A protocol for the interpretation of side-chain dynamics based on NMR relaxation: Application to phenylalanines in antamanide

A new protocol fur the interpretation of NMR relaxation data in terms of intramolecular motion is described. At first, a long molecular dynamics simulation of the system is generated and analyzed with respect to nuclear spin relaxation-active motional modes. In a second step, an analytical model is conceived on the basis of the computational results. Finally, the model parameters are determined numerically by a least-squares fit to the experimental NMR data. This protocol was applied to the phenylalanine side-chain dynamics in the cyclic decapeptide antamanide. A 100 ns Langevin dynamics simulation was analyzed in terms of dihedral angle fluctuations, correlation functions, and potentials of mean force. For (chi 1) and (chi 2), motion in a harmonic potential is observed which is interrupted by occasional jumps between different rotamers over relatively high barriers. This behavior leads to an analytical Gaussian axial fluctuation and jump model, which is an extension of the previously proposed GAF model (Bruschweiler, R.;Wright, P. E. J. Am. Chem. Soc, 1994, 116, 8426).