Simulating cyclodextrin interactions with peptides and proteins

Laurent Duroux (Speaker)

Activity: Talks and presentationsTalks and presentations in private or public companies


The interaction of cyclodextrins (CD) with the surface of biological macromolecules such as polypeptides and proteins is poorly understood. Nevertheless, beta-CD forms inclusion com-plexes with native solvent-exposed hydrophobic amino-acid residues at the surface of poly-peptides and proteins. This feature has been exploited in order to inhibit aggregation of un-folded species as well as to increase the solubility of peptide drugs. Alternatively, the intro-duction of synthetic groups at the surface of proteins has been used for specific complex for-mation with CDs and protein immobilization onto solid surfaces. In order to better understand the mechanisms of CD interactions with peptides and pro-teins, molecular modelling methods were applied. We used peptides, native protein structures as well as designed protein mutants, where a solvent-accessible benzophenone moiety was introduced. Blind docking simulations were performed with AUTODOCK to scan the protein surface and docking solutions were further processed with Molecular Dynamics using YASARA. Results showed preferential complex formation of CDs with aromatic groups. Binding energy showed a dependency on the type of CD, on the conformation and on the solvent accessibility of the aromatic groups. This approach should prove useful in designing high-affinity and specific sites for immobilization of proteins to various CD-based materials.
Period5 Jun 2012
Event titleAdvanced Macromolecular Systems Across the Length Scales: Smart, nanostructured systems for controlled molecular release and biological interfaces
Event typeConference
LocationSiofok, Hungary