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Parameterization of Peptide 13 C Carbonyl Chemical Shielding Anisotropy in Molecular Dynamics Simulations Effects of Dynamic Local Distortions on 13 C Carbonyl NMR Relaxation.

Wiley Blackwell (John Wiley & Sons)
Publication Date
  • Biology
  • Chemistry
  • Mathematics
  • Physics


NMR chemical shielding anisotropy (CSA) relaxation is an important tool in the study of dynamical processes in proteins and nucleic acids in solution. Herein, we investigate how dynamical variations in local geometry affect the chemical shielding anisotropy relaxation of the carbonyl carbon nucleus, using the following protocol: 1) Using density functional theory, the carbonyl 13 C′ CSA is computed for 103 conformations of the model peptide group N -methylacetamide (NMA). 2) The variations in computed 13 C′ CSA parameters are fitted against quadratic hypersurfaces containing cross terms between the variables. 3) The predictive quality of the CSA hypersurfaces is validated by comparing the predicted and de novo calculated 13 C′ CSAs for 20 molecular dynamics snapshots. 4) The CSA fluctuations and their autocorrelation and cross correlation functions due to bond-length and bond-angle distortions are predicted for a chemistry Harvard molecular mechanics (CHARMM) molecular dynamics trajectory of Ca 2+ -saturated calmodulin and GB3 from the hypersurfaces, as well as for a molecular dynamics (MD) simulation of an NMA trimer using a quantum mechanically correct forcefield. We find that the fluctuations can be represented by a 0.93 scaling factor of the CSA tensor for both R 1 and R 2 relaxations for residues in helix, coil, and sheet alike. This result is important, as it establishes that 13 C′ relaxation is a valid tool for measurement of interesting dynamical events in proteins.

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