.2    Cook, W.J.3
  • 30
    • 0031718310 scopus 로고    scopus 로고
    • Homology modeling, model and software evaluation: Three related resources
    • Rodriguez R, Chinea G, Lopez N, Pons T, Vriend G (1998) Homology modeling, model and software evaluation: Three related resources. Bioinformatics 14:523-528.
    • (1998) Bioinformatics , vol.14 , pp. 523-528
    • Rodriguez, R.1    Chinea, G.2    Lopez, N.3    Pons, T.4    Vriend, G.5
  • 31
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: A program for display and analysis of macromolecular structures. J Mol Graphics 14:51-55.
    • (1996) J Mol Graphics , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wüthrich, K.3
  • 32
    • 20144387833 scopus 로고    scopus 로고
    • Robotic cloning and protein production platform of the Northeast Structural Genomics Consortium
    • Acton TB, et al. (2005) Robotic cloning and protein production platform of the Northeast Structural Genomics Consortium. Methods Enzymol 394:210-243.
    • (2005) Methods Enzymol , vol.394 , pp. 210-243
    • Acton, T.B.1
  • 33
    • 0033954256 scopus 로고    scopus 로고
    • The Protein Data Bank
    • Berman HM, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242.
    • (2000) Nucleic Acids Res , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 34
    • 0001731773 scopus 로고
    • Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
    • Némethy G, et al. (1992) Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem 96:6472-6484.
    • (1992) J Phys Chem , vol.96 , pp. 6472-6484
    • Némethy, G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.