Can all-atom protein dynamics be reconstructed from the knowledge of C-alpha time evolution?

TL;DR

This study investigates how well peptide plane and side chain atom dynamics can be reconstructed from C-alpha atom trajectories, finding that statistical methods outperform others and that all atom dynamics are largely determined by C-alpha motion.

Contribution

The paper introduces a statistical reconstruction method for peptide plane and side chain atom dynamics from C-alpha trajectories, demonstrating its superior accuracy over existing tools.

Findings

Statistical method outperforms other reconstruction approaches.

All atom dynamics are largely governed by C-alpha atom motion.

Results can improve force fields and reconstruction methods for protein structures.

Abstract

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.