Normal Mode Analysis of Thermophilic Cellulase FnCel5A Using Elastic Network Models

Abstract

Normal mode analysis (NMA) based on elastic network models is an efficient, cost-effective and powerful, computational approach for characterizing protein flexibility and the resulting dynamics. In this study, we have analyzed a single protein structure, a hyperthermophylic enzyme (FnCel5A) with a given PDB ID: 3rjy, in order to calculate deformation energies, Eigenvalues, atomic fluctuations and displacements, and overlap and correlation matrices that display correlations among all of the C-alpha-atom motions in the FnCel5A structure. The WEBnm@ server was used to provide a quick automated computational low-frequency normal protein structure mode analysis. Single mode analysis using NMA has been applied on the web server, which can provide recently improved functionality for the single protein structures. This includes new visualization of protein motions, inter-amino acids correlations, and conformational transition analysis applying the overlap analysis. Furthermore, we have studied the structural and single mode FnCel5A (PDB: 3rjy) analysis in order to calculate the lowest and normal frequency protein modes. This study provides enough information about the loop flexibility and highest B-factors regions of FnCel5A which play an important role in rational and semi-rational designing to engineer this enzyme for improved activity.