In-silico characterization of a thermophilic serine protease via homology modeling, docking and molecular dynamics simulations

One of the major categories of industrial enzymes, proteases is crucial to the survival of living things. The purpose of this research was to newly thermostable protease from the thermophilum Geobacillus stearothermophilus. With the conserved catalytic tetrad, protease (Protease JJ) is closely related to the serine proteases from the subtilisin S8 peptidase, according to phylogenetic tree analysis. The tertiary structure of Protease JJ was predicted structurally using RoseTTAFold, and it is a sandwich structure overall. Homology modeling validation showed Protease JJ was modeled in X-ray's protein areas, and it has gained a favored Ramachandran graph regarding Phi/Psi angels. Protease JJ showed structure stability through Molecular dynamics simulation in the presence of Tween20 and Methanol in 1% concentration. Also, Protease JJ exhibited thermal stability at 60 to 90 degrees C so that amino acid exposure of Protease JJ was low and constant throughout the MD simulation. Docking results of Protease JJ with BSA and beta casein were simulated via MD and it was found that Protease JJ could interact with both BSA and beta casein strongly. MM/PBSA analysis showed Protease JJ may be involved via more amino acids with BSA as well as established more interaction hydrogen bonds. Overall, evidence suggests Protease JJ probably has merit for future experimental investigation as a thermostable protease.

Automated summary

The purpose of this study was to identify a thermostable protease from a thermophilic bacterium, Geobacillus stearothermophilus, named Protease JJ. Structural prediction and molecular dynamics simulations revealed that Protease JJ exhibited good structural and thermal stability, and it showed strong interactions with BSA and β-casein. The findings suggest that Protease JJ has potential as a thermostable protease for further research.