Smoothing molecular interactions: The “kinetic buffer” effect of intrinsically disordered proteins

Authors

  • Yongqi Huang,

    1. State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, and Center for Theoretical Biology, Peking University, Beijing 100871, People's Republic of China
    2. Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People's Republic of China
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  • Zhirong Liu

    Corresponding author
    1. State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, and Center for Theoretical Biology, Peking University, Beijing 100871, People's Republic of China
    2. Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People's Republic of China
    • College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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Abstract

Intrinsically disordered proteins (IDPs) widely participate in molecular recognition and signaling processes in cells by interacting with other molecules. Compared with ordered proteins, IDPs usually possess stronger intermolecular interactions in binding. As a result, the interface structure of IDPs in complexes is distinct from that of ordered-protein complexes, and this difference may have essential effect on the response to various perturbations in a cell. In this study, we examined the perturbations of intermolecular interactions and temperature on the coupled folding and binding processes of pKID to KIX domains by performing molecular dynamics simulations. By comparing a series of virtual pKID systems with various degree of disorder, we found that the complex stability and the binding kinetics of the disordered systems were less sensitive to the perturbations than the ordered systems. The origin of the lower response sensitivity of IDPs was attributed to their higher flexibility in the complex interface, which was further supported by an analysis on protein complex structures. On the basis of our simulations and results from the literature, we speculate IDPs may not only interact with their biological partners with high specificity and low affinity but also may be resistant to the perturbations in the environment and transmit signals fast and smooth. We proposed to name it the “kinetic buffer” effect. Proteins 2010. © 2010 Wiley-Liss, Inc.

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