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Simulations suggest double sodium binding induces unexpected conformational changes in thrombin.

Dizhou Wu1, Freddie R Salsbury2

  • 1Department of Physics, Wake Forest University, Winston-Salem, 27106, NC, USA.

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Sodium ions binding to thrombin may involve two sites, influencing its activity. Molecular dynamics simulations reveal potential allosteric pathways and suggest a multi-step binding mechanism.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Chemistry

Background:

  • Thrombin, a serine protease, regulates blood coagulation.
  • It possesses both procoagulant and anticoagulant activities.
  • Existing research focused on a single sodium-binding site in thrombin.

Purpose of the Study:

  • To investigate the potential for two sodium-binding sites in thrombin.
  • To explore the effects of different sodium-binding modes on thrombin structure and function.
  • To elucidate the allosteric mechanisms and kinetic pathways of sodium binding to thrombin.

Main Methods:

  • 12 independent 2-microsecond all-atom molecular dynamics simulations of wild-type thrombin.
  • Analysis of root-mean-square fluctuations (RMSF) and correlation matrices.
  • Application of Amorim-Hennig (AH) clustering, principal component analysis (PCA), and solvent-accessible surface area (SASA) calculations.

Main Results:

  • Identified distinct changes in atomic fluctuations in specific thrombin loops (60s, 170s, 220s) and connecting regions based on sodium binding modes.
  • Revealed potential allosteric pathways and conformational changes in exosite I and the catalytic triad.
  • Observed that simultaneous dual sodium binding might represent an inactive thrombin conformation.

Conclusions:

  • The study suggests a more complex, potentially multi-step mechanism for sodium binding to thrombin, beyond the previously assumed two-step model.
  • Dual sodium binding may lead to an inactive state of thrombin.
  • These findings offer insights into thrombin's allosteric regulation by sodium ions.