Exploring THz Protein Vibrations by Means of Modal Analysis: All-Atom vs Coarse-Grained Model

Abstract

It is strongly believed among the scientific community that protein dynamics constitutes the fundamental link existing between structure and function. Indeed, by means of modal analysis, it has been shown that low-frequency vibrational modes are strictly related to protein conformational transitions. In the last years, some of the authors made use of all-atom mechanical models, treating proteins like elastic lattice structures, in order to investigate the expansion-contraction vibrational modes. In particular, low-frequency modes were found to involve the whole protein structure and occur in the so-called terahertz (THz) range. Vibrations at THz frequencies, especially around or below 1 THz, were also detected experimentally on lysozyme and Na+/K+-ATPase powder samples by means of Raman spectroscopy using modern ultra-low frequency (ULF) filters. In order to focus mostly on low-frequency vibrations occurring in the THz range, different finite-element coarse-grained models, based on the coordinates of Cα atoms, are then proposed in this contribution. In particular, the case of HIV-1 protease subunit is investigated and its THz mechanical vibrations are analyzed.