A finite-element-based coarse-grained model for global protein vibration

Protein mechanical vibrations play a pivotal role in biological activity. In particular, low-frequency (terahertz) modes are related to protein conformational changes, which represent the foundations for a correct protein functionality. Relying on the fact that such low-frequency motions involve large protein portions, thus modeling of local details is not necessary, coarse-grained models have proven their efficacy in capturing the essential dynamic behavior. In this paper, we show that a coarse-grained finite element space truss model is suitable for investigating protein vibrations. Hen egg-white lysozyme is selected as a case study and modal analysis is performed in order to investigate the protein dynamics; the influence of interaction cutoff values on optimal force constant, obtained vibrational frequencies and mode shapes is also explored. The validity of the structural model is demonstrated by comparing the calculated B-factors with the experimental ones. Moreover, from the methodology framework the truss model is shown to be consistent with the well-known anisotropic network model and this has been confirmed by the obtained results. The proposed truss model is then believed to be a simple yet powerful tool to investigate protein dynamics, and it could also be used to analyze conformational changes and protein stability from a Structural Mechanics viewpoint.