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Quasi-harmonic fluctuations of two bound peptides.
MedLine Citation:
PMID:  22890690     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
Binding of two short peptides of sequences ASN-ASP-MET-PHE-ARG-LEU and LEU-LEU-PHE-MET-GLN-HIS and their bound complex structures is studied. Molecular dynamics simulations of the three structures around their respective minimum energy conformations are performed and a quasi-harmonic analysis is performed over the trajectories generated. The fluctuation correlation matrix is constructed for all C(α) -atoms of the peptides for the full trajectory. The spring constant matrix between peptide C(α) -atoms is obtained from the correlation matrix. Statistical thermodynamics of fluctuations, the energies, entropies and the free energies of binding are discussed in terms of the quasi-harmonic model. Sites contributing to the stability of the system and presenting high affinity for binding are determined. Contribution of hydrophobic forces to binding is discussed. Quasi-harmonic approximation identifies the essential subspace of motions, the important interactions and binding sites, gives the energetic contribution of each individual interaction and filters out noise observed in MD due to uncorrelated motions. Comparison of the molecular dynamics results with those of the quasi-harmonic model shows the importance of entropy change resulting from water molecules being liberated from the surfaces of the two peptides upon binding. Proteins 2012. © 2012 Wiley Periodicals, Inc.
Authors:
Mert Gur; Burak Erman
Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-8-14
Journal Detail:
Title:  Proteins     Volume:  -     ISSN:  1097-0134     ISO Abbreviation:  Proteins     Publication Date:  2012 Aug 
Date Detail:
Created Date:  2012-8-14     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8700181     Medline TA:  Proteins     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
Copyright © 2012 Wiley Periodicals, Inc.
Affiliation:
Center for Computational Biology and Bioinformatics, Koc University, Sariyer, 34450, Istanbul, Turkey. meg78@pitt.edu.
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