Browsing by Author "Savolainen, Heini"

Palmitoylation is an important posttranslational modification, which can change the function of proteins by the addition of fatty acids. In this thesis, I studied how palmitoylation affects the behavior of proteins and their interactions with the membranes. I also investigated the molecular mechanism of acetyl-palmitoyl recruitment by DHHC20, an important step in the palmitoyl transfer reaction. To this end, I used atomistic molecular dynamics simulations, which is a common computational method for studying biomolecules. In the first part of the thesis, I present my simulations and free energy calculations that show that palmitoylation enhances the partitioning of cysteines to the membranes and the spontaneous adsorption of amphipathic helices onto the membrane surface. At high levels, membrane cholesterol negatively impacts both of these properties both in the presence and absence of palmitoylation. However, palmitoylation strongly subdues the negative effect of increasing cholesterol. Moreover, palmitoylation helps proteins to maintain their helical conformation upon membrane binding. Overall, palmitoylation appears to be important for membrane interactions and the structural stability of proteins, especially under conditions of high membrane cholesterol. In the second part of my thesis, I investigated how its ligand, acetylpalmitoyl molecules, enters into the binding site of DHHC20. These simulations revealed that a short amphipathic helix at the gate of the ligand binding may play an important role in ligand recruitment and the overall stability of the enzyme. Moreover, I discovered that the protonation state of the cysteine residues that coordinate zinc cofactors is important for the stability of the zinc ions.