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Design, Fabrication, and Experimental Characterization of Plasmonic Photoconductive Terahertz Emitters
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Terahertz vibration modes in Na/K-ATPase.

Alberto Carpinteri1, Gianfranco Piana1, Andrea Bassani1

  • 1a Department of Structural, Geotechnical and Building Engineering , Politecnico di Torino , Corso Duca degli Abruzzi 24, 10129 , Torino , Italy.

Journal of Biomolecular Structure & Dynamics
|January 10, 2018
PubMed
Summary

This study uses normal-mode analysis to model low-frequency vibrations in the sodium-potassium pump (Na/K-ATPase). Numerical results confirm experimental findings and reveal new vibrational modes linked to the pump

Keywords:
THz vibrationall-atom simulationlattice modelmodal analysissodium-potassium pump

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Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Dynamics

Background:

  • Terahertz mechanical vibrations are linked to protein functionality.
  • The sodium-potassium pump (Na/K-ATPase) is crucial for cellular ion transport.
  • Previous Raman spectroscopy revealed unassigned peaks in Na/K-ATPase spectra below 500 cm⁻¹.

Purpose of the Study:

  • To perform normal-mode analysis on an all-atom model of Na/K-ATPase.
  • To investigate low-frequency vibrational modes.
  • To interpret experimental Raman spectroscopy data and identify specific vibrational modes.

Main Methods:

  • All-atom molecular dynamics simulation.
  • Normal-mode analysis (modal analysis).
  • Comparison with experimental Raman spectroscopy data.

Main Results:

  • Numerical confirmation of experimentally observed vibrational modes at 27, 190, and 300 cm⁻¹.
  • Identification of additional low-frequency vibrational modes not detectable experimentally.
  • These modes involve vibrations of the protein ends, crucial for the pump's mechanism.

Conclusions:

  • Normal-mode analysis provides a valuable tool for interpreting experimental vibrational spectroscopy of proteins.
  • The identified low-frequency modes are directly related to the functional mechanism of the Na/K-ATPase.
  • This study enhances the understanding of protein dynamics and their role in biological function.