MOLECULAR-DYNAMICS ANALYSIS OF NMR RELAXATION IN A ZINC-FINGER PEPTIDE

The dynamical behavior of the 25-residue "zinc-finger" peptide xfin31 has been modeled through molecular dynamics simulations in vacuum and in water, and by normal mode and by Langevin mode analyses. The effects of internal motion on dipolar nuclear magnetic relaxation of C-H, N-H, and H-H spin pairs have been calculated, and the results for C-H pairs are compared to experimental results. Calculated internal correlation functions for directly bonded C-H and N-H spin pairs and for H-H spin pairs show rapid, subpicosecond initial decays followed by slower transitions to nearly constant "plateau" values. The fast initial decay contains underdamped oscillations in the gas-phase analysis and in the molecular dynamics simulations but is overdamped in the Langevin analysis. Quantum effects (estimated from the normal mode results) reduce the correlation functions at early times by about 0.05 for directly bonded C-H and N-H pairs and by less than 0.01 for H-H spin pairs. Correction factors relating cross-relaxation rate constants for inter-residue H-H spin pairs in rigid and nonrigid molecular models display a reasonably narrow distribution with an average value near 1. Calculated order parameters from solvated molecular dynamics simulations are in good agreement with experiment at most carbon positions. Implications of the results for the interpretation of "model-free" analyses of NMR relaxation rate constants and for NMR-based structural refinements are discussed.