Improving stability of nitrile hydratase by bridging the salt-bridges in specific thermal-sensitive regions

Journal of Biotechnology

Volumn 164, Issue 2, 2012, Pages 354-362

  Chen, Jie ^a   Yu, Huimin ^a   Liu, Changchun ^a   Liu, Jie ^a   Shen, Zhongyao ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

C terminal salt bridge strategy; Enzyme stability; Molecular dynamic simulation; Nitrile hydratase; Thermal sensitive region

Indexed keywords

C-TERMINAL SALT-BRIDGE STRATEGY; ENZYME STABILITY; GLOBAL CHANGE; NITRILE HYDRATASES; PSEUDONOCARDIA; RHODOCOCCUS RUBER; THERMAL-SENSITIVE; ULTRA-SONICATION;

BACTERIOLOGY; COMPUTER SIMULATION; CYANIDES; ENZYMES; MOLECULAR DYNAMICS;

STABILITY;

NITRILE HYDRATASE;

ARTICLE; BACILLUS; CARBOXY TERMINAL SEQUENCE; ENZYME ACTIVITY; ENZYME STABILITY; MOLECULAR DYNAMICS; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PSEUDONOCARDIA THERMOPHILA; PSEUDONOCARDIACEAE; THERMOSTABILITY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; ENZYME STABILITY; ESCHERICHIA COLI; GRAM-POSITIVE BACTERIA; HOT TEMPERATURE; HYDRO-LYASES; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN SUBUNITS; RECOMBINANT FUSION PROTEINS;

PSEUDONOCARDIA THERMOPHILA; RHODOCOCCUS RUBER;

EID: 84875233565     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2013.01.021     Document Type: Article

References (40)

1. Arnold F.H., Volkov A.A. Directed evolution of biocatalysts. Current Opinion in Chemical Biology 1999, 3:54-59.
2. Brooks B.R., Brooks C., Mackerell A., Nilsson L., Petrella R., Roux B., Won Y., Archontis G., Bartels C., Boresch S. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry 2009, 30:1545-1614.
3. Barlow D.J., Thornton J. Ion-pairs in proteins. Journal of Molecular Biology 1983, 168:867-885.
4. Dürrschmidt P., Mansfeld J., Ulbrich-Hofmann R. Differentiation between conformational and autoproteolytic stability of the neutral protease from Bacillus stearothermophilus containing an engineered disulfide bond. European Journal of Biochemistry 2001, 268:3612-3618.
5. Eijsink V.G.H., Bjørk A., Gåseidnes S., Sirevåg R., Synstad B., Burg B., Vriend G. Rational engineering of enzyme stability. Journal of Biotechnology 2004, 113:105-120.
6. Fernandez-Lafuente R. Stabilization of multimeric enzymes: strategies to prevent subunit dissociation. Enzyme and Microbial Technology 2009, 45:405-418.
7. Garcia-Galan C., Berenguer-Murcia A., Fernandez-Lafuente R., Rodrigues R.C. Potential of different enzyme immobilization strategies to improve enzyme performance. Advanced Synthesis & Catalysis 2011, 353:2885-2904.
8. Geourjon C., Deleage G. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics 1995, 11:681-684.
9. Gurry T., Nerenberg P.S., Stultz C.M. The contribution of interchain salt bridges to triple-helical stability in collagen. Biophysical Journal 2010, 98:2634-2643.
10. Hourai S., Miki M., Takashima Y., Mitsuda S., Yanagi K. Crystal structure of nitrile hydratase from a thermophilic Bacillus smithii. Biochemical and Biophysical Research Communications 2003, 312:340-345.
11. Komeda H., Kobayashi M., Shimizu S. Characterization of the gene cluster of high-molecular-mass nitrile hydratase (H-NHase) induced by its reaction product in Rhodococcus rhodochrous J1. Proceedings of the National Academy of Sciences of the United States of America 1996, 93:4267-4272.
12. Li J., Matsumura Y., Shinjo M., Kojima M., Kihara H. A stable [alpha]-helix-rich intermediate is formed by a single mutation of the [beta]-sheet protein, src SH3, at pH 3. Journal of Molecular Biology 2007, 372:747-755.
13. Liu J., Yu H., Shen Z. Insights into thermal stability of thermophilic nitrile hydratases by molecular dynamics simulation. Journal of Molecular Graphics and Modelling 2008, 27:529-535.
14. Lutz S. Beyond directed evolution-semi-rational protein engineering and design. Current Opinion in Biotechnology 2010, 21:734-743.
15. Ma Y., Yu H. Engineering of Rhodococcus cell catalysts for tolerance improvement by sigma factor mutation and active plasmid partition. Journal of Industrial Microbiology and Biotechnology 2012, 39:1421-1430.
16. Ma Y., Yu H., Pan W., Liu C., Zhang S., Shen Z. Identification of nitrile hydratase-producing Rhodococcus ruber TH and characterization of an amiE-negative mutant. Bioresource Technology 2010, 101:285-291.
17. Makhatadze G.I., Loladze V.V., Ermolenko D.N., Chen X.F., Thomas S.T. Contribution of surface salt bridges to protein stability: guidelines for protein engineering. Journal of Molecular Biology 2003, 327:1135-1148.
18. Miyanaga A., Fushinobu S., Ito K., Shoun H., Wakagi T. Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding. European Journal of Biochemistry 2004, 271:429-438.
19. Nagasawa T., Shimizu H., Yamada H. The superiority of the third-generation catalyst Rhodococcus rhodochrous J1 nitrile hydratase, for industrial production of acrylamide. Applied Microbiology and Biotechnology 1993, 40:189-195.
20. Nestl B.M., Nebel B.A., Hauer B. Recent progress in industrial biocatalysis. Current Opinion in Chemical Biology 2011, 15:187-193.
21. Okamoto S., Petegem F.V., Patrauchan M.A., Eltis L.D. AnhE, a metallochaperone involved in the maturation of a cobalt-dependent nitrile hydratase. Journal of Biological Chemistry 2010, 285:25126-25133.
22. Otten L.G., Hollmann F., Arends I.W.C.E. Enzyme engineering for enantioselectivity: from trial-and-error to rational design?. Trends in Biotechnology 2010, 28:46-54.
23. Pace C.N., Fu H., Fryar K.L., Landua J., Trevino S.R., Shirley B.A., Hendricks M.M.N., Iimura S., Gajiwala K., Scholtz J.M. Contribution of hydrophobic interactions to protein stability. Journal of Molecular Biology 2011, 408:514-528.
24. Pereira R.A., Graham D., Rainey F.A., Cowan D.A. A novel thermostable nitrile hydratase. Extremophiles 1998, 2:347-357.
25. Perl D., Mueller U., Heinemann U., Schmid F.X. Two exposed amino acid residues confer thermostability on a cold shock protein. Nature Structural & Molecular Biology 2000, 7:380-383.
26. Rahman R.N.Z.A., Fujiwara S., Nakamura H., Takagi M., Imanaka T. Ion pairs involved in maintaining a thermostable structure of glutamate dehydrogenase from a hyperthermophilic archaeon. Biochemical and Biophysical Research Communications 1998, 248:920-926.
27. Rodrigues R.C., Berenguer-Murcia á., Fernandez-Lafuente R. Coupling chemical modification and immobilization to improve the catalytic performance of enzymes. Advanced Synthesis & Catalysis 2011, 353:2216-2238.
28. Rodrigues R.C., Ortiz C., Berenguer-Murcia á., Torres R., Fernández-Lafuente R. Modifying enzyme activity and selectivity by immobilization. Chemical Society Reviews 2013, 10.1039/C2CS35231A.
29. Shi Y., Yu H., Sun X., Tian Z., Shen Z. Cloning of the nitrile hydratase gene from Nocardia sp. in Escherichia coli and Pichia pastoris and its functional expression using site-directed mutagenesis. Enzyme and Microbial Technology 2004, 35:557-562.
30. Szilágyi A., Závodszky P. Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure 2000, 8:493-504.
31. Sun X., Yu H., Shen Z. Deactivation kinetics of nitrile hydratase in free resting cells. Chinese Journal of Chemical Engineering 2009, 17:822-828.
32. Teilum K., Olsen J.G., Kragelund B.B. Protein stability, flexibility and function. Biochimica et Biophysica Acta - Proteins and Proteomics 2011, 1814:969-976.
33. Tsujimura M., Dohmae N., Odaka M., Chijimatsu M., Takio K., Yohda M., Hoshino M., Nagashima S., Endo I. Structure of the photoreactive iron center of the nitrile hydratase from Rhodococcus sp. N-771. Journal of Biological Chemistry 1997, 272:29454-29459.
34. van Pelt S., Quignard S., Kubac D., Sorokin D.Y., van Rantwijk F., Sheldon R.A. Nitrile hydratase CLEAs: the immobilization and stabilization of an industrially important enzyme. Green Chemistry 2008, 10:395-400.
35. Wang J., Cieplak P., Kollman P.A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?. Journal of Computational Chemistry 2000, 21:1049-1074.
36. Wang M., Si T., Zhao H. Biocatalyst development by directed evolution. Bioresource Technology 2012, 115:117-125.
37. Yip K., Stillman T., Britton K., Artymiuk P., Baker P., Sedelnikova S., Engel P., Pasquo A., Chiaraluce R., Consalvi V. The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures. Structure 1995, 3:1147-1158.
38. Yokota K., Satou K., Ohki S. Comparative analysis of protein thermostability: differences in amino acid content and substitution at the surfaces and in the core regions of thermophilic and mesophilic proteins. Science and Technology of Advanced Materials 2006, 7:255-262.
39. Yu H., Liu J., Shen Z. Modeling catalytic mechanism of nitrile hydratase by semi-empirical quantum mechanical calculation. Journal of Molecular Graphics and Modelling 2008, 27:522-528.
40. Yu H.M., Shi Y., Luo H., Tian Z.L., Zhu Y.Q., Shen Z.Y. An over expression and high efficient mutation system of a cobalt-containing nitrile hydratase. Journal of Molecular Catalysis B: Enzymatic 2006, 43:80-85.