Characterization of protein dynamics from residual dipolar couplings using the three dimensional Gaussian axial fluctuation model.
Residual dipolar couplings are potentially very powerful probes of slower protein motions, providing access to dynamic events occurring on functionally important timescales up to the millisecond. One recent approach uses the three dimensional Gaussian Axial Fluctuation model (3D GAF) to determine the major directional modes and associated amplitudes of motions along the peptide chain. In this study we have used standard and accelerated molecular dynamics simulations to determine the accuracy of 3D GAF-based approaches in characterizing the nature and extent of local molecular motions. We compare modes determined directly from the trajectories with motional parameterization derived from RDCs simulated from the same trajectories. Three approaches are tested, that either suppose a known three-dimensional structure, simultaneously determine backbone structure and dynamics, or determine dynamic modes in the absence of a structural model. The results demonstrate the robustness of the 3D GAF analysis even in the presence of large-scale motions, and illustrate the remarkably quantitative nature of the extracted amplitudes. These observations suggest that the approach can be generally used for the study of functionally interesting biomolecular motions.
Bouvignies
Guillaume
G
Institute de Biologie Structurale Jean-Pierre Ebel, CNRS; CEA; UJF; UMR 5075, 41 rue Jules Horowitz, F-38027 Grenoble, Cedex, France.
Markwick
Phineus R L
PR
Blackledge
Martin
M
D008722:Methods; D008958:Models, Molecular; D009038:Motion; D011506:Proteins / Q000737:chemistry*
D011506:Proteins