Local dynamic amplitudes on the protein backbone from dipolar couplings: toward the elucidation of slower motions in biomolecules.
Local protein backbone dynamics on time scales reaching up to milliseconds have been investigated using residual dipolar couplings (RDC) using an analytical description of conformational averaging under the influence of anisotropic peptide plane dynamics. We have applied this technique to RDC from protein G and find that sites in the alpha-helix exhibit overall higher-order parameters than loops, suggesting a high degree of conformational integrity even over this extended time period. The approach is shown to be stable when using data from a smaller number of alignment media. Order parameters derived from combinations of independent subsets of two and three of the five alignment media from protein G reveal results essentially identical to those from the complete data set. Structures of lysozyme determined at different crystal diffraction resolutions ranging from 0.9 to 2.1 A give similar dynamic parameters using this method, demonstrating robustness with respect to structural error.
Bernadó
Pau
P
Institut de Biologie Structurale - Jean-Pierre Ebel C.N.R.S.-C.E.A.-UJF 41, rue Jules Horowitz - 38027 Grenoble Cedex - France.
Blackledge
Martin
M
D008958:Models, Molecular; D009010:Monte Carlo Method; D009113:Muramidase / Q000737:chemistry*; D009419:Nerve Tissue Proteins / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary
C029152:G-substrate; D009419:Nerve Tissue Proteins; D009113:Muramidase