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    Free Energy Calculations of the Interactions of c-Jun-based Synthetic Peptides with the c-Fos Protein

    Access Status
    Fulltext not available
    Authors
    Zuo, Zhili
    Gandhi, Neha
    Arndt, K.
    Mancera, Ricardo
    Date
    2012
    Type
    Journal Article
    
    Metadata
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    Citation
    Zuo, Z. and Gandhi, N. and Arndt, K. and Mancera, R. 2012. Free Energy Calculations of the Interactions of c-Jun-based Synthetic Peptides with the c-Fos Protein. Biopolymers. 97 (11): pp. 899-909.
    Source Title
    Biopolymers
    DOI
    10.1002/bip.22099
    ISSN
    0006-3525
    School
    School of Biomedical Sciences
    URI
    http://hdl.handle.net/20.500.11937/43767
    Collection
    • Curtin Research Publications
    Abstract

    The c-Fos–c-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.

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