Homology Modeling and Molecular Dynamics Simulation of Recombinant Laccase

Today, due to the abundant use of recombinant and engineered proteins in various fields,predicting the tertiary structure of proteins opens a new window in understanding their function. In thisstudy, the sequence of recombinant laccase was used, and homology modeling was done byMODELLER software version ۱۰.۰۴ [۱]. The maize laccase (PDB ID: ۶KLG [۲]) was considered as atemplate. A Python script did the prediction and construction of ۱۰۰ models. DOPE and GA۳۴۱ methodswere employed to evaluate the quality of the models. To validate the ۳D structures, the UCLA-DOELAB SAVES tool was utilized. Following the identification of the best model, we assessed the structuralstability of the enzyme through ۱۰ ns molecular dynamics simulation using Gromacs ۲۰۲۲ [۳]. Thesimulated structure exhibited notable stability, as indicated by consistent RMSD values observed duringthe simulation. In comparison to the reference protein, our novel enzyme displayed an RMSD value of۱.۲۳ Å. The recombinant laccase formed a significant number of intra-structure hydrogen bonds,totaling ۱۶,۹۹۳, while the reference protein formed only ۴۵۸. Additionally, the solvent-accessiblesurface area (SASA) of the structures differed, with values of ۲۰,۵۳۴.۴۷ and ۱۹,۳۷۷.۱۴ Ų/kcal for thereference protein and recombinant enzyme, respectively. The novel enzyme's ۳D structure opensavenues for both experimental and computational investigations, such as predicting binding sites withligands and engineering enhancements through residue design in future studies.

کلیدواژه ها:

tertiary structure ، recombinant laccase ، homology modeling ، molecular dynamics simulation