메뉴 건너뛰기




Volumn 18, Issue 8, 2010, Pages 923-933

Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins

Author keywords

Proteins

Indexed keywords

PROTEIN;

EID: 77955498721     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2010.04.016     Document Type: Article
Times cited : (126)

References (40)
  • 1
    • 70350348011 scopus 로고    scopus 로고
    • NMR spectroscopy brings invisible protein states into focus
    • Baldwin A.J., Kay L.E. NMR spectroscopy brings invisible protein states into focus. Nat. Chem. Biol. 2009, 5:808-814.
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 808-814
    • Baldwin, A.J.1    Kay, L.E.2
  • 2
    • 0033654297 scopus 로고    scopus 로고
    • Generalized born models of macromolecular solvation effects
    • Bashford D., Case D.A. Generalized born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. 2000, 51:129-152.
    • (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 129-152
    • Bashford, D.1    Case, D.A.2
  • 3
    • 34547563370 scopus 로고    scopus 로고
    • The RCI server: Rapid and accurate calculation of protein flexibility using chemical shifts
    • Berjanskii M.V., Wishart D.S. The RCI server: Rapid and accurate calculation of protein flexibility using chemical shifts. Nucleic Acids Res. 2007, 35:W531-W537.
    • (2007) Nucleic Acids Res. , vol.35
    • Berjanskii, M.V.1    Wishart, D.S.2
  • 5
    • 37049014272 scopus 로고    scopus 로고
    • Version 1.2 of the crystallography and NMR system
    • Brunger A.T. Version 1.2 of the crystallography and NMR system. Nat. Protoc. 2007, 2:2728-2733.
    • (2007) Nat. Protoc. , vol.2 , pp. 2728-2733
    • Brunger, A.T.1
  • 7
    • 27844498431 scopus 로고    scopus 로고
    • Application of torsion angle molecular dynamics for efficient sampling of protein conformations
    • Chen J.H., Im W., Brooks C.L. Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J. Comput. Chem. 2005, 26:1565-1578.
    • (2005) J. Comput. Chem. , vol.26 , pp. 1565-1578
    • Chen, J.H.1    Im, W.2    Brooks, C.L.3
  • 8
    • 0032568556 scopus 로고    scopus 로고
    • New methods of structure refinement for macromolecular structure determination by NMR
    • Clore G.M., Gronenborn A.M. New methods of structure refinement for macromolecular structure determination by NMR. Proc. Natl. Acad. Sci. USA 1998, 95:5891-5898.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 5891-5898
    • Clore, G.M.1    Gronenborn, A.M.2
  • 9
    • 0033003335 scopus 로고    scopus 로고
    • Backbone angle restraints from searching a database for chemical shift and sequence homology
    • Cornilescu G., Delaglio F., Bax A. Backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 1999, 13:289-302.
    • (1999) J. Biomol. NMR , vol.13 , pp. 289-302
    • Cornilescu, G.1    Delaglio, F.2    Bax, A.3
  • 10
    • 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
  • 12
    • 70450194574 scopus 로고    scopus 로고
    • Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins
    • De Simone A., Cavalli A., Hsu S.T.D., Vranken W., Vendruscolo M. Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins. J. Am. Chem. Soc. 2009, 131:16332-16333.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 16332-16333
    • De Simone, A.1    Cavalli, A.2    Hsu, S.T.D.3    Vranken, W.4    Vendruscolo, M.5
  • 13
    • 0034620764 scopus 로고    scopus 로고
    • Protein structure determination using molecular fragment replacement and NMR dipolar couplings
    • Delaglio F., Kontaxis G., Bax A. Protein structure determination using molecular fragment replacement and NMR dipolar couplings. J. Am. Chem. Soc. 2000, 122:2142-2143.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 2142-2143
    • Delaglio, F.1    Kontaxis, G.2    Bax, A.3
  • 14
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    • Duan Y., Wu C., Chowdhury S., Lee M.C., Xiong G.M., Zhang W., Yang R., Cieplak P., Luo R., Lee T., et al. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 2003, 24:1999-2012.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Chowdhury, S.3    Lee, M.C.4    Xiong, G.M.5    Zhang, W.6    Yang, R.7    Cieplak, P.8    Luo, R.9    Lee, T.10
  • 16
    • 70349627256 scopus 로고    scopus 로고
    • Fast and accurate predictions of protein NMR chemical shifts from interatomic distances
    • Kohlhoff K.J., Robustelli P., Cavalli A., Salvatella X., Vendruscolo M. Fast and accurate predictions of protein NMR chemical shifts from interatomic distances. J. Am. Chem. Soc. 2009, 131:13894-13895.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 13894-13895
    • Kohlhoff, K.J.1    Robustelli, P.2    Cavalli, A.3    Salvatella, X.4    Vendruscolo, M.5
  • 17
    • 0029314335 scopus 로고
    • The impact of direct refinement against proton chemical-shifts on protein-structure determination by NMR
    • Kuszewski J., Gronenborn A.M., Clore G.M. The impact of direct refinement against proton chemical-shifts on protein-structure determination by NMR. J. Magn. Reson. B. 1995, 107:293-297.
    • (1995) J. Magn. Reson. B. , vol.107 , pp. 293-297
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 19
    • 0038703404 scopus 로고    scopus 로고
    • Proshift: protein chemical shift prediction using artificial neural networks
    • Meiler J. Proshift: protein chemical shift prediction using artificial neural networks. J. Biomol. NMR 2003, 26:25-37.
    • (2003) J. Biomol. NMR , vol.26 , pp. 25-37
    • Meiler, J.1
  • 20
    • 56749151048 scopus 로고    scopus 로고
    • Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex
    • Montalvao R.W., Cavalli A., Salvatella X., Blundell T.L., Vendruscolo M. Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex. J. Am. Chem. Soc. 2008, 130:15990-15996.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 15990-15996
    • Montalvao, R.W.1    Cavalli, A.2    Salvatella, X.3    Blundell, T.L.4    Vendruscolo, M.5
  • 21
    • 0038407231 scopus 로고    scopus 로고
    • Rapid and accurate calculation of protein H-1, C-13 and N-15 chemical shifts
    • Neal S., Nip A.M., Zhang H.Y., Wishart D.S. Rapid and accurate calculation of protein H-1, C-13 and N-15 chemical shifts. J. Biomol. NMR 2003, 26:215-240.
    • (2003) J. Biomol. NMR , vol.26 , pp. 215-240
    • Neal, S.1    Nip, A.M.2    Zhang, H.Y.3    Wishart, D.S.4
  • 22
    • 0345674016 scopus 로고
    • Molecular orbital theory of aromatic ring currents
    • Pople J.A. Molecular orbital theory of aromatic ring currents. Mol. Physiol. 1958, 1:175-180.
    • (1958) Mol. Physiol. , vol.1 , pp. 175-180
    • Pople, J.A.1
  • 23
    • 57049170316 scopus 로고    scopus 로고
    • Determination of protein structures from solid-state NMR chemical shifts
    • Robustelli P., Cavalli A., Vendruscolo M. Determination of protein structures from solid-state NMR chemical shifts. Structure 2008, 16:1764-1769.
    • (2008) Structure , vol.16 , pp. 1764-1769
    • Robustelli, P.1    Cavalli, A.2    Vendruscolo, M.3
  • 24
    • 66549130822 scopus 로고    scopus 로고
    • Folding of small proteins by Monte Carlo simulations with chemical shift restraints without the use of molecular fragment replacement or structural homology
    • Robustelli P., Cavalli A., Dobson C.M., Vendruscolo M., Salvatella X. Folding of small proteins by Monte Carlo simulations with chemical shift restraints without the use of molecular fragment replacement or structural homology. J. Phys. Chem. B 2009, 113:7890-7896.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 7890-7896
    • Robustelli, P.1    Cavalli, A.2    Dobson, C.M.3    Vendruscolo, M.4    Salvatella, X.5
  • 25
    • 33646940952 scopus 로고
    • Numerical-integration of cartesian equations of motion of a system with constraints-molecular-dynamics of n-alkanes
    • Ryckaert J.P., Ciccotti G., Berendsen H.J.C. Numerical-integration of cartesian equations of motion of a system with constraints-molecular-dynamics of n-alkanes. J. Comp. Physiol. 1977, 23:327-341.
    • (1977) J. Comp. Physiol. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 27
    • 0035742323 scopus 로고    scopus 로고
    • Internal coordinates for molecular dynamics and minimization in structure determination and refinement
    • Schwieters C.D., Clore G.M. Internal coordinates for molecular dynamics and minimization in structure determination and refinement. J. Magn. Reson. 2001, 152:288-302.
    • (2001) J. Magn. Reson. , vol.152 , pp. 288-302
    • Schwieters, C.D.1    Clore, G.M.2
  • 29
    • 34547179849 scopus 로고    scopus 로고
    • Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology
    • Shen Y., Bax A. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J. Biomol. NMR 2007, 38:289-302.
    • (2007) J. Biomol. NMR , vol.38 , pp. 289-302
    • Shen, Y.1    Bax, A.2
  • 31
    • 58149468410 scopus 로고    scopus 로고
    • De novo protein structure generation from incomplete chemical shift assignments
    • Shen Y., Vernon R., Baker D., Bax A. De novo protein structure generation from incomplete chemical shift assignments. J. Biomol. NMR 2009, 43:63-78.
    • (2009) J. Biomol. NMR , vol.43 , pp. 63-78
    • Shen, Y.1    Vernon, R.2    Baker, D.3    Bax, A.4
  • 32
    • 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., Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 1997, 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
  • 33
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita Y., Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999, 314:141-151.
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 35
    • 50149085281 scopus 로고    scopus 로고
    • Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy
    • Vallurupalli P., Hansen D.F., Kay L.E. Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy. Proc. Natl. Acad. Sci. USA 2008, 105:11766-11771.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 11766-11771
    • Vallurupalli, P.1    Hansen, D.F.2    Kay, L.E.3
  • 36
    • 0034923356 scopus 로고    scopus 로고
    • Use of chemical shifts in macromolecular structure determination
    • Wishart D.S., Case D.A. Use of chemical shifts in macromolecular structure determination. Methods Enzymol. 2001, 338:3-34.
    • (2001) Methods Enzymol. , vol.338 , pp. 3-34
    • Wishart, D.S.1    Case, D.A.2
  • 37
    • 0026410969 scopus 로고
    • Relationship between nuclear-magnetic-resonance chemical-shift and protein secondary structure
    • Wishart D.S., Sykes B.D., Richards F.M. Relationship between nuclear-magnetic-resonance chemical-shift and protein secondary structure. J. Mol. Biol. 1991, 222:311-333.
    • (1991) J. Mol. Biol. , vol.222 , pp. 311-333
    • Wishart, D.S.1    Sykes, B.D.2    Richards, F.M.3
  • 38
    • 48449095850 scopus 로고    scopus 로고
    • Cs23d: a web server for rapid protein structure generation using NMR chemical shifts and sequence data
    • Wishart D.S., Arndt D., Berjanskii M., Tang P., Zhou J., Lin G. Cs23d: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res. 2008, 36:W496-W502.
    • (2008) Nucleic Acids Res. , vol.36
    • Wishart, D.S.1    Arndt, D.2    Berjanskii, M.3    Tang, P.4    Zhou, J.5    Lin, G.6
  • 39
    • 0037114648 scopus 로고    scopus 로고
    • Probing multiple effects on N-15, C-13 alpha, C-13 beta, and C-13 ' chemical shifts in peptides using density functional theory
    • Xu X.P., Case D.A. Probing multiple effects on N-15, C-13 alpha, C-13 beta, and C-13 ' chemical shifts in peptides using density functional theory. Biopolymers 2002, 65:408-423.
    • (2002) Biopolymers , vol.65 , pp. 408-423
    • Xu, X.P.1    Case, D.A.2
  • 40
    • 0037354231 scopus 로고    scopus 로고
    • RefDB: a database of uniformly referenced protein chemical shifts
    • Zhang H., Neal S., Wishart D.S. RefDB: a database of uniformly referenced protein chemical shifts. J. Biomol. NMR 2003, 25:173-195.
    • (2003) J. Biomol. NMR , vol.25 , pp. 173-195
    • Zhang, H.1    Neal, S.2    Wishart, D.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.