Molecular dynamics simulations of a hyperthermophilic and a mesophilic protein L30e

Molecular dynamics (MD) simulations were used to study the hyperthermophilic ribosomal protein L30e from archaeon Thermococcus celer at 300 and 350 K, and its mesophilic homologue, yeast L30e, at 300 K in explicit solvent for a period of 5.0 ns. Three trajectories obtained from the MD simulations were stable throughout the simulation period, such as total potential energy, radius of gyration, root-mean-square deviation, and secondary structures assignment. At 300 K, T. celer L30e is less flexible than its mesophilic homologue, and this difference becomes more pronounced at 350 K. Salt bridge networks, one triad and one hexad, are present at the surface of T. celer L30e. The ion pairs forming these salt bridges maintain close contact at a higher temperature, suggesting that these networks contribute to the protein’s hyperthermal stability. By contrast, we found no such networks to be present in yeast L30e. For charged residue I in T. celer L30e, the ΔΔGsolvI value and its corresponding ΔECoulI value possess opposite signs. This indicates that for T. celer L30e, a change in the solvation free energy of a charged residue due to increasing temperature is compensated by a change in the residude’s Coulombic interaction energy with the rest of the protein.