Molecular Dynamics Analysis of Lysozyme Protein in Ethanol- Water Mixed Solvent.

摘要

Effect of protein-solvent interaction on the protein structure is widely studied with experimental and computational techniques. Despite this, molecular level understanding of proteins and some simple solvents is still not fully understood. This work focuses on detailed molecular dynamics simulations of solvent effect on lysozyme protein, using water, ethanol, and different concentrations of water-ethanol mixtures as solvents. The lysozyme protein structure in water, ethanol and ethanol-water mixture (0 12% ethanol) was studied using GROMACS molecular dynamics simulation (MD) code. Compared to water environment, the lysozyme structure showed remarkable changes in water-ethanol with increasing ethanol concentration. Significant changes were observed in the protein secondary structure involving alpha helices. A study of thermodynamic and structural properties indicate that increasing ethanol concentration resulted in a systematic increase in total energy, enthalpy, root mean square deviation (RMSD), and radius of gyration of lysozyme. A polynomial interpolation approach is presented to determine these quantities for any intermediate alcohol percentage, and compared with the values obtained from a full MD simulation. Results from MD simulation were in reasonably good agreement with those from the interpolation approach. The polynomial approach eliminates the need for computationally intensive full MD analysis for the concentrations within the range of 0 - 12%.