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    Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein

    Access Status
    Fulltext not available
    Authors
    Yang, A.
    Mancera, Ricardo
    Date
    2008
    Type
    Journal Article
    
    Metadata
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    Citation
    Yang, Ami and Mancera, Ricardo. 2008. Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein. Journal of Computer-Aided Molecular Design 22: pp. 799-814.
    Source Title
    Journal of Computer-Aided Molecular Design
    DOI
    10.1007/s10822-008-9215-6
    ISSN
    0920654X
    Faculty
    Faculty of Health Sciences
    Western Australian Biomedical Research Institute
    Biomedical Science and Pharmacy
    School
    School of Biomedical Sciences
    URI
    http://hdl.handle.net/20.500.11937/4951
    Collection
    • Curtin Research Publications
    Abstract

    The periplasmic lysine-, arginine-, ornithine-binding protein (LAOBP) traps its ligands by a large hinge bending movement between two globular domains. The overall geometry of the binding site remains largely unchanged between the open (unliganded) and closed (liganded) forms, with only a small number of residues exhibiting limited movement of their side chains. However, in the case of the ornithine-bound structure, the backbone peptide bond between Asp11 and Thr12 undergoes a large rotation. Molecular dynamics simulations have been used to investigate the origin and mechanism of this backbone movement. Simulations allowing flexibility of a limited region and of the whole binding site, with and without bound ligands, suggest that this conformational change is induced by the binding of ornithine, leading to the stabilisation of an energetically favourable alternative conformation.

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