Molecular Dynamics Studies of the Effects of Alcohols on Chymotrypsin Inhibitor 2

Abstract

The folded native structure of a protein is highly sensitive towards the nature of solvent under specific environmental conditions. With the change of solvent’s physicochemical properties protein’s native structure can be disrupted. The use of cosolvent may also perturb protein stability. The primary objective of this thesis has been to obtain a microscopic understanding of the influence of cosolvent alcohols on the structure and dynamics of a protein. To achieve our goal, extensive molecular dynamics (MD) simulations of a protein Chymotrypsin Inhibitor 2 in water-alcohol binary mixtures were carried out with varying alcohol concentrations and temperatures. The thesis consists of six chapters. Chapter 1 provides a short account of the current status of research in this area. The methodologies employed in this thesis are also described briefly in this chapter. In Chapter 2 we present MD simulations of the protein in water-ethanol binary mixtures. Detailed investigations were carried out to explore the structural transformations of the protein in presence of ethanol. Further the local structure and dynamics of the surrounding water and ethanol were explored. Considering the importance of the heterogeneous surface of a protein in unfolding process, in Chapter 3 we have explored the
origin of locally heterogeneous correlated properties of water as well as ethanol around the secondary segments, namely, helix, loop and sheet of the protein in its folded and unfolded forms at several ethanol concentrations. In Chapter 4 the residue specific solvation of the unfolded protein and the interactions between the individual amino acid residues of the protein with ethanol as well as water have been investigated by using combined MD simulations and ONIOM study. Further, emphasis has been given to explore the residue’s preferential site of attraction towards the nature of the solvents. The importance of formation of hydrogen bonds between water and each residue of the protein was explored. A small number of key-residues in a protein sequence play vital roles in the function, stability and folding of proteins. Therefore, in Chapter 5 we made an attempt to identify the key-residues of the protein that trigger unfolding. Further the properties of the solvents around these residues as well as the dynamics of key-residue-water and key-residue-ethanol hydrogen bond were explored to investigate how the presence of ethanol may help these residues to initiate the unfolding. In Chapter 6 we present the comparative denaturing role of methanol, ethanol and 2,2,2-trifluoroethanol (TFE) under thermal stress. Efforts have been made to identify whether the alcohol governed unfolding of the protein involves direct interactions or it is an indirect process in which presence of alcohol alters the water properties and hence promotes unfolding.