On the Molecular Understanding of Protein Stability In Water, in Chemical Chaperone, and Its Intercalation to DNA

Abstract

Protein and DNA are two very important macromolecules in living organisms. Both have different kind of functions. DNA encodes the genetic information whereas proteins catalyse the biological reaction. To perform the biological function, proteins have to be in a folded native state. The conformational change or misfolding of protein causes disease in living organisms. For example, misfolding of prion protein causes neurodegenerative disease in all mammals. Prion protein is a glycoprotein, located at brain cell. It has three helices and an anti-parallel β-sheet. The cellular prion protein, termed as PrPC, converts to a toxic, more β-rich conformation (PrPSc). Various studies, including experimental and computational, have been performed to find the mechanism of prion protein conversion. Yet the mechanism is unclear. In this thesis, we have used the molecular dynamic simulation with enhanced sampling techniques to understand the mechanism of full prion unfolding for the first time in molecular detail. Our finding shows that the cellular prion protein is an intrinsically disordered protein and it is in a metastable state in which any small perturbation would lead to a more stable unfolded state. As mention above, protein conformational change would cause the fatal disease in living organisms. The protein folding, unfolding, or conformational changes are extremely dependent on the environment of proteins. It has been proposed that the inorganic salts (e.g. Na2So4, CaCl2) perturb the protein folding/unfolding. Similarly, isolated amino acids (AA) also act as chemical chaperones and perturb the folding and stability of the protein. The unique feature of amino acids is that they can exist in zwitterion and this way they would interact with the positive (ARG and LYS) and negative (ASP and GLU) residues of a protein. In this thesis we have investigated the effect of glycine and other AA on protein folding. We have observed that this AA interact with the charged residues of the protein. Moreover, among these charged residues they preferentially bind to the side chain of the ARG and LYS in protein using the carboxyl group. Proteins also bind to DNA to perform some biological functions. The protein binding is sometimes very specific. The binding of certain proteins such as transcription factors (TFs) involves a conformational change in DNA e.g. bending and kinking. It has been shown that the conformation change in DNA is the reason for specific DNA-protein complex formation. The crystal structure of all these complexes shows a partial intercalation of AA at the kinked site. Here, we have investigated the role of intercalation in DNA kinking. We have observed that the bending alone does not kink the DNA, but a partial intercalation of AA does. Further, we have investigated the mechanism of AA intercalation into DNA using two different systems (SOX4-DNA and Sac7d-DNA) and observed that bending, kinking and an intercalation is a simultaneous event. In summary, the current thesis contains my findings on the unfolding mechanism of prion protein (a neurodegenerative disease causing protein), the roll of amino acids as chemical chaperons in protein folding, and the molecular mechanism of protein intercalation into DNA and its kinking.