Citation: BAI Shu, ZHOU Rong, LIU Fu-Feng. Rational Design of Affinity Ligand for the Oriented Immobilization of Trypsin[J]. Acta Physico-Chimica Sinica, ;2013, 29(02): 439-448. doi: 10.3866/PKU.WHXB201211272 shu

Rational Design of Affinity Ligand for the Oriented Immobilization of Trypsin

1.
Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, P. R. China

Received Date: 20 September 2012
Available Online: 27 November 2012
Fund Project: 国家自然科学基金(20906068) (20906068)天津市应用基础与前沿技术研究计划项目(10JCYBJC04500)资助 (10JCYBJC04500)

Based on the three-dimensional (3D) structure of trypsin, 2-nitrophenyl-β-D-glucopyranoside was selected from the ZINC database to be a candidate affinity ligand for trypsin. The affinity between trypsin and the ligand was analyzed. It is found that the interactions between the ligand and the protein are dominated by van der Waals interactions and hydrogen bonding. Molecular dynamics (MD) simulations were used to verify the affinity between the ligand and trypsin; the simulations indicate that the complex remains stable, and the distance between the ligand and the target protein changes only a little. It is found that one water molecule acts as a bridge between the ligand and the protein pocket via hydrogen bonding. Finally, the ligand was coupled to Sepharose CL-6B gel, and was used to immobilize trypsin in an oriented fashion. It is found that the enzyme activity and specific activity of the oriented immobilized trypsin are 340.8 U·g^-1 and 300.3 U·mg^-1, respectively. These values are 10 and 5 times that of the free enzyme. The results of this work indicate that the combination of docking and MD simulations are promising for the rational design of ligands for oriented immobilization.
- Enzyme catalysis,
- Affinity ligand,
- Molecular docking,
- Molecular dynamics simulation,
- Oriented immobilization
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