Biomolecules in Binary Solvents: Computer Simulation Study of Lysozyme Protein in Ethanol-Water Mixed Solvent Environment - Abstract
Proteins are building blocks of biological systems and play an important role from the health and medical perspective in the drug reactions and efficiency. Proteins function well in their natural water solvent environments and are influenced by modified solvent environments such as alcohol. Effect of protein-solvent interaction on the protein structure is widely studied with experimental and computational techniques. However, molecular level understanding of proteins interaction with many solvents is still not fully understood. The present work aims to obtain a detailed understanding of solvent effect on lysozyme protein, using water, ethanol, and different concentrations of waterethanol mixtures as solvents. We use detailed atomistic molecular dynamics simulations to study using GROMACS code. Compared to neat water environment, the lysozome structure shows remarkable changes in water-ethanol mixed solvent, with increasing ethanol concentration. Significant changes were observed in the protein secondary structure involving alpha helices. We found that increasing ethanol concentration results in a systematic increase in total energy, enthalpy, root mean square deviation (RMSD), and radius of gyration of lysozyme protein. 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 good agreement with those obtained from the interpolation approach. The polynomial approach eliminates the need for computationally intensive full MD analysis for the concentrations within the range (0-12%) studied.