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"Multiple loop conformations of peptides predicted by molecular dynamics simulations are compatible with NMR" Heiko Carstens, Christian Renner, Alexander G. Milbradt, Luis Moroder, and Paul TavanBiochemistry 44, 4829-4840 (2005). Abstract: The affinity and selectivity of protein-protein interactions can be fine-tuned by varying the size, flexibility and amino acid composition of involved surface loops. As a model for such surface loops we study the conformational landscape of an octapeptide, whose flexibility is chemically steered by two different types of covalent ring-closures integrating an azobenzene dye into and by a disulfide bridge additionally constraining the peptide backbone. Because the covalently integrated azobenzene dyes can be switched by light between a bent cis-state and an elongated trans-state, six cyclic peptide models of strongly different flexibilities are obtained. The conformational states of these peptide models are sampled by NMR and by unconstrained molecular dynamics simulations. Prototypical conformations and the free energy landscapes in the high-dimensional space spanned by the Φ/Ψ angles at the peptide backbone are obtained by clustering techniques from the MD trajectories. Multiple open loop conformations are shown to be predicted by MD particularly in the very flexible cases and are shown to comply with the NMR data despite the fact that such open loop conformations are missing in the refined NMR structures. BMO authors (in alphabetic order): Heiko Carstens Paul Tavan Assoziierte Projekte: Photoswitchable model peptides and their conformational dynamics |
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Letzte Änderung: 2016-09-14 13:34
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