胰蛋白酶定向固定化亲和配基的理性设计

doi:10.3866/PKU.WHXB201211272

Abstract

Abstract:

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.

Key words: Enzyme catalysis, Affinity ligand, Molecular docking, Molecular dynamics simulation, Oriented immobilization

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

References

(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) Schmid, A.; Dordick, J. S.; Hauer, B.; Kiener, A.;Wubbolts, M.;Witholt, B. Nature 2001, 409, 258. doi: 10.1038/35051736
(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) Zhang, B.;Weng, Y.; Xu, H.; Mao, Z. Appl. Microbiol. Biotechnol. 2012, 93, 61. doi: 10.1007/s00253-011-3672-x
(5) Sheldon, R. A. Chem. Soc. Rev. 2012, 41, 1437. doi: 10.1039/c1cs15219j
(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) Hu, Y.; Liu,W. M.; Zou, B.; Tang, S. S.; Huang, H. Prog. Chem.2010, 22, 1656.
(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) 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) Park, B.W.; Yoon, D. Y.; Kim, D. S. Biosens. Bioelectron. 2010,26, 1. doi: 10.1016/j.bios.2010.04.033
(11) Kato, M.; Inuzuka, K.; Sakai-Kato, K.; Toyo'oka, T. Anal. Chem.2005, 77, 1813. doi: 10.1021/ac048388u
(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) Jung, Y.; Lee, J. M.; Jung, H.; Chung, B. H. Anal. Chem. 2007,79, 6534. doi: 10.1021/ac070484i
(14) Limoges, B.; Marchal, D.; Mavre, F.; Saveant, J. M. J. Am. Chem. Soc. 2006, 128, 2084. doi: 10.1021/ja0569196
(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) Rusmini, F.; Zhong, Z. Y.; Feijen, J. Biomacromolecules 2007,8, 1775. doi: 10.1021/bm061197b
(17) Turkova, J. J. Chromatogr. B 1999, 722, 11. doi: 10.1016/S0378-4347(98)00434-4
(18) Cao, L.; Chen, H. J. Chin. Biotechnol. 2003, 23, 22.
(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) 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) Hernandez, K.; Fernandez-Lafuente, R. Enzyme Microb. Technol. 2011, 48, 107. doi: 10.1016/j.enzmictec.2010.10.003
(22) Gohlke, H.; Klebe, G. Angew. Chem. Int. Edit. 2002, 41, 2645.
(23) Huang, B.; Liu, F. F.; Dong, X. Y.; Sun, Y. J. Phys. Chem. B2011, 115, 4168. doi: 10.1021/jp111216g
(24) Huang, B.; Liu, F. F.; Dong, X. Y.; Sun, Y. J. Phys. Chem. B2012, 116, 424. doi: 10.1021/jp205770p
(25) Lin, D. Q.; Tong, H. F.;Wang, H. Y.; Yao, S. J. J. Phys. Chem. B2012, 116, 1393. doi: 10.1021/jp206817b
(26) Alonso, H.; Bliznyuk, A. A.; Gready, J. E. Med. Res. Rev. 2006,26, 531.
(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) Liu, F. F.;Wang, T.; Dong, X. Y.; Sun, Y. J. Chromatogr. A2007, 1146, 41. doi: 10.1016/j.chroma.2007.01.130
(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) Morris, G. M.; Huey, R.; Lindstrom,W.; Sanner, M. F.; Belew,R. K.; Goodsell, D. S.; Olson, A. J. J. Comput. Chem. 2009, 30,2785. doi: 10.1002/jcc.v30:16
(31) Dundas, J.; Ouyang, Z.; Tseng, J.; Binkowski, A.; Turpaz, Y.;Liang, J. Nucleic. Acids Res. 2006, 34,W116.
(32) Irwin, J. J.; Sterling, T.; Mysinger, M. M.; Bolstad, E. S.;Coleman, R. G. J. Chem. Inf. Model. 2012, 52, 1757.
(33) Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart,W. E.; Belew, R. K.; Olson, A. J. J. Comput. Chem. 1998, 19,1639.
(34) Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J. Mol. Biol.1996, 261, 470. doi: 10.1006/jmbi.1996.0477
(35) Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435. doi: 10.1021/ct700301q
(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) 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) Hess, B.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463.
(39) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98,10089. doi: 10.1063/1.464397
(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) Humphrey,W.; Dalke, A.; Schulten, K. J. Mol. Graph. 1996, 14,33. doi: 10.1016/0263-7855(96)00018-5
(42) Plewczynski, D.; Lazniewski, M.; Augustyniak, R.; Ginalski, K.J. Comput. Chem. 2011, 32, 742. doi: 10.1002/jcc.v32.4
(43) Lu, I. L.;Wang, H. J. Comput. Biol. 2012, 19, 1215. doi: 10.1089/cmb.2012.0188
(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) 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) Huang, S. Y.; Grinter, S. Z.; Zou, X. Q. Phys. Chem. Chem. Phys. 2010, 12, 12899.
(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) 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) 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) Liu, F. F.; Dong, X. Y.; Sun, Y. J. Mol. Graph. Model. 2008, 27,421. doi: 10.1016/j.jmgm.2008.07.002
(51) Levy, Y.; Onuchic, J. N. Annu. Rev. Biophys. Biomol. Struct.2006, 35, 389. doi: 10.1146/annurev.biophys.35.040405.102134
(52) Liu, F. F.; Ji, L.; Dong, X. Y.; Sun, Y. J. Phys. Chem. B 2009,113, 11320. doi: 10.1021/jp905580j

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Rational Design of Affinity Ligand for the Oriented Immobilization of Trypsin

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