Interaction of cibacron blue attached magnetic polymers with albumin using computational tools

Human plasma contains a vast amount of human serum albumin (HSA). Almost 60% of human plasma protein contains HSA. Blood volume regulation based on colloid osmotic pressure is a vital role of serum albumins. In order to hide their hydrophobic nature, they can be seen transferring some low water-soluble molecules. These molecules consisted of some steroid hormones, some salts, free fatty acids, calcium, and some drugs. Low or high level of albumin almost always caused several diseases. Besides, albumin should be removed from blood plasma in some cases, since high abundancy of albumin hinders biomarkers in proteome studies. Affinity chromatography is a standard method, which used for protein purification and separation studies due to its specificity, selectivity. There are several affinity chromatography methods, such as dye affinity, immobilized metal chelated affinity, and affinity electrophoresis. Cibacron Blue F3GA (CBD), as a dye ligand, is one of the most used dyes amongst dye affinity chromatography. CBD is ideally suited for HSA purification for several years. However, even though CBD has many purification applications, there is not much research focused on the interaction between CBD and HSA in molecular simulation. In this thesis, interactions between CBD and HSA were simulated via AutoDock molecular docking software in this study. Investigated possibilities resulted in six different conformations on different locations, which light the way to variable connectivity of CBD. Thus, it is determined that the most favorable binding is conformation 5, with its lowest binding energy, which is energetically favorable.