Model selection for the interpretation of protein side chain methyl dynamics.
A number of different dynamics models are considered for fitting (13)C and (2)H 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 (15)N 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.
Choy
Wing-Yiu
WY
The Protein Engineering Network Center of Excellence, University of Toronto, Toronto, Ontario, Canada M5S 1A8.
Kay
Lewis E
LE
D000596:Amino Acids; D007554:Isotopes; D008697:Methane; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D013997:Time Factors
D000596:Amino Acids; D007554:Isotopes; D011506:Proteins; D008697:Methane