Applying flexible molecular docking to simulate protein retention behavior in hydrophobic interaction chromatography

作者：Peng Zhou; FeiFei Tian; ZhiLiang Li^*

来源：Science in China Series B-Chemistry, 2007, 50(5): 675-682.

DOI：10.1007/S11426-007-0044-6

• hydrophobic interaction chromatography
• flexible molecular docking
• genetic algorithm
• protein
• salting-in factor

Interaction between proteins and stationary phase in hydrophobic interaction chromatography (HIC) is differentiated into two thermodynamic processes involving direct nonbonding/conformation interaction and surface hydrophobic effect of proteins, hence quantitatively giving rise to a binary linear relation between HIC retention time (RT) at concentrated salting liquid and ligand-protein binding free energy. Then, possible binding manners for 27 proteins of known crystal structures with hydrophobic ligands are simulated and analyzed via ICM flexible molecular docking and genetic algorithm, with results greatly consistent with experimental values. By investigation, it is confirmed local hydrophobic effects of proteins and nonbinding/conformation interaction between ligand and protein both notably influence HIC chromatogram retention behaviors, mainly focusing on exposed portions on the protein surface.

• 出版日期2007-10
• 单位重庆大学