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.
Highlights
Most of the known biological functions are only conceivable because of the wide range of operations performed by proteins [1,2]
Shorter links can be associated with covalent bonds, the longer ones are related to weaker interactions due to electrostatic and Van der Waals effects
The static geometrical description made available in the PDB file for the crystallized hen-egg white lysozyme was used to analyze the dynamic properties of the resulting structure
Summary
Most of the known biological functions are only conceivable because of the wide range of operations performed by proteins [1,2]. The study of the three-dimensional protein structure is rather complex, allowing many different approaches to the problem. The atomically-detailed models can, to some extent, contribute to further and more accurate information [5]. To this purpose, molecular dynamics (MD) dives deeper into higher accuracy evaluation of the actual phenomena in place. Its high computational burden often prevents its applicability in studying the large-scale slow motions of the protein, which are known to be correlated with the biological function
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