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
1. [1]
  
  (1) Bornscheuer, U. T.; Huisman, G.W.; Kazlauskas, R. J.; Lutz, S.;Moore, J. C.; Robins, K. Nature 2012, 485, 185. doi: 10.1038/nature11117
2. [2]
  (2) Schmid, A.; Dordick, J. S.; Hauer, B.; Kiener, A.;Wubbolts, M.;Witholt, B. Nature 2001, 409, 258. doi: 10.1038/35051736
3. [3]
  (3) Nestl, B. M.; Nebel, B. A.; Hauer, B. Curr. Opin. Chem. Biol.2011, 15, 187. doi: 10.1016/j.cbpa.2010.11.019
4. [4]
  (4) Zhang, B.;Weng, Y.; Xu, H.; Mao, Z. Appl. Microbiol. Biotechnol. 2012, 93, 61. doi: 10.1007/s00253-011-3672-x
5. [5]
  (5) Sheldon, R. A. Chem. Soc. Rev. 2012, 41, 1437. doi: 10.1039/c1cs15219j
6. [6]
  (6) Huang, Z. L.; Zhang, C.;Wu, X.; Su, N.; Xing, X. H. Chin. J. Biotech. 2012, 28, 393. [黄子亮, 张翀, 吴希, 苏楠,刑新会. 生物工程学报, 2012, 28, 393.]
7. [7]
  (7) Hu, Y.; Liu,W. M.; Zou, B.; Tang, S. S.; Huang, H. Prog. Chem.2010, 22, 1656.
8. [8]
  (8) Liu, P.; Xing, G.W.; Li, X.W.; Ye, Y. H. Acta Phys. -Chim. Sin.2010, 26, 1113. [刘平, 邢国文, 李宣文, 叶蕴华. 物理化学学报, 2010, 26, 1113.] doi: 10.3866/PKU.WHXB20100448
9. [9]
  (9) Lei, Q. J.; Gao, B. J.; Zhang, Z. G. Acta Phys. -Chim. Sin. 2011,27, 2697. [雷青娟, 高保娇, 张正国. 物理化学学报, 2011, 27,2697.] doi: 10.3866/PKU.WHXB20111122
10. [10]
  (10) Park, B.W.; Yoon, D. Y.; Kim, D. S. Biosens. Bioelectron. 2010,26, 1. doi: 10.1016/j.bios.2010.04.033
11. [11]
  (11) Kato, M.; Inuzuka, K.; Sakai-Kato, K.; Toyo'oka, T. Anal. Chem.2005, 77, 1813. doi: 10.1021/ac048388u
12. [12]
  (12) Knezevic, Z.; Milosavic, N.; Bezbradica, D.; Jakovljevic, Z.;Prodanovic, R. Biochem. Eng. J. 2006, 30, 269. doi: 10.1016/j.bej.2006.05.009
13. [13]
  (13) Jung, Y.; Lee, J. M.; Jung, H.; Chung, B. H. Anal. Chem. 2007,79, 6534. doi: 10.1021/ac070484i
14. [14]
  (14) Limoges, B.; Marchal, D.; Mavre, F.; Saveant, J. M. J. Am. Chem. Soc. 2006, 128, 2084. doi: 10.1021/ja0569196
15. [15]
  (15) Chen, M. L.; Adak, A. K.; Yeh, N. C.; Yang,W. B.; Chuang, Y.J.;Wong, C. H.; Hwang, K. C.; Hwu, J. R. R.; Hsieh, S. L.; Lin,C. C. Angew. Chem. Int. Edit. 2008, 47, 8627. doi: 10.1002/anie.v47:45
16. [16]
  (16) Rusmini, F.; Zhong, Z. Y.; Feijen, J. Biomacromolecules 2007,8, 1775. doi: 10.1021/bm061197b
17. [17]
  (17) Turkova, J. J. Chromatogr. B 1999, 722, 11. doi: 10.1016/S0378-4347(98)00434-4
18. [18]
  (18) Cao, L.; Chen, H. J. Chin. Biotechnol. 2003, 23, 22.
19. [19]
  (19) Zhou,W.W.; Lian, J.; Hu, K. J.; Gao, Y. H.; Xu, B. Acta Phys. -Chim. Sin. 2010, 26, 2821. [周稳稳, 廉洁, 胡科家,高云华, 徐百. 物理化学学报, 2010, 26, 2821.] doi: 10.3866/PKU.WHXB20101016
20. [20]
  (20) Zhou, J. Q.; Chen, S. H.;Wang, J.W. Chin. J. Biotech. 2008, 24,617. [周建芹, 陈韶华, 王剑文. 生物工程学报, 2008, 24,617.] doi: 10.1016/S1872-2075(08)60031-X
21. [21]
  (21) Hernandez, K.; Fernandez-Lafuente, R. Enzyme Microb. Technol. 2011, 48, 107. doi: 10.1016/j.enzmictec.2010.10.003
22. [22]
  (22) hlke, H.; Klebe, G. Angew. Chem. Int. Edit. 2002, 41, 2645.
23. [23]
  (23) Huang, B.; Liu, F. F.; Dong, X. Y.; Sun, Y. J. Phys. Chem. B2011, 115, 4168. doi: 10.1021/jp111216g
24. [24]
  (24) Huang, B.; Liu, F. F.; Dong, X. Y.; Sun, Y. J. Phys. Chem. B2012, 116, 424. doi: 10.1021/jp205770p
25. [25]
  (25) Lin, D. Q.; Tong, H. F.;Wang, H. Y.; Yao, S. J. J. Phys. Chem. B2012, 116, 1393. doi: 10.1021/jp206817b
26. [26]
  (26) Alonso, H.; Bliznyuk, A. A.; Gready, J. E. Med. Res. Rev. 2006,26, 531.
27. [27]
  (27) Liu, F. F.; Dong, X. Y.;Wang, T.; Sun, Y. J. Chromatogr. A2007, 1175, 249. doi: 10.1016/j.chroma.2007.10.074
28. [28]
  (28) Liu, F. F.;Wang, T.; Dong, X. Y.; Sun, Y. J. Chromatogr. A2007, 1146, 41. doi: 10.1016/j.chroma.2007.01.130
29. [29]
  (29) Transue, T. R.; Krahn, J. M.; Gabel, S. A.; DeRose, E. F.;London, R. E. Biochemistry-us 2004, 43, 2829. doi: 10.1021/bi035782y
30. [30]
  (30) Morris, G. M.; Huey, R.; Lindstrom,W.; Sanner, M. F.; Belew,R. K.; odsell, D. S.; Olson, A. J. J. Comput. Chem. 2009, 30,2785. doi: 10.1002/jcc.v30:16
31. [31]
  (31) Dundas, J.; Ouyang, Z.; Tseng, J.; Binkowski, A.; Turpaz, Y.;Liang, J. Nucleic. Acids Res. 2006, 34,W116.
32. [32]
  (32) Irwin, J. J.; Sterling, T.; Mysinger, M. M.; Bolstad, E. S.;Coleman, R. G. J. Chem. Inf. Model. 2012, 52, 1757.
33. [33]
  (33) Morris, G. M.; odsell, D. S.; Halliday, R. S.; Huey, R.; Hart,W. E.; Belew, R. K.; Olson, A. J. J. Comput. Chem. 1998, 19,1639.
34. [34]
  (34) Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J. Mol. Biol.1996, 261, 470. doi: 10.1006/jmbi.1996.0477
35. [35]
  (35) Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435. doi: 10.1021/ct700301q
36. [36]
  (36) Van Gunsteren,W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger,P. H.; Krüger, P.; Mark, A. E.; Scott,W. R. P.; Tironi, I. G. TheGROMOS96 Manual and User Guide. In Biomolecular Simulation; Zürich, Groninigen, 1996.
37. [37]
  (37) Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren,W. F.;Hermans, J. In Intermolecular Forces; Pullman, B. Ed.; Reidel:Dordecht, holland, 1981, p 331.
38. [38]
  (38) Hess, B.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463.
39. [39]
  (39) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98,10089. doi: 10.1063/1.464397
40. [40]
  (40) Beredsen, H. J. C.; Postma, J. P. M.; van Gunsteren,W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684. doi: 10.1063/1.448118
41. [41]
  (41) Humphrey,W.; Dalke, A.; Schulten, K. J. Mol. Graph. 1996, 14,33. doi: 10.1016/0263-7855(96)00018-5
42. [42]
  (42) Plewczynski, D.; Lazniewski, M.; Augustyniak, R.; Ginalski, K.J. Comput. Chem. 2011, 32, 742. doi: 10.1002/jcc.v32.4
43. [43]
  (43) Lu, I. L.;Wang, H. J. Comput. Biol. 2012, 19, 1215. doi: 10.1089/cmb.2012.0188
44. [44]
  (44) Li, X.; Li, Y.; Cheng, T. J.; Liu, Z. H.;Wang, R. X. J. Comput. Chem. 2010, 31, 2109. doi: 10.1002/jcc.v31:11
45. [45]
  (45) Cheng, T. J.; Li, X.; Li, Y.; Liu, Z. H.;Wang, R. X. J. Chem. Inf. Model. 2009, 49, 1079. doi: 10.1021/ci9000053
46. [46]
  (46) Huang, S. Y.; Grinter, S. Z.; Zou, X. Q. Phys. Chem. Chem. Phys. 2010, 12, 12899.
47. [47]
  (47) Liu, F. F.; Ji, L.; Dong, X. Y. Acta Phys. -Chim. Sin. 2010, 26,2813. [刘夫锋, 纪络, 董晓燕. 物理化学学报, 2010, 26,2813.] doi: 10.3866/PKU.WHXB20101011
48. [48]
  (48) Sun, H.; Jiang, Y. J.; Yu, Q. S.; Zou, J.W. Acta Phys. -Chim. Sin.2009, 25, 635. [孙浩, 蒋勇军, 俞庆森, 邹建卫. 物理化学学报, 2009, 25, 635.] doi: 10.3866/PKU.WHXB20090405
49. [49]
  (49) Zhao, Y. S.; Zheng, Q. C.; Zhang, H. X.; Chu, H. Y.; Sun, C. C.Acta Phys. -Chim. Sin. 2009, 25, 417. [赵勇山, 郑清川, 张红星, 楚慧郢, 孙家钟. 物理化学学报, 2009, 25, 417.] doi: 10.3866/PKU.WHXB20090304
50. [50]
  (50) Liu, F. F.; Dong, X. Y.; Sun, Y. J. Mol. Graph. Model. 2008, 27,421. doi: 10.1016/j.jmgm.2008.07.002
51. [51]
  (51) Levy, Y.; Onuchic, J. N. Annu. Rev. Biophys. Biomol. Struct.2006, 35, 389. doi: 10.1146/annurev.biophys.35.040405.102134
52. [52]
  (52) Liu, F. F.; Ji, L.; Dong, X. Y.; Sun, Y. J. Phys. Chem. B 2009,113, 11320. doi: 10.1021/jp905580j
1. [1]
  Zhi Zhou , Yu-E Lian , Yuqing Li , Hui Gao , Wei Yi . New Insights into the Molecular Mechanism Behind Clinical Tragedies of “Cephalosporin with Alcohol”. University Chemistry, 2025, 40(3): 42-51. doi: 10.12461/PKU.DXHX202403104
2. [2]
  Congying Lu , Fei Zhong , Zhenyu Yuan , Shuaibing Li , Jiayao Li , Jiewen Liu , Xianyang Hu , Liqun Sun , Rui Li , Meijuan Hu . Experimental Improvement of Surfactant Interface Chemistry: An Integrated Design for the Fusion of Experiment and Simulation. University Chemistry, 2024, 39(3): 283-293. doi: 10.3866/PKU.DXHX202308097
3. [3]
  Zhenming Xu , Yibo Wang , Zhenhui Liu , Duo Chen , Mingbo Zheng , Laifa Shen . Experimental Design of Computational Materials Science and Computational Chemistry Courses Based on the Bohrium Scientific Computing Cloud Platform. University Chemistry, 2025, 40(3): 36-41. doi: 10.12461/PKU.DXHX202403096
4. [4]
  Shule Liu . Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments. University Chemistry, 2024, 39(4): 338-342. doi: 10.3866/PKU.DXHX202310029
5. [5]
  Shanghua Li , Malin Li , Xiwen Chi , Xin Yin , Zhaodi Luo , Jihong Yu . 基于高离子迁移动力学的取向ZnQ分子筛保护层实现高稳定水系锌金属负极的构筑. Acta Physico-Chimica Sinica, 2025, 41(1): 2309003-. doi: 10.3866/PKU.WHXB202309003
6. [6]
  Yaping Li , Sai An , Aiqing Cao , Shilong Li , Ming Lei . The Application of Molecular Simulation Software in Structural Chemistry Education: First-Principles Calculation of NiFe Layered Double Hydroxide. University Chemistry, 2025, 40(3): 160-170. doi: 10.12461/PKU.DXHX202405185
7. [7]
  Yue Wu , Jun Li , Bo Zhang , Yan Yang , Haibo Li , Xian-Xi Zhang . Research on Kinetic and Thermodynamic Transformations of Organic-Inorganic Hybrid Materials for Fluorescent Anti-Counterfeiting Application information: Introducing a Comprehensive Chemistry Experiment. University Chemistry, 2024, 39(6): 390-399. doi: 10.3866/PKU.DXHX202403028
8. [8]
  Yufang GAO , Nan HOU , Yaning LIANG , Ning LI , Yanting ZHANG , Zelong LI , Xiaofeng LI . Nano-thin layer MCM-22 zeolite: Synthesis and catalytic properties of trimethylbenzene isomerization reaction. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1079-1087. doi: 10.11862/CJIC.20240036
9. [9]
  You Wu , Chang Cheng , Kezhen Qi , Bei Cheng , Jianjun Zhang , Jiaguo Yu , Liuyang Zhang . ZnO/D-A共轭聚合物S型异质结高效光催化产H₂O₂及其电荷转移动力学研究. Acta Physico-Chimica Sinica, 2024, 40(11): 2406027-. doi: 10.3866/PKU.WHXB202406027
10. [10]
  Yan Li , Xinze Wang , Xue Yao , Shouyun Yu . 基于激发态手性铜催化的烯烃E→Z异构的动力学拆分——推荐一个本科生综合化学实验. University Chemistry, 2024, 39(5): 1-10. doi: 10.3866/PKU.DXHX202309053
11. [11]
  Wenyan Dan , Weijie Li , Xiaogang Wang . The Technical Analysis of Visual Software ShelXle for Refinement of Small Molecular Crystal Structure. University Chemistry, 2024, 39(3): 63-69. doi: 10.3866/PKU.DXHX202302060
12. [12]
  Zhifang SU , Zongjie GUAN , Yu FANG . Process of electrocatalytic synthesis of small molecule substances by porous framework materials. Chinese Journal of Inorganic Chemistry, 2024, 40(12): 2373-2395. doi: 10.11862/CJIC.20240290
13. [13]
  Heng Zhang . Determination of All Rate Constants in the Enzyme Catalyzed Reactions Based on Michaelis-Menten Mechanism. University Chemistry, 2024, 39(4): 395-400. doi: 10.3866/PKU.DXHX202310047
14. [14]
  Yaling Chen . Basic Theory and Competitive Exam Analysis of Dynamic Isotope Effect. University Chemistry, 2024, 39(8): 403-410. doi: 10.3866/PKU.DXHX202311093
15. [15]
  Jiayu Gu , Siqi Wang , Jun Ling . Kinetics of Living Copolymerization: A Brief Discussion. University Chemistry, 2025, 40(4): 100-107. doi: 10.12461/PKU.DXHX202406012
16. [16]
  .
  CCS Chemistry | 超分子活化底物为自由基促进高效选择性光催化氧化
  . CCS Chemistry, 2025, 7(10.31635/ccschem.025.202405229): -.
17. [17]
  Pingping Zhu , Yongjun Xie , Yuanping Yi , Yu Huang , Qiang Zhou , Shiyan Xiao , Haiyang Yang , Pingsheng He . Excavation and Extraction of Ideological and Political Elements for the Virtual Simulation Experiments at Molecular Level: Taking the Project “the Simulation and Computation of Conformation, Morphology and Dimensions of Polymer Chains” as an Example. University Chemistry, 2024, 39(2): 83-88. doi: 10.3866/PKU.DXHX202309063
18. [18]
  Jinfu Ma , Hui Lu , Jiandong Wu , Zhongli Zou . Teaching Design of Electrochemical Principles Course Based on “Cognitive Laws”: Kinetics of Electron Transfer Steps. University Chemistry, 2024, 39(3): 174-177. doi: 10.3866/PKU.DXHX202309052
19. [19]
  Yeyun Zhang , Ling Fan , Yanmei Wang , Zhenfeng Shang . Development and Application of Kinetic Reaction Flasks in Physical Chemistry Experimental Teaching. University Chemistry, 2024, 39(4): 100-106. doi: 10.3866/PKU.DXHX202308044
20. [20]
  Lijun Huo , Mingcun Wang , Tianyi Zhao , Mingjie Liu . Exploration of Undergraduate and Graduate Integrated Teaching in Polymer Chemistry with Aerospace Characteristics. University Chemistry, 2024, 39(6): 103-111. doi: 10.3866/PKU.DXHX202312059

Get Citation

PDF

XML

Metrics

PDF Downloads(1015)
Abstract views(1038)
HTML views(5)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142