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Adhesive water networks facilitate binding of protein interfaces

Author

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  • Mazen Ahmad

    (Center for Bioinformatics, Saarland University, Building E 2.1, Postfach 15 11 50, Saarbruecken 66041, Germany.)

  • Wei Gu

    (Center for Bioinformatics, Saarland University, Building E 2.1, Postfach 15 11 50, Saarbruecken 66041, Germany.)

  • Tihamér Geyer

    (Center for Bioinformatics, Saarland University, Building E 2.1, Postfach 15 11 50, Saarbruecken 66041, Germany.)

  • Volkhard Helms

    (Center for Bioinformatics, Saarland University, Building E 2.1, Postfach 15 11 50, Saarbruecken 66041, Germany.)

Abstract

Water structure has an essential role in biological assembly. Hydrophobic dewetting has been documented as a general mechanism for the assembly of hydrophobic surfaces; however, the association mechanism of hydrophilic interfaces remains mysterious and cannot be explained by simple continuum water models that ignore the solvent structure. Here we study the association of two hydrophilic proteins using unbiased extensive molecular dynamics simulations that reproducibly recovered the native bound complex. The water in the interfacial gap forms an adhesive hydrogen-bond network between the interfaces stabilizing early intermediates before native contacts are formed. Furthermore, the interfacial gap solvent showed a reduced dielectric shielding up to distances of few nanometres during the diffusive phase. The interfacial gap solvent generates an anisotropic dielectric shielding with a strongly preferred directionality for the electrostatic interactions along the association direction.

Suggested Citation

  • Mazen Ahmad & Wei Gu & Tihamér Geyer & Volkhard Helms, 2011. "Adhesive water networks facilitate binding of protein interfaces," Nature Communications, Nature, vol. 2(1), pages 1-7, September.
    • Handle: RePEc:nat:natcom:v:2:y:2011:i:1:d:10.1038_ncomms1258
    DOI: 10.1038/ncomms1258
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    Cited by:

    1. Iain H Moal & Paul A Bates, 2012. "Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding," PLOS Computational Biology, Public Library of Science, vol. 8(1), pages 1-13, January.
    2. In Jung Kim & Hyuntae Na, 2022. "An efficient algorithm calculating common solvent accessible volume," PLOS ONE, Public Library of Science, vol. 17(3), pages 1-24, March.

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