In silico Analysis and Molecular Dynamic Modeling of Three-dimensional Structure of Glutelin type-B 5-like Proteins from Proso Millet: Effects of Temperature and Electric Field

Abstract

This study determined the 3D structure of glutelin type-B 5-like (GTB) protein from proso millet using homology modeling and investigated the effects of simulated temperature and static electric field on its secondary structures, solvent accessibility surface area (SASA), the radius of gyration (Rg), root mean square deviation (RMSD), and total dipole moment. The result showed that the structure of GTB is majorly a protomer that comprises three monomers with one jelly-like β-barrel and two extended helix domains, and the remaining 35% as coils. Based on the molecular dynamic simulation, the secondary structure of the protein was not disrupted at temperatures between 300–400 K and static electric fields of between 0.1-3 V/nm, albeit the loss of a few amino acid residues. The RMSD increased significantly with an increase in temperature, static electric field, and simulation time. But the Rg and SASA decreased for the same conditions, suggesting that, the protein structure is compacting during thermal and electrical treatment.