Understanding the effects of salinity and temperature variations on conformational changes in a thermohalostable lipase: Insights from molecular dynamics simulations

Abstract

The interplay between side-chain hydrogen bonds and salt bridge networks stabilises thermohalostable enzymes. This study examined the effects of NaCl (0.6, 2.0, and 4.0 M) and temperature (300, 343, and 373 K) on the conformation of thermohalostable lipase using molecular dynamics simulations. The simulation was done using the AMBER with the ff14sb force field for 100 ns in the TIP3P solvent. The enzyme showed minimal structural changes across various temperatures and NaCl concentrations, as indicated by slight variations in the root mean square deviation (RMSD), radius of gyration (Rg), and solvent-accessible surface area (SASA). While increasing temperature raised root mean square fluctuation (RMSF) values, NaCl concentration effects were only significant at 373 K. Minimal changes in the secondary structure composition support the suggestion of overall structural stability. The catalytic site remained stable, with slight differences in the RMSF values for the catalytic triad and oxyanion hole residues, although their orientation was altered. Higher temperatures decreased the number of hydrogen bonds, but salt ions compensated for this loss by enhancing electrostatic interactions with charged residues, which incurred energy costs. The 0.6 M NaCl concentration was optimal for lipase stability across the tested conditions. These results advance our understanding of the structural stability mechanisms in thermohalostable enzymes and may be used in the development of novel enzymes for industrial applications.