Modal Analysis of the Lysozyme Protein Considering All-Atom and Coarse-Grained Finite Element Models

Abstract

Proteins are the fundamental entities of several organic activities. They are essential for a broad range of tasks in a way that their shapes and folding processes are crucial to achieving proper biological functions. Low-frequency modes, generally associated with collective movements at terahertz (THz) and sub-terahertz frequencies, have been appointed as critical for the conformational processes of many proteins. Dynamic simulations, such as molecular dynamics, are vastly applied by biochemical researchers in this field. However, in the last years, proposals that define the protein as a simplified elastic macrostructure have shown appealing results when dealing with this type of problem. In this context, modal analysis based on different modelization techniques, i.e., considering both an all-atom (AA) and coarse-grained (CG) representation, is proposed to analyze the hen egg-white lysozyme. This work presents new considerations and conclusions compared to previous analyses. Experimental values for the B-factor, considering all the heavy atoms or only one representative point per amino acid, are used to evaluate the validity of the numerical solutions. In general terms, this comparison allows the assessment of the regional flexibility of the protein. Besides, the low computational requirements make this approach a quick method to extract the protein’s dynamic properties under scrutiny.

Keywords

• lysozyme
• modal analysis
• B-factor
• finite element model
• all-atom model
• coarse-grained model