Alternatives for the simulation of the lysozyme protein structure

Resumo

The application of solid mechanics has recently expanded to various new fields, which were unthinkable
a few years ago. Studies focusing on structural characteristics of microscopic entities have helped other areas such
as biochemistry to enhance our understanding of complex phenomena. Special attention has been given to proteins,
where the dynamic, flexibility, and vibration analysis are fundamental to comprehend their biological activities.
This work seeks to evaluate the protein's structure through a frame representation where the links simulate the
chemical bonds, using finite element method and optimization procedures to verify the feasibility of solid
mechanics techniques. The numerical simulation of three conformational states of the lysozyme protein is
performed (PDB code: 1DPX, 1DPW, and 4YM8), where modal analysis is used to investigate the protein
dynamics, obtaining vibrational frequencies, modes shapes, and a local measure of flexibility. Special attention is
given to the influence of the secondary bonds on the protein's behavior. The results are compared using Pearson's
correlation of the temperature factor distribution obtained experimentally for each atom. The application of
optimization tools utilizing the temperature factor to define the links' stiffness increased the correlation with
experimental results. The method brought acceptable outputs with low computational cost, with potential for
improvements, indicating the technique's feasibility.