Journal
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
Volume 37, Issue 1, Pages 256-264Publisher
TAYLOR & FRANCIS INC
DOI: 10.1080/07391102.2018.1425638
Keywords
sodium-potassium pump; THz vibration; all-atom simulation; modal analysis; lattice model
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Mechanical vibration in the Terahertz range is believed to be connected with protein functions. In this paper, we present the results of a normal-mode analysis (modal analysis) of a Na/K-ATPase all-atom model, focusing the attention on low-frequency vibration modes. The numerical model helps in the interpretation of experimental results previously obtained by the authors via Raman spectroscopy of Na/K-ATPase samples, where several unassigned peaks were found in the sub-500 cm(-1) range. In particular, vibration modes corresponding to peaks at 27, 190 and 300 cm(-1), found experimentally, are confirmed here numerically, together with some other modes at lower frequencies (wavenumbers) that were not possible to observe in the experimental test. All the aforementioned modes correspond to vibrations involving the protein ends, i.e. portions directly related to the operating mechanism of the sodium-potassium pump.
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