The development of a thermostable CiP (Coprinus cinereus peroxidase) through in silico design

Biotechnology Progress

Volumn 26, Issue 4, 2010, Pages 1038-1046

  Kim, Su Jin ^a   Lee, Jeong Ah ^a   Joo, Jeong Chan ^b   Yoo, Young Je ^b   Kim, Yong Hwan ^a,c   Song, Bong Keun ^a  

^a Korea Research Institute of Chemical Technology   (South Korea)

^b Seoul National University   (South Korea)

^c Kwangwoon University   (South Korea)

Author keywords

B factor; Coprinus cinereus peroxidase; Flexibility; RosettaDesign; Thermostability

Indexed keywords

B-FACTOR; COPRINUS CINEREUS; FLEXIBILITY; ROSETTADESIGN; THERMOSTABILITY;

BIOCHEMICAL ENGINEERING; CATALYST ACTIVITY; ENZYMES; GENETIC ENGINEERING; MUTAGENESIS; PHENOLS; POLYMERIZATION; PORPHYRINS;

THERMODYNAMIC STABILITY;

PEROXIDASE;

ARTICLE; CHEMISTRY; COPRINUS; ENZYME STABILITY; ENZYMOLOGY; FLUOROMETRY; GENETICS; METABOLISM; MOLECULAR DYNAMICS; SITE DIRECTED MUTAGENESIS; THERMODYNAMICS;

COPRINUS; ENZYME STABILITY; FLUOROMETRY; MOLECULAR DYNAMICS SIMULATION; MUTAGENESIS, SITE-DIRECTED; PEROXIDASE; THERMODYNAMICS;

COPRINOPSIS CINEREA; COPRINUS;

EID: 77957131531     PISSN: 87567938     EISSN: 15206033     Source Type: Journal    
DOI: 10.1002/btpr.408     Document Type: Article

References (40)

1. Azerad R. Biocatalysis in organic synthesis. Adv Org Synth. 2005;1:455-518.
2. Radivojac P, Obradovic Z, Smith DK, Zhu G, Vucetic S, Brown CJ, Lawson JD, Dunker AK. Protein flexibility and intrinsic disorder. Protein Sci. 2004;13:71-81.
3. McLachlan MJ, Johannes TW, Zhao, H., Further improvement of phosphite dehydrogenase thermostability by saturation mutagenesis. Biotechnol Bioeng. 2007;99:268-274.
4. Palackal N, Brennan Y, Callen WN, Dupree P, Frey G, Goubet F, Hazlewood GP, Healey S, Kang YE, Kretz KA, Lee E, Tan X, Tomlinson GL, Verruto J, Wong VWK, Mathur EJ, Short JM, Robertson DE, Steer BA. An evolutionary route to xylanase process fitness. Protein Sci. 2004;13:494-503.
5. Giver L, Gershenson A, Freskgard P-O, Arnold FH. Directed evolution of a thermostable esterase. Proc Natl Acad Sci USA. 1998;95:12809-12813.
6. Cherry JR, Lamsa MH, Schneider P, Vind J, Svendsen A, Jones A, Pedersen AH. Directed evolution of a fungal peroxidase. Nat Biotechnol. 1999;17:179-184.
7. Abraham T, Pack Sp, Yoo YJ. Stabilization of Bacillus subtilis lipase A by increasing the residual packing. Biocatal Biotransformation. 2005;23:217-224.
8. Kima SH, Pokhrela S, Yoo YJ. Mutation of non-conserved amino acids surrounding catalytic site to shift pH optimum of Bacillus circulans xylanase. J Mol Catal B Enzym. 2008;55:130-136.
9. Vihinen M. Relationship of protein flexibility to thermostability. Protein Eng. 1987;1:477-480.
10. Karplus PA, Schulz GE. Prediction of chain flexibility in proteins. Naturwissenschaften 1985;72:212-213.
11. Kraemer-Pecore CM, Wollacott AM, Desjarlais JR. Computational protein design. Curr Opin Chem Biol. 2001;5:690-695.
12. Street AG, Mayo SL. Computational protein design. Structure. 1999;7:105-109.
13. Dahiyat BI. In silico design for protein stabilization. Curr Opin Biotechnol. 1999;10:387-390.
14. Luo P, Hayes RJ, Chan C, Stark DM, Hwang MY, Jacinto JM, Juvvadi P, Chung HS, Kundu A, Ary ML, Dahiyat BI. Development of a cytokine analog with enhanced stability using computational ultrahigh throughput screening. Protein Sci. 2002;11:1218-1226.
15. Dantas G, Kuhlman B, Callender D, Wong M, Baker D. A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol. 2003;332:449-460.
16. Liu Y, Kuhlman B, RosettaDesign server for protein design. Nucleic Acids Res. 2006;34:235-238.
17. Korkegian A, Black ME, Baker D, Stoddard BL. Computational thermostabilization of an enzyme. Science 2005;308:857-860.
18. Abelskov AK, Smith AT, Rasmussen CB, Dunford HB, Welinder, K. G., pH dependence and structural interpretation of the reactions of Coprinus cinereus peroxidase with hydrogen peroxide, ferulic acid, and 2,2'-Azinobis(3-ethylbenzthiazoline-6-sulfonic aicd). Biochemistry 1997;36:9453-9463.
19. Poulos TL, Kraut, J., The stereochemistry of peroxidase catalysis. J Biol Chem. 1980;255:8199-8205.
20. Kim YH, An ES, Song BK, Kim DS, Chelikani R. Polymerization of cardanol using soybean peroxidase and its potential application as anti-biofilm coating material. Biotechnol Lett 2003;25:1521-1524.
21. Won K, Kim YH, An ES, Lee YS, Song BK. Horseradish peroxidase-catalyzed polymerization of cardanol in the presence of redox mediators. Biomacromolecules 2004;5:1-4.
22. Kim YH, Won, Kh.; Kwon JM, Jeong HS, Park SY, An ES, Song BK. Synthesis of polycardanol from a renewable resource using a fungal peroxidase from Coprinus cinereus. J Mol Catal B Enzym 2005;34:33-38.
23. Kim YH, An ES, Park SY, Lee J-O, Kim JH, Song BK. Polymerization of bisphenol a using Coprinus cinereus peroxidase (CiP) and its application as a photoresist resin. J Mol Catal B Enzym 2007;44:149-154.
24. Kunishima N, Fukuyama K, Matsubara H, Hatanaka H, Shibano Y, Amachi T. Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1-9 A ° resolution: structural comparisons with the lignin and cytochrome c peroxidases. J Mol Biol. 1994;235:331-344.
25. Kim SJ, Lee JA, Kim YH, Song, B. K., Functional expression of Coprinus cinereus peroxidase in Pichia pastoris. Process Biochem. 2009;44:731-735.
26. Mackay GA, Hulett MD, Cook JPD, Trist HM, Henry AJ, McDonnell J, Beavil AJ, Beavil RL, Sutton BJ, Hogarth PM, Gould HJ. Mutagenesis within human FcRI differentially affects human and murine IgE binding. J Immunol. 2002;168:1787-1795.
27. Niesen FH, Berglund H, Vedadi M. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc. 2007;2:2212-2221.
28. Laberge M, Vanderkooi JM, Sharp KA. Effect of a protein electric-field on the CO stretch frequency. Finite difference Poisson-Boltzmann calculations on carbonmonoxycytochromes c. J Phys Chem B. 1996;100:10793-10801.
29. Laberge M, Sharp KA, Vanderkooi JM. Protein electric field effects on the CO stretch frequency of carbonmonoxycytochromes c as a function of carbonyl tilting and bending investigated with a continuum electrostatic approach. J Phys Chem B 1997;101:7364-7367.
30. Rossello A, Bertini S, Lapucci A, Macchia M, Martinelli A, Rapposelli S, Herreros E, Macchia B, Synthesis, antifungal activity, and molecular modeling studies of new inverted oxime ethers of oxiconazole. J Med Chem. 2002;45:4903-4912.
31. Vihinen, M., Relationship of protein flexibility to thermostability. Protein Eng. 1987;1:477-480.
32. Sun L, Petrounia IP, Yagasaki M, Bandara G, Arnold, F. H., Expression and stabilization of galactose oxidase in Escherichia coli by directed evolution. Protein Eng. 2001;14:699-704.
33. Senisterra GA, Finerty PJJ. High throughput methods of assessing protein stability and aggregation. Mol Biosyst. 2009;5:217-223.
34. Iwakura M, Honda S. Stability and reversibility of thermal denaturation are greatly improved by limiting terminal flexibility of Escherichia coli dihydrofolate reductase. J Biochem. 1996; 119:414-420.
35. Gershenson A, Schauerte JA, Giver L, Arnold FH. Tryptophan phosphorescence study of enzyme flexibility and unfolding in laboratory-evolved thermostable esterases. Biochemistry 2000; 39:4658-4665.
36. Merlino A, Graziano G, Mazzarella L. Structural and dynamic effects of alpha-Helix deletion in Sso7d: implications for protein thermal stability. Proteins 2004;57:692-701.
37. Reid KSC, Lindley PF, Thornton JM. Sulfur-aromatic interactions in proteins. FEBS Lett. 1985;190:209-213.
38. Zauhar RJ, Colbert CL, Morgan RS, Welsh WJ. Evidence for a strong sulfur-aromatic interaction derived from crystallographic data. Biopolymers 2000;53:233-248.
39. Ma Y, Evans D, Logue S, Langridge P. Mutations of barley bamylase that improve substrate-binding affinity and thermostability. Mol Genet Genomics. 2001;266:1617-4615.
40. Jain RR, Dani V, Mitra A, Srivastava S, Sarma SP, Varadarajan R, Ramakumar S. Structural consequences of replacement of an a-helical Pro residue in Escherichia coli thioredoxin. Protein Eng. 2002;15:627-633.