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Early mechanistic events in biotin dissociation from streptavidin

Abstract

The streptavidin–biotin system has provided a unique opportunity to investigate the molecular details of ligand dissociation pathways. An underlying mechanistic question is whether ligand dissociation proceeds with a relatively ordered process of bond breaking and ligand escape. Here we report a joint computational and crystallographic study of the earliest events in biotin dissociation. In molecular dynamics potential of mean force simulations, a water molecule from a defined access channel intercalated into the hydrogen bond between Asp 128 and biotin, bridging them and stabilizing an intermediate state. In forced biotin dissociation simulations, this event led to subsequent bond breaking steps and ligand escape. In equilibrium simulations, the water molecule was sometimes observed to move back to the access channel with re-formation of the biotin hydrogen bond. Analysis of streptavidin crystal structures revealed a close overlap of crystallographically defined and simulated waters in the water access channel. These results suggest that biotin dissociation is initiated by stochastic coupling of water entry with lengthening of a specific biotin hydrogen-bonding interaction.

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Figure 1: Location of the water-access channel within the wild type crystal structure of streptavidin24.
Figure 2: Location and history of water molecules.
Figure 3: Graphs of inter-atomic distances for atoms involved in the bridged Asp 128 OD…biotin N2 hydrogen bond.

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Acknowledgements

This work was supported by grants from the NIH.

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Correspondence to Ronald E. Stenkamp, Terry P. Lybrand or Patrick S. Stayton.

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The authors declare no competing financial interests.

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Hyre, D., Amon, L., Penzotti, J. et al. Early mechanistic events in biotin dissociation from streptavidin. Nat Struct Mol Biol 9, 582–585 (2002). https://doi.org/10.1038/nsb825

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