Correlation Between Protein Bond Vector And Dihedral Fluctuations

Coordination between residues of protein is essential for various biophysical phenomena. The coordination can be best understood in terms of correlation between dihedral angles of these residues. Since these fluctuations take place at nanoseconds time scale, they are experimentally not easily accessible. NMR experiments probe bond vector fluctuations given in terms of cross correlated relaxation (CCR) rates. Theoretically this CCR rates can be expressed as low frequency (omega -> 0) limit of spectral function of these fluctuations. Here we illustrate correlation between protein bond vector and dihedral angle using molecular dynamics simulation of a small protein ubiquitin. We compute the spectral function for both kinds of fluctuations and find good correlation. Hence our work may provide an indirect way to set up a connection between theoretical and experimental result.