Detecting protein atom correlations using correlation of probability of recurrence

ABSTRACT 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 seri...

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Bibliographic Details
Published in:Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2014-09, Vol.82 (9), p.2180-2189
Main Authors: Fataftah, Hiba, Karain, Wael
Format: Article
Language:English
Subjects:
Bacterial Proteins - chemistry
Bacterial Proteins - genetics
beta-Lactamase Inhibitors - metabolism
beta-Lactamases - metabolism
BLIP
cross-correlation
molecular dynamics
Molecular Dynamics Simulation
Mutation
mutual information
Protein Interaction Mapping
Protein Interaction Maps
Protein Structure, Tertiary
Streptomyces - enzymology
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Summary:ABSTRACT 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. Proteins 2014; 82:2180–2189. © 2014 Wiley Periodicals, Inc.
ISSN:0887-3585
1097-0134
DOI:10.1002/prot.24574