Molecular Modeling Study on the Three-dimensional Structure of the Luciferase Protein inVibrio-qinghaiensissp.-Q67

Hormesis of some organic solvents on Vibrio qinghaiensis sp.-Q67 from first binding to the β subunit of luciferase

“…The atomic coordinates of Q67 luciferase with FMN (avin mononucleotide) were taken from the structure le constructed by Chen et al 22 We named the subunits of Q67 luciferase as Q67Luca and Q67Lucb. The molecular docking and molecular dynamics (MD) simulations were used to simulate the structure of the organic solvent-luciferase complex.…”

“…The system was gradually heated from 0 to 300 K within 50 ps and subsequently simulated at 300 K for the equilibration and production phases. 22 The ptraj module was used to analyze the root mean-square displacements (RMSD) between the trajectory structures and the rst snapshot structure in 1st ns trajectory and root mean-square uctuation (RMSF) of various residues. All systems were equilibrated at 5 ns, and the MDs were prolonged for another 3 ns.…”

“…As the natural substrates of the photobacterium luminous reaction, FMN binds to Q67Luca. 22 For Q67Luca, the uctuation of the residue Thr179a of the a-helix can make it bigger and easier for FMN binding to occur. In addition, the loop of the residues Ser145a-Arg165a has high exibility, which enables the uctuation of the a-helix.…”

“…The Q67 luciferase has two subunits, a and b (Fig. 1), 22 which we named as Q67Luca and Q67Lucb. As the natural substrates of the luminous reaction in photobacterium, FMN binds to Q67Luca.…”

“…As the natural substrates of the luminous reaction in photobacterium, FMN binds to Q67Luca. 22 Molecular docking 23 examines whether the two molecules can bind and predicts the binding mode based on the threedimensional structures of molecules. Docking methods are fast and oen able to identify the correct binding site and ligand poses, though they rarely yield accurate binding affinities.…”