Detecting protein atom correlations using correlation of probability of recurrence.
The dynamic cross-correlation Map(DCCM) technique has been used extensively to study protein dynamics. In this work, we introduce the use of the method of correlation of probability of recurrence (CPR) as a complementary method to detect correlations between protein residue atoms. Time series of the distances of the Cα atoms of the β-lactamase inhibitory protein (BLIP) from a reference position are analyzed using CPR and mutual information (MI). The results are compared to those provided by DCCM. In comparison to MI, CPR is found to detect more of the correlations present in DCCM. It is also able to detect a small number of significant correlations between distant residues that are not detected by DCCM.
Department of Physics, Birzeit University, Birzeit, Palestine.
Hiba
H
Fataftah
Wael
W
Karain
D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics*; D056004:Molecular Dynamics Simulation; D009154:Mutation; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D017434:Protein Structure, Tertiary; D013302:Streptomyces / Q000201:enzymology*; D065093:beta-Lactamase Inhibitors / Q000378:metabolism; D001618:beta-Lactamases / Q000378:metabolism
D001426:Bacterial Proteins; D065093:beta-Lactamase Inhibitors; C065596:beta-lactamase-inhibitor protein, Streptomyces; D001618:beta-Lactamases
BLIP; cross-correlation; molecular dynamics; mutual information