Abstract
A number of different dynamics models are considered for fitting 13C and 2H side chain methyl relaxation rates. It is shown that in cases where nanosecond time scale dynamics are present the extended Lipari–Szabo model which is explicitly parameterized to include the effects of slow motions can produce wide distributions of fitting parameters even in cases where the errors are relatively small and large numbers of relaxation rates are considered. In contrast, fits of 15N backbone dynamics using this model are far more robust. The origin of this difference is analyzed and can be explained by the different functional forms of the spectral density in these two cases. The utility of a number of models for the analysis of methyl side chain dynamics is presented.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Brooks, C.L., Karplus, M. and Pettitt, B.M. (1988) Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics, John Wiley and Sons, New York, NY.
Choy, W.Y., Shortle, D. and Kay, L.E. (2003) J. Am. Chem. Soc., 125, 1748-1758.
Clore, G.M., Szabo, A., Bax, A., Kay, L.E., Driscoll, P.C. and Gronenborn, A.M. (1990) J. Am. Chem. Soc., 112, 4989-4991.
Cordier, F., Brutscher, B. and Marion, D. (1996) J. Biomol. NMR, 7, 163-168.
Dayie, K.T. and Wagner, G. (1997) J. Am. Chem. Soc., 119, 7797-7806.
Edwards, A.M., Arrowsmith, C.H., Christendat, D., Dharamsi, A., Friesen, J.D., Greenblatt, J.F. and Vedadi, M. (2000) Nat. Struct. Biol. Suppl., 7, 970-972.
Engelke, J. and Rüterjans, H. (1995) J. Biomol. NMR, 5, 173-182.
Farrow, N.A., Muhandiram, R., Singer, A.U., Pascal, S.M., Kay, C.M., Gish, G., Shoelson, S.E., Pawson, T., Forman-Kay, J.D. and Kay, L.E. (1994) Biochemistry, 33, 5984-6003.
Fersht, A. (1985) Enzyme Structure and Mechanism, 2nd edn., Freeman and Co., New York.
Ishima, R. and Torchia, D.A. (2000) Nat. Struct. Biol., 7, 740-743.
Ishima, R., Louis, J.M. and Torchia, D.A. (1999) J. Am. Chem. Soc., 121, 11589-11590.
Ishima, R., Petkova, A.P., Louis, J.M. and Torchia, D.A. (2001) J. Am. Chem. Soc., 123, 6164-6171.
Kay, L.E. (1998) Nat. Struct. Biol. NMR Suppl., 5, 513-516.
Lee, A.L., Flynn, P.F. and Wand, A.J. (1999) J. Am. Chem. Soc., 121, 2891-2902.
Lee, A.L., Urbauer, J.L. and Wand, A.J. (1997) J. Biomol. NMR, 9, 437-440.
LeMaster, D.M. and Kushlan, D.M. (1996) J. Am. Chem. Soc., 118, 9255-9264.
Lipari, G. and Szabo, A. (1982a) J. Am. Chem. Soc., 104, 4546-4559.
Lipari, G. and Szabo, A. (1982b) J. Am. Chem. Soc., 104, 4559-4570.
Millet, O., Muhandiram, D.R., Skrynnikov, N.R. and Kay, L.E. (2002) J. Am. Chem. Soc., 124, 6439-6448.
Muhandiram, D.R., Johnson, P.E., Yang, D., Zhang, O., McIntosh, L.P. and Kay, L.E. (1997) J. Biomol. NMR, 10, 283-288.
Muhandiram, D.R., Yamazaki, T., Sykes, B.D. and Kay, L.E. (1995) J. Am. Chem. Soc., 117, 11536-11544.
Palmer, A.G., Williams, J. and McDermott, A. (1996) J. Phys. Chem., 100, 13293-13310.
Press, W.H., Flannery, B.P., Teukolsky, S.A. and Vetterling, W.T. (1988) Numerical Recipes in C, Cambridge University Press, Cambridge.
Skrynnikov, N.R., Millet, O. and Kay, L.E. (2002) J. Am. Chem. Soc., 124, 6449-6460.
Yamazaki, T., Muhandiram, R. and Kay, L.E. (1994) J. Am. Chem. Soc., 116, 8266-8278.
Yang, D., Mittermaier, A., Mok, Y.K. and Kay, L.E. (1998) J. Mol. Biol., 276, 939-954.
Zeng, L., Fischer, M.W.F. and Zuiderweg, E.R.P. (1996) J. Biomol. NMR, 7, 157-162.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Choy, WY., Kay, L.E. Model selection for the interpretation of protein side chain methyl dynamics. J Biomol NMR 25, 325–333 (2003). https://doi.org/10.1023/A:1023065310430
Issue Date:
DOI: https://doi.org/10.1023/A:1023065310430