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

Ghadir A. Jamal, Ehsan Jahangirian, Michael R. Hamblin, Masoud Shirali, Hamed Mirzaei, Hossein Tarrahimofrad

Research output: Contribution to journalArticlepeer-review


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 °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 βcasein were simulated via MD and it was found that Protease JJ could interact with both BSA and βcasein 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. Communicated by Ramaswamy H. Sarma.

Original languageEnglish
JournalJournal of Biomolecular Structure and Dynamics
Publication statusAccepted/In press - 2023


  • Bacillus
  • docking
  • molecular dynamics
  • protease
  • thermostable

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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