Computer Aided Simulations Of The Interactions Between Immobilized Ligands And Proteins

In order to obtain the molecular docking method which can be used for simulation and calculation the interactions between ligands and proteins in chromatography research, an improved molecular docking technology based on DOCK5.3.0 software was applied to analysis the factor of immobilization, and finally the reasonable molecular docking technology is achieved. In this paper, the mainly issues are focused on the performance of the software docking on the whole receptor protein surfaces, the characters of ligands which well binded on IgG, the impact of the immobilization on the simulation and two novel instruments used for analysis the interaction between immobilized ligands and receptor.The results show that: (1) DOCK software has a good performance on the whole protein surface docking, and it can be used to analysis binding sites with natural ligands and artificial probe. For non-ligand small molecules, there are multiple binding sites on the protein surfaces, and the cluster sizes play an important role in locating them; for the natural ligands, they bind on active pockets by their own characters of structures. (2) The types of ligands which have good energy scores are related to the structure of IgG. Ligands with increased hydrophobic, hydrogen bond receptor number and negative charge will be more conducive to absorption. At the same time, comprehensive analysis shows that design and synthetic absorbent for Fc fragment will be more easily. (3)The immobilization plays an important role in the interaction between ligands and proteins in chromatography study, including reducing the freedom of ligands and restricting adsorption on protein surface. Using virtual surface is an effective way to reduce the side effects of immobilization and increase the accuracy of molecular docking, and the best choice of roll ball size would be in a radius of 5.0 A|°- 8.0|°. (4)The model of multiple sites binding is the major way of the adsorption between small ligands and receptors. Analysis of binding site number and energy score distribution will be two kinds of novel and useful instruments.