  We inquire to what extent protein peptide plane and side chain dynamics can
be reconstructed from knowledge of C-alpha dynamics. Due to lack of
experimental data we analyze all atom molecular dynamics trajectories from
Anton supercomputer, and for clarity we limit our attention to the peptide
plane O atoms and side chain C-beta atoms. We try and reconstruct their
dynamics using four different approaches. Three of these are the publicly
available reconstruction programs Pulchra, Remo Scwrl4. The fourth, Statistical
Method, builds entirely on statistical analysis of Protein Data Bank (PDB)
structures. All four methods place the O and C-beta atoms accurately along the
Anton trajectories. However, the Statistical Method performs best. The results
suggest that under physiological conditions, the all atom dynamics is slaved to
that of C-alpha atoms. The results can help improve all atom force fields, and
advance reconstruction and refinement methods for reduced protein structures.
The results provide impetus for development of effective coarse grained force
fields in terms of reduced coordinates.
