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Volumn 443, Issue , 2008, Pages 229-255

Nuclear magnetic resonance-based modeling and refinement of protein three-dimensional structures and their complexes

Author keywords

Docking; NMR; Refinement; Structure calculation; Validation of structures

Indexed keywords


EID: 84934435926     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-177-2_13     Document Type: Article
Times cited : (2)

References (60)
  • 3
    • 0001875657 scopus 로고    scopus 로고
    • Vicinal coupling constants & conformation of biomolecules
    • Harris, D. M. G. a. K. R, Ed. John Wiley, London
    • Altona, C., Vicinal coupling constants & conformation of biomolecules. In Encyclopedia of Nuclear Magnetic Resonance, Harris, D. M. G. a. K. R., Ed. John Wiley, London: 1996; pp 4909-4922.
    • (1996) Encyclopedia of Nuclear Magnetic Resonance , pp. 4909-4922
    • Altona, C.1
  • 4
    • 0034919243 scopus 로고    scopus 로고
    • Dipolar couplings in macromolecular structure determination
    • Bax, A., Kontaxis, G. and Tjandra, N. (2001) Dipolar couplings in macromolecular structure determination. Methods in Enzymology 339, 127-174.
    • (2001) Methods in Enzymology , vol.339 , pp. 127-174
    • Bax, A.1    Kontaxis, G.2    Tjandra, N.3
  • 5
    • 0031714689 scopus 로고    scopus 로고
    • Structure calculation of biological macromolecules from NMR data
    • Guntert, P. (1998) Structure calculation of biological macromolecules from NMR data. Quarterly Reviews of Biophysics 31, 145-237.
    • (1998) Quarterly Reviews of Biophysics , vol.31 , pp. 145-237
    • Guntert, P.1
  • 9
    • 0037039335 scopus 로고    scopus 로고
    • Mapping protein-protein interactions in solution by NMR spectroscopy
    • Zuiderweg, E. R. (2002) Mapping protein-protein interactions in solution by NMR spectroscopy. Biochemistry 41, 1-7.
    • (2002) Biochemistry , vol.41 , pp. 1-7
    • Zuiderweg, E.R.1
  • 10
    • 12544256528 scopus 로고    scopus 로고
    • Data-driven docking for the study of biomolecular complexes
    • van Dijk, A. D. J., Boelens, R., and Bonvin, A. M. J. J. (2005) Data-driven docking for the study of biomolecular complexes. Febs Journal 272, 293-312.
    • (2005) Febs Journal , vol.272 , pp. 293-312
    • van Dijk, A.D.J.1    Boelens, R.2    Bonvin, A.M.J.J.3
  • 12
    • 0037316363 scopus 로고    scopus 로고
    • Aria: Automated NOE assignment and NMR structure calculation
    • Linge, J. P., Habeck, M., Rieping, W. and Nilges, M. (2003) Aria: Automated NOE assignment and NMR structure calculation. Bioinformatics 19, 315-316.
    • (2003) Bioinformatics , vol.19 , pp. 315-316
    • Linge, J.P.1    Habeck, M.2    Rieping, W.3    Nilges, M.4
  • 13
    • 0037442962 scopus 로고    scopus 로고
    • Haddock: A protein-protein docking approach based on biochemical or biophysical information
    • Dominguez, C., Boelens, R. and Bonvin, A. M. J. J. (2003) Haddock: A protein-protein docking approach based on biochemical or biophysical information. Journal of the American Chemical Society 125, 1731-1737.
    • (2003) Journal of the American Chemical Society , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.J.J.3
  • 14
    • 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 and Wishart, D. S. (2003) Rapid and accurate calculation of protein h-1, c-13 and n-15 chemical shifts. Journal of Biomolecular NMR 26, 215-240.
    • (2003) Journal of Biomolecular NMR , vol.26 , pp. 215-240
    • Neal, S.1    Nip, A.M.2    Zhang, H.Y.3    Wishart, D.S.4
  • 15
    • 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. Journal of Biomolecular NMR 21, 321-333.
    • (2001) Journal of Biomolecular NMR , vol.21 , pp. 321-333
    • Xu, X.P.1    Case, D.A.2
  • 16
    • 0028988451 scopus 로고
    • Application of h-1-NMR chemical-shifts to measure the quality of protein structures
    • Williamson, M. P., Kikuchi, J. and Asakura, T. (1995) Application of h-1-NMR chemical-shifts to measure the quality of protein structures. Journal of Molecular Biology 247, 541-546.
    • (1995) Journal of Molecular Biology , vol.247 , pp. 541-546
    • Williamson, M.P.1    Kikuchi, J.2    Asakura, T.3
  • 17
    • 0038703404 scopus 로고    scopus 로고
    • Proshift: Protein chemical shift prediction using artificial neural networks
    • Meiler, J. (2003) Proshift: Protein chemical shift prediction using artificial neural networks. Journal of Biomolecular NMR 26, 25-37.
    • (2003) Journal of Biomolecular NMR , vol.26 , pp. 25-37
    • Meiler, J.1
  • 18
    • 0032568556 scopus 로고    scopus 로고
    • New methods of structure refinement for macromolecular structure determination by NMR
    • Clore, G. M. and Gronenborn, A. M. (1998) New methods of structure refinement for macromolecular structure determination by NMR. Proceedings-National Academy of Sciences USA 95, 5891-5898.
    • (1998) Proceedings-National Academy of Sciences USA , vol.95 , pp. 5891-5898
    • Clore, G.M.1    Gronenborn, A.M.2
  • 21
    • 12244297937 scopus 로고
    • Vicinal proton coupling in nuclear magnetic resonance
    • Karplus, M. (1963) Vicinal proton coupling in nuclear magnetic resonance. Journal American Chemistry Society 85, 2870-2871.
    • (1963) Journal American Chemistry Society , vol.85 , pp. 2870-2871
    • Karplus, M.1
  • 22
    • 0025613125 scopus 로고
    • Refinement of the NMR structures for acyl carrier protein with scalar coupling data
    • Kim, Y. P., J. H. Prestegard (1990) Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Proteins 8, 377-385.
    • (1990) Proteins , vol.8 , pp. 377-385
    • Kim, Y.P.1    Prestegard, J.H.2
  • 23
  • 24
    • 0020483829 scopus 로고
    • Amide proton exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution
    • Wagner, G. and Wüthrich, K (1982) Amide proton exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution. Journal Molecular Biology 160, 343-361.
    • (1982) Journal Molecular Biology , vol.160 , pp. 343-361
    • Wagner, G.1    Wüthrich, K.2
  • 26
    • 0033209607 scopus 로고    scopus 로고
    • Observation of through-hydrogen-bond 2hjhc' in a perdeuterated protein
    • Cordier, F., Rogowski, M., Grzesiek, S. and Bax, A. (1999) Observation of through-hydrogen-bond 2hjhc' in a perdeuterated protein. Journal of Magnetic Resonance 140, 510-512.
    • (1999) Journal of Magnetic Resonance , vol.140 , pp. 510-512
    • Cordier, F.1    Rogowski, M.2    Grzesiek, S.3    Bax, A.4
  • 28
    • 0037215324 scopus 로고    scopus 로고
    • Weak alignment offers new NMR opportunities to study protein structure and dynamics
    • Bax, A. (2003) Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Science 12, 1-16.
    • (2003) Protein Science , vol.12 , pp. 1-16
    • Bax, A.1
  • 29
    • 25844506708 scopus 로고    scopus 로고
    • Weak alignment NMR: A hawk-eyed view of biomolecular structure
    • Bax, A. and Grishaev, A. (2005) Weak alignment NMR: A hawk-eyed view of biomolecular structure. Current Opinion in Structural Biology 15, 563-570.
    • (2005) Current Opinion in Structural Biology , vol.15 , pp. 563-570
    • Bax, A.1    Grishaev, A.2
  • 30
    • 4344648452 scopus 로고    scopus 로고
    • Residual dipolar couplings in structure determination of biomolecules
    • Prestegard, J. H., Bougault, C. M. and Kishore, A. I. (2004) Residual dipolar couplings in structure determination of biomolecules. Chemical Reviews 104, 3519-3540.
    • (2004) Chemical Reviews , vol.104 , pp. 3519-3540
    • Prestegard, J.H.1    Bougault, C.M.2    Kishore, A.I.3
  • 32
    • 2942544364 scopus 로고    scopus 로고
    • Determining domain orientation in macromolecules by using spin-relaxation and residual dipolar coupling measurements
    • Fushman, D., Varadan, R., Assfalg, M. and Walker, O. (2004) Determining domain orientation in macromolecules by using spin-relaxation and residual dipolar coupling measurements. Progress in Nuclear Magnetic Resonance Spectroscopy 44, 189-214.
    • (2004) Progress in Nuclear Magnetic Resonance Spectroscopy , vol.44 , pp. 189-214
    • Fushman, D.1    Varadan, R.2    Assfalg, M.3    Walker, O.4
  • 33
    • 0030963093 scopus 로고    scopus 로고
    • Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy
    • Tjandra, N., Garrett, D. S., Gronenborn, A. M., Bax, A. and Clore, G. M. (1997) Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy. Nature Structural Biology 4, 443-449.
    • (1997) Nature Structural Biology , vol.4 , pp. 443-449
    • Tjandra, N.1    Garrett, D.S.2    Gronenborn, A.M.3    Bax, A.4    Clore, G.M.5
  • 34
  • 36
    • 0038188962 scopus 로고    scopus 로고
    • Paramagnetic constraints: An aid for quick solution structure determination of paramagnetic metalloproteins
    • Bertini, I., Luchinat, C. and Parigi, G. (2002) Paramagnetic constraints: An aid for quick solution structure determination of paramagnetic metalloproteins. Concepts in Magnetic Resonance 14, 259-286.
    • (2002) Concepts in Magnetic Resonance , vol.14 , pp. 259-286
    • Bertini, I.1    Luchinat, C.2    Parigi, G.3
  • 38
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program dyana
    • Guntert, P., Mumenthaler, C. and Wuthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program dyana. Journal of Molecular Biology 273, 283-298.
    • (1997) Journal of Molecular Biology , vol.273 , pp. 283-298
    • Guntert, P.1    Mumenthaler, C.2    Wuthrich, K.3
  • 39
    • 0034685602 scopus 로고    scopus 로고
    • De novo determination of protein structure by NMR using orientational and long-range order restraints
    • Hus, J. C., Marion, D. and Blackledge, M. (2000) De novo determination of protein structure by NMR using orientational and long-range order restraints. Journal of Molecular Biology 298, 927-936.
    • (2000) Journal of Molecular Biology , vol.298 , pp. 927-936
    • Hus, J.C.1    Marion, D.2    Blackledge, M.3
  • 43
    • 0034254909 scopus 로고    scopus 로고
    • Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear Overhauser enhancement data and dipolar couplings by rigid body minimization
    • Clore, G. M. (2000) Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear Overhauser enhancement data and dipolar couplings by rigid body minimization. Proc Natl Acad Sci U S A 97, 9021-9025.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 9021-9025
    • Clore, G.M.1
  • 44
    • 0034051065 scopus 로고    scopus 로고
    • A novel NMR method for determining the interfaces of large protein-protein complexes
    • Takahashi, H., Nakanishi, T., Kami, K., Arata, Y. and Shimada, I. (2000) A novel NMR method for determining the interfaces of large protein-protein complexes. Nature Structural Biology 7, 220-223.
    • (2000) Nature Structural Biology , vol.7 , pp. 220-223
    • Takahashi, H.1    Nakanishi, T.2    Kami, K.3    Arata, Y.4    Shimada, I.5
  • 45
    • 17744364511 scopus 로고    scopus 로고
    • An NMR method for the determination of protein-binding interfaces using dioxygen-induced spinlattice relaxation enhancement
    • Sakakura, M., Noba, S., Luchette, P A., Shimada, I. and Prosser, R. S. (2005) An NMR method for the determination of protein-binding interfaces using dioxygen-induced spinlattice relaxation enhancement. Journal of the American Chemical Society 127, 5826-5832.
    • (2005) Journal of the American Chemical Society , vol.127 , pp. 5826-5832
    • Sakakura, M.1    Noba, S.2    Luchette, P.A.3    Shimada, I.4    Prosser, R.S.5
  • 46
    • 0037433504 scopus 로고    scopus 로고
    • Docking of protein-protein complexes on the basis of highly ambiguous intermolecular distance restraints derived from 1H/15N chemical shift mapping and backbone 15N-1H residual dipolar couplings using conjoined rigid body/torsion angle dynamics
    • Clore, G. M. and Schwieters, C. D. (2003) Docking of protein-protein complexes on the basis of highly ambiguous intermolecular distance restraints derived from 1H/15N chemical shift mapping and backbone 15N-1H residual dipolar couplings using conjoined rigid body/torsion angle dynamics. J Am Chem Soc 125, 2902-2912.
    • (2003) J Am Chem Soc , vol.125 , pp. 2902-2912
    • Clore, G.M.1    Schwieters, C.D.2
  • 47
    • 0041319073 scopus 로고    scopus 로고
    • Filtering and selection of structural models: Combining docking and NMR
    • Dobrodumov, A. and Gronenborn, A. M. (2003) Filtering and selection of structural models: Combining docking and NMR. Proteins 53, 18-32.
    • (2003) Proteins , vol.53 , pp. 18-32
    • Dobrodumov, A.1    Gronenborn, A.M.2
  • 48
    • 0037138706 scopus 로고    scopus 로고
    • Treedock: A tool for protein docking based on minimizing Van der Waals energies
    • Fahmy, A. and Wagner, G. (2002) Treedock: A tool for protein docking based on minimizing Van der Waals energies. J Am Chem Soc 124, 1241-1250.
    • (2002) J Am Chem Soc , vol.124 , pp. 1241-1250
    • Fahmy, A.1    Wagner, G.2
  • 49
    • 0037070536 scopus 로고    scopus 로고
    • Structures of protein-protein complexes are docked using only NMR restraints from residual dipolar coupling and chemical shift perturbations
    • McCoy, M. A. and Wyss, D. F. (2002) Structures of protein-protein complexes are docked using only NMR restraints from residual dipolar coupling and chemical shift perturbations. JAm Chem Soc 124, 2104-2105.
    • (2002) JAm Chem Soc , vol.124 , pp. 2104-2105
    • McCoy, M.A.1    Wyss, D.F.2
  • 50
    • 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. and Wuthrich, K. (2002) Protein NMR structure determination with automated NOE assignment using the new software candid and the torsion angle dynamics algorithm dyana. Journal of Molecular Biology 319, 209-227.
    • (2002) Journal of Molecular Biology , vol.319 , pp. 209-227
    • Herrmann, T.1    Guntert, P.2    Wuthrich, K.3
  • 52
    • 0033003335 scopus 로고    scopus 로고
    • Protein backbone angle restraints from searching a database for chemical shift and sequence homology
    • Cornilescu, G., Delaglio, F and Bax, A. (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. Journal of Biomolecular NMR 13, 289-302.
    • (1999) Journal of Biomolecular NMR , vol.13 , pp. 289-302
    • Cornilescu, G.1    Delaglio, F.2    Bax, A.3
  • 53
    • 0028673594 scopus 로고
    • Chemical shifts as a tool for structure determination
    • Wishart, D. S. and Sykes, B. D. (1994) Chemical shifts as a tool for structure determination. Methods In Enzymology, 363.
    • (1994) Methods In Enzymology , pp. 363
    • Wishart, D.S.1    Sykes, B.D.2
  • 54
    • 0034919240 scopus 로고    scopus 로고
    • Automated assignment of ambiguous nuclear Overhauser effects with aria
    • Linge, J. P., O'Donoghue, S. I. and Nilges, M. (2001) Automated assignment of ambiguous nuclear Overhauser effects with aria. Methods in Enzymology 339, 71-90.
    • (2001) Methods in Enzymology , vol.339 , pp. 71-90
    • Linge, J.P.1    O'Donoghue, S.I.2    Nilges, M.3
  • 55
    • 0033104825 scopus 로고    scopus 로고
    • Conformational and functional variability supported by the bpti fold: Solution structure of the ca2+ channel blocker calcicludine
    • Gilquin, B., Lecoq, A., Desne, F., Guenneugues, M., Zinn-Justin, S. and Menez, A. (1999) Conformational and functional variability supported by the bpti fold: Solution structure of the ca2+ channel blocker calcicludine. Proteins 34, 520-532.
    • (1999) Proteins , vol.34 , pp. 520-532
    • Gilquin, B.1    Lecoq, A.2    Desne, F.3    Guenneugues, M.4    Zinn-Justin, S.5    Menez, A.6
  • 58
    • 0025398721 scopus 로고
    • What if-a molecular modeling and drug design program
    • Vriend, G. (1990) What if-a molecular modeling and drug design program. Journal of Molecular Graphics 8, 52-56.
    • (1990) Journal of Molecular Graphics , vol.8 , pp. 52-56
    • Vriend, G.1
  • 60
    • 0029881007 scopus 로고    scopus 로고
    • Molmol: A program for display and analysis of macromolecular structures
    • Koradi, R., Billeter, M. and Wüthrich, K. (1996) Molmol: A program for display and analysis of macromolecular structures. Journal Molecular Graphics 14, 51-55.
    • (1996) Journal Molecular Graphics , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wüthrich, K.3


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