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Chapter J3 - Structure and dynamics studies

from Part J - Nuclear magnetic resonance

Published online by Cambridge University Press:  05 November 2012

Igor N. Serdyuk ,
Nathan R. Zaccai  and
Joseph Zaccai
Igor N. Serdyuk
Affiliation:
Institute of Protein Research, Moscow
Nathan R. Zaccai
Affiliation:
University of Bristol
Joseph Zaccai
Affiliation:
Institut de Biologie Structurale, Grenoble
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Type
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Information
Methods in Molecular Biophysics
Structure, Dynamics, Function
 , pp. 1039 - 1075
Publisher: Cambridge University Press
Print publication year: 2007

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References

Wuthrich, K., Wider, G., Wagner, G., and Braun, W. (1982). Sequential resonance assignments as a basis for determination of spatial protein structures by high resolution proton nuclear magnetic resonance. J. Mol. Biol., 155, 311–319.CrossRefGoogle ScholarPubMed
Spronk, C. A. E. M., Linge, J. P., Hilbers, C. W., and Vuister, G. W. (2002). Improving the quality of protein structures derived by NMR spectroscopy. J. Biomolecular NMR, 22, 281–289.CrossRefGoogle ScholarPubMed
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. Nat. Struct. Biol., 4, 443–449.CrossRefGoogle ScholarPubMed
Tjandra, N., Omichinski, J. G., Gronenborn, A. M., Clore, G. M., and Bax, A. (1997). Use of dipolar 1H–15N and 1H–13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nat. Struct. Biol., 4, 732–738.CrossRefGoogle ScholarPubMed
Wuthrich, K. (1995). NMR – This other method for protein and nucleic acid structure determination. Acta Cryst., D51, 249–270.Google Scholar
Wider, G., and Wuthrich, K. (1999). NMR spectroscopy of large molecules and multimolecular assemblies in solution. Curr. Opin. Struct. Biol., 9, 594–601.CrossRefGoogle ScholarPubMed
Garret, D. S., Seok, Y.-J., et al. (1997). Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpuruvate: sugar phosphotransferase system by multidimensional NMR. Biochemistry, 36, 2517–2530.CrossRefGoogle Scholar
Flaux, J., Bertelsen, E. B., Horwich, A. L., and Wuthrich, K. (2002). NMR analysis of a 900K GroEL–GroES complex. Nature, 418, 207–211.Google Scholar
Wuthrich, K. (2000). Protein recognition by NMR. Nat. Struct. Biol. 7, 188–189.CrossRefGoogle Scholar
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. Nat. Struct. Biol. 7, 220–223.Google ScholarPubMed
Zidek, L., Stefl, R., and Sklenar, V. (2001). NMR methodology for the study of nucleic acids. Curr. Opin. Struct. Biol., 11, 275–281.CrossRefGoogle Scholar
Tjandra, N., Tate, S., Ono, A., Kainosho, M., and Bax, A. (2000). The NMR structure of a DNA dodecamer in an aqueous dilute liquid crystalline phase. JACS, 122, 6190–6200.CrossRefGoogle Scholar
Mollova, E. T., Hansen, M. R., and Pardi, A. (2000). Global structure of RNA determined with residual dipolar coupling. JACS, 122, 11561–11562.CrossRefGoogle Scholar
Tian, F., Al-Hashimi, H. M., Craighead, J. L., and Prestegard, J. H. (2001). Conformational analysis of a flexible oligosaccharide using residual dipolar coupling. JACS, 123, 485–492.CrossRefGoogle Scholar
Ishima, R., and Torchia, D. (2000). Protein dynamics from NMR, Nat. Str. Biol., 7, 740–743.CrossRefGoogle ScholarPubMed
Stejskal, E. O., and Tanner, J. E. (1965). Spin diffusion measurements: spin echoes in the presence of a time dependent field gradient. J. Chem. Phys., 42, 288–292.CrossRefGoogle Scholar
Jones, J. A., Wilkins, D. K., Smith, L. J., and Dobson, C. M. (1997). Characterization of protein unfolding by NMR diffusion measurements. J. Biomolecular NMR, 10, 199–203.CrossRefGoogle Scholar
Smith, S. O., and Peersen, O. B. (1992). Solid-state NMR approaches for studying membrane protein structure. Ann. Rev. Biophys. Biomol. Str., 21, 25–47.CrossRefGoogle ScholarPubMed
Opella, S. J., and Stewart, P. L. (1989). Solid-state nuclear magnetic resonance structural studies of proteins. Meth. Enzymol., 176, 242–275.CrossRefGoogle ScholarPubMed
Marassi, F. M., Ma, C., et al. (1999). Correlation of the structural and functional domains in the membrane protein Vpu from HIV-1. PANS, 96, 14336–14341.CrossRefGoogle ScholarPubMed
Smith, L. J., Redfield, C., et al. (1994). Comparison of four independently determined structures of human recombinant interleikin-4. Struct. Biol., 1, 301–310.CrossRefGoogle Scholar
Schwabe, J. W. R., Chapman, L., Finch, J. T., Rhodes, D., and Neuhaus, D. (1993). DNA recognition by the oestrogen receptor: From solution to the crystal. Structure, 1, 187–204.CrossRefGoogle ScholarPubMed
Prestegard, J. H., Valafar, H., Glushka, J., and Tian, F. (2001). Nuclear magnetic resonance in the era of structural Genomics. Biochemistry, 40, 8677–8685.CrossRefGoogle ScholarPubMed
Jacobs, R. E., Ahrens, E. T., Meade, T. J., and Fraser, S. E. (1999). Looking deeper into vertebrate development. TIBS, 9, 73–76.Google ScholarPubMed
Wuthrich, K., Wider, G., Wagner, G., and Braun, W. (1982). Sequential resonance assignments as a basis for determination of spatial protein structures by high resolution proton nuclear magnetic resonance. J. Mol. Biol., 155, 311–319.CrossRefGoogle ScholarPubMed
Spronk, C. A. E. M., Linge, J. P., Hilbers, C. W., and Vuister, G. W. (2002). Improving the quality of protein structures derived by NMR spectroscopy. J. Biomolecular NMR, 22, 281–289.CrossRefGoogle ScholarPubMed
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. Nat. Struct. Biol., 4, 443–449.CrossRefGoogle ScholarPubMed
Tjandra, N., Omichinski, J. G., Gronenborn, A. M., Clore, G. M., and Bax, A. (1997). Use of dipolar 1H–15N and 1H–13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nat. Struct. Biol., 4, 732–738.CrossRefGoogle ScholarPubMed
Wuthrich, K. (1995). NMR – This other method for protein and nucleic acid structure determination. Acta Cryst., D51, 249–270.Google Scholar
Wider, G., and Wuthrich, K. (1999). NMR spectroscopy of large molecules and multimolecular assemblies in solution. Curr. Opin. Struct. Biol., 9, 594–601.CrossRefGoogle ScholarPubMed
Garret, D. S., Seok, Y.-J., et al. (1997). Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpuruvate: sugar phosphotransferase system by multidimensional NMR. Biochemistry, 36, 2517–2530.CrossRefGoogle Scholar
Flaux, J., Bertelsen, E. B., Horwich, A. L., and Wuthrich, K. (2002). NMR analysis of a 900K GroEL–GroES complex. Nature, 418, 207–211.Google Scholar
Wuthrich, K. (2000). Protein recognition by NMR. Nat. Struct. Biol. 7, 188–189.CrossRefGoogle Scholar
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. Nat. Struct. Biol. 7, 220–223.Google ScholarPubMed
Zidek, L., Stefl, R., and Sklenar, V. (2001). NMR methodology for the study of nucleic acids. Curr. Opin. Struct. Biol., 11, 275–281.CrossRefGoogle Scholar
Tjandra, N., Tate, S., Ono, A., Kainosho, M., and Bax, A. (2000). The NMR structure of a DNA dodecamer in an aqueous dilute liquid crystalline phase. JACS, 122, 6190–6200.CrossRefGoogle Scholar
Mollova, E. T., Hansen, M. R., and Pardi, A. (2000). Global structure of RNA determined with residual dipolar coupling. JACS, 122, 11561–11562.CrossRefGoogle Scholar
Tian, F., Al-Hashimi, H. M., Craighead, J. L., and Prestegard, J. H. (2001). Conformational analysis of a flexible oligosaccharide using residual dipolar coupling. JACS, 123, 485–492.CrossRefGoogle Scholar
Ishima, R., and Torchia, D. (2000). Protein dynamics from NMR, Nat. Str. Biol., 7, 740–743.CrossRefGoogle ScholarPubMed
Stejskal, E. O., and Tanner, J. E. (1965). Spin diffusion measurements: spin echoes in the presence of a time dependent field gradient. J. Chem. Phys., 42, 288–292.CrossRefGoogle Scholar
Jones, J. A., Wilkins, D. K., Smith, L. J., and Dobson, C. M. (1997). Characterization of protein unfolding by NMR diffusion measurements. J. Biomolecular NMR, 10, 199–203.CrossRefGoogle Scholar
Smith, S. O., and Peersen, O. B. (1992). Solid-state NMR approaches for studying membrane protein structure. Ann. Rev. Biophys. Biomol. Str., 21, 25–47.CrossRefGoogle ScholarPubMed
Opella, S. J., and Stewart, P. L. (1989). Solid-state nuclear magnetic resonance structural studies of proteins. Meth. Enzymol., 176, 242–275.CrossRefGoogle ScholarPubMed
Marassi, F. M., Ma, C., et al. (1999). Correlation of the structural and functional domains in the membrane protein Vpu from HIV-1. PANS, 96, 14336–14341.CrossRefGoogle ScholarPubMed
Smith, L. J., Redfield, C., et al. (1994). Comparison of four independently determined structures of human recombinant interleikin-4. Struct. Biol., 1, 301–310.CrossRefGoogle Scholar
Schwabe, J. W. R., Chapman, L., Finch, J. T., Rhodes, D., and Neuhaus, D. (1993). DNA recognition by the oestrogen receptor: From solution to the crystal. Structure, 1, 187–204.CrossRefGoogle ScholarPubMed
Prestegard, J. H., Valafar, H., Glushka, J., and Tian, F. (2001). Nuclear magnetic resonance in the era of structural Genomics. Biochemistry, 40, 8677–8685.CrossRefGoogle ScholarPubMed
Jacobs, R. E., Ahrens, E. T., Meade, T. J., and Fraser, S. E. (1999). Looking deeper into vertebrate development. TIBS, 9, 73–76.Google ScholarPubMed

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