Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin

PLoS One. 2015 Oct 23;10(10):e0140713. doi: 10.1371/journal.pone.0140713. eCollection 2015.

Abstract

Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm "dynamics govern specificity" might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Computer Simulation
  • Entropy
  • Fibrinogen / metabolism*
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Peptides / metabolism
  • Protein Binding
  • Substrate Specificity
  • Thermodynamics
  • Thrombin / chemistry
  • Thrombin / metabolism*
  • Water

Substances

  • Peptides
  • Water
  • Fibrinogen
  • Thrombin

Grants and funding

The work was supported by the following: Austrian Science Fund, P23051, www.fwf.ac.at and Austrian Academy of Sciences, DOC-grant to JEF, RGH, BJW, www.oeaw.ac.at. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.