2019/01/21 by Jiaojiao Liu, Liu, Jiaojiao, Jin Dai +7
Biochemistry, Genetics and Molecular Biology · Chemistry · Physics and Astronomy · #Advanced Proteomics Techniques and Applications #Biological Physics (physics.bio-ph) #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Physical sciences #Mass Spectrometry Techniques and Applications #Protein Structure and Dynamics #Soft Condensed Matter (cond-mat.soft) #cond-mat.soft #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.48550/arxiv.1901.06864
24 figures
arxiv created 2019/01/21 · openalex publication_date 2019/01/21 · arxiv updated 2019/01/23 · openalex created_date 2019/02/21 · openalex updated_date 2026/07/28
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.