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    Optimization of protein-protein docking for predicting Fc-protein interactions

    Access Status
    Fulltext not available
    Authors
    Agostino, Mark
    Mancera, R.
    Ramsland, P.
    Fernández-Recio, J.
    Date
    2016
    Type
    Journal Article
    
    Metadata
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    Abstract

    The antibody crystallizable fragment (Fc) is recognized by effector proteins as part of the immune system. Pathogens produce proteins that bind Fc in order to subvert or evade the immune response. The structural characterization of the determinants of Fc-protein association is essential to improve our understanding of the immune system at the molecular level and to develop new therapeutic agents. Furthermore, Fc-binding peptides and proteins are frequently used to purify therapeutic antibodies. Although several structures of Fc-protein complexes are available, numerous others have not yet been determined. Protein-protein docking could be used to investigate Fc-protein complexes; however, improved approaches are necessary to efficiently model such cases. In this study, a docking-based structural bioinformatics approach is developed for predicting the structures of Fc-protein complexes. Based on the available set of X-ray structures of Fc-protein complexes, three regions of the Fc, loosely corresponding to three turns within the structure, were defined as containing the essential features for protein recognition and used as restraints to filter the initial docking search. Rescoring the filtered poses with an optimal scoring strategy provided a success rate of approximately 80% of the test cases examined within the top ranked 20 poses, compared to approximately 20% by the initial unrestrained docking. The developed docking protocol provides a significant improvement over the initial unrestrained docking and will be valuable for predicting the structures of currently undetermined Fc-protein complexes, as well as in the design of peptides and proteins that target Fc.

    Citation
    Agostino, M. and Mancera, R. and Ramsland, P. and Fernández-Recio, J. 2016. Optimization of protein-protein docking for predicting Fc-protein interactions. Journal of Molecular Recognition. 29 (11): pp. 555-568.
    Source Title
    Journal of Molecular Recognition
    DOI
    10.1002/jmr.2555
    ISSN
    0952-3499
    School
    School of Biomedical Sciences
    URI
    http://hdl.handle.net/20.500.11937/28838
    Collection
    • Curtin Research Publications

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