Thermostabilization of Bacillus circulans xylanase via computational design of a flexible surface cavity

Journal of Biotechnology

Volumn 146, Issue 1-2, 2010, Pages 31-39

  Joo, Jeong Chan ^a   Pohkrel, Subarna ^a   Pack, Seung Pil ^b   Yoo, Young Je ^a  

^a Seoul National University   (South Korea)

^b Korea University   (South Korea)

Author keywords

Activity; Bacillus circulans xylanase; Cavity; Computational design; Flexibility; Thermostability

Indexed keywords

BACILLUS CIRCULANS XYLANASE; CATALYTIC ACTIVITY; CATALYTIC EFFICIENCIES; CAVITY DESIGN; CAVITY FILLING; COMPUTATIONAL DESIGN; FILLING METHODS; FLEXIBLE MOTION; FLEXIBLE SURFACES; LOCAL INTERACTIONS; NO REDUCTION; PROTEIN CAVITY; PROTEIN SURFACE; RATIONAL DESIGN; SINGLE MUTANT; STRUCTURAL FEATURE; SURFACE CAVITY; THERMOSTABILIZATION; TRIPLE MUTANTS; WILD TYPES; XYLANASES;

BACTERIOLOGY; DESIGN; ENZYME ACTIVITY; ENZYMES; ISOMERS; SURFACE PROPERTIES;

COMPUTATIONAL METHODS;

BACTERIAL ENZYME; GLUTAMIC ACID DERIVATIVE; XYLAN ENDO 1,3 BETA XYLOSIDASE;

ARTICLE; BACILLUS CIRCULANS; CATALYSIS; COMPUTER ANALYSIS; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME STABILITY; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR INTERACTION; MUTATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; STRUCTURE ANALYSIS; SURFACE CHARGE; SURFACE PROPERTY; WILD TYPE;

ALGORITHMS; BACILLUS; COMPUTATIONAL BIOLOGY; ENDO-1,4-BETA XYLANASES; ENZYME STABILITY; KINETICS; MUTAGENESIS, SITE-DIRECTED; PROTEIN BINDING; PROTEIN ENGINEERING; TEMPERATURE;

BACILLUS CIRCULANS;

EID: 77249085574     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2009.12.021     Document Type: Article

References (38)

1. Abraham T., Pack S.P., and Yoo Y.J. Stabilization of Bacillus subtilis Lipase A by increasing the residual packing. Biocatal. Biotransform. 23 (2004) 217-224
2. Akasako A., Haruki M., Oobatake M., and Kanaya S. Conformational stabilities of Escherichia coli RNase HI variants with a series of amino acid substitutions at a cavity within the hydrophobic core. J. Biol. Chem. 272 (1997) 18686-18693
3. Bailey M.J., Biely P., and Poutanen K. Interlaboratory testing of methods for assay of xylanase activity. J. Biotechnol. 23 (1992) 257-270
4. Bogin O., Levin I., Hacham Y., Tel-Or S., Peretz M., Frolow F., and Burstein Y. Structural basis for the enhanced thermal stability of alcohol dehydrogenase mutants from the mesophilic bacterium Clostridium beijerinckii: contribution of salt bridging. Protein Sci. 11 (2002) 2561-2574
5. Bowie J.U., Reidhaar-Olson J.F., Lim W.A., and Sauer R.T. Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science 247 (1990) 1306-1310
6. Bueno M., Cremades N., Neira J.L., and Sancho J. Filling small, empty protein cavities: structural and energetic consequences. J. Mol. Biol. 358 (2006) 701-712
7. Chakravarty S., and Varadarajan R. Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (1999) 723-732
8. Cordes M.H.J., and Sauer R.T. Tolerance of a protein to multiple polar-to-hydrophobic surface substitutions. Protein Sci. 8 (1999) 318-325
9. Dubey V.K., and Jagannadham M.V. Roles for cavities in protein structure: new insights. Curr. Proteomics 5 (2008) 157-160
10. Dundas J., Ouyang Z., Tseng J., Binkowski A., Turpaz Y., and Liang J. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res. 34 (2006) W116-W118
11. Eijsink V.G., Dijkstra D.W., Vriend A., Van der Zee J.R., Veltman O.R., Van der Vinne B., Van den Burg B., Kempe S., and Venema G. The effect of cavity-filling mutations on the thermostability of Bacillus stearothermophilus neutral protease. Protein Eng. 5 (1992) 421-426
12. Eijsink V.G., Bjørk A., Gåseidnes S., Sirevåg R., Synstad B., van den Burg B., and Vriend G. Rational engineering of enzyme stability. J. Biotechnol. 113 (2004) 105-120
13. Eijsink V.G., Gåseidnes S., Borchert T.V., and van den Burg B. Directed evolution of enzyme stability. Biomol. Eng. 22 (2005) 21-30
14. Gallivan J.P., and Dougherty D.A. Cation-pi interactions in structural biology. Proc. Natl. Acad. Sci. U.S.A. 96 (1999) 9459-9464
15. Guo H.H., Choe J., and Loeb L.A. Protein tolerance to random amino acid change. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 9205-9210
16. Hubbard S.J., Gross K.-H., and Argos P. Intramolecular cavities in globular proteins. Protein Eng. 7 (1994) 613-626
17. Kim S.H., Pokhrel S., and Yoo Y.J. Mutation of non-conserved amino acids surrounding catalytic site to shift pH optimum of Bacillus circulans xylanase. J. Mol. Catal. B: Enzym. 55 (2008) 130-136
18. Korkegian A., Black M.E., Baker D., and Stoddard B.L. Computational thermostabilization of an enzyme. Science 308 (2005) 857-860
19. Lazar G.A., and Handel T.M. Hydrophobic core packing and protein design. Curr. Opin. Chem. Biol. 2 (1998) 675-679
20. Lee C., Maeng J.-S., Kocher J.-P., Lee B., and Yu M.-H. Cavities of alpha-antitrypsin that play structural and functional roles. Protein Sci. 10 (2001) 1446-1453
21. Liu Y., and Kuhlman B. RosettaDesign server for protein design. Nucleic Acids Res. 34 (2006) W235-W238
22. Matthews B.W. Structural and genetic analysis of protein stability. Annu. Rev. Biochem. 62 (1993) 139-160
23. Pack S.P., and Yoo Y.J. Protein thermostability: structure-based difference of residual properties between thermophilic and mesophilic proteins. J. Mol. Catal. B: Enzym. 26 (2003) 257-264
24. Parfrey H., Mahadeva R., Ravenhill N.A., Zhou A., Dafforn T.R., Foreman R.C., and Lomas D.A. Targeting a surface cavity of α1-antitrypsin to prevent conformational disease. J. Biol. Chem. 278 (2003) 33060-33066
25. Purmonen M., Valjakka J., Takkinen K., Laitinen T., and Rouvinen J. Molecular dynamics studies on the thermostability of family 11 xylanases. Protein Eng. Des. Sel. 20 (2007) 551-559
26. Reetz M.T., Carballeira J.D., and Vogel A. Iterative saturation mutagenesis on the basis of b factors as a strategy for increasing protein thermostability. Angew. Chem. Int. Ed. 45 (2006) 7745-7751
27. Szilágyi A., and Závodszky P. Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure 15 (2000) 493-504
28. Schweiker K.I., Zarrine-Afsar A., Davidson A.R., and Makhatadze G.I. Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge-charge interactions. Protein Sci. 16 (2007) 2694-2702
29. Tina K.G., Bhadra R., and Srinivasan N. PIC: protein interactions calculator. Nucleic Acids Res. 35 (2007) W473-W476
30. Tokuriki N., Stricher F., Schymkowitz J., Serrano L., and Tawfik D.S. The stability effects of protein mutations appear to be universally distributed. J. Mol. Biol. 369 (2007) 1318-1322
31. Tsodikov O.V., Thomas Record Jr. M., and Sergeev Y.V. Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J. Comput. Chem. 23 (2002) 600-609
32. Vriend G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graphics 8 (1990) 52-56
33. Wakarchuk W.W., Sung W.L., Campbell R.L., Cunningham A., Watson D.C., and Yaguchi M. Thermostabilization of the Bacillus circulans xylanase by the introduction of disulfide bonds. Protein Eng. 7 (1994) 1379-1386
34. Wells S., Menor S., Hespenheide B.M., and Thorpe M.F. Constrained geometric simulation of the diffusive motions in proteins. Phys. Biol. 2 (2005) S127-S136
35. Woolfson D.N. Core-directed protein design. Curr. Opin. Struct. Biol. 11 (2001) 464-471
36. Xiong H., Fenel F., Leisola M., and Turunen O. Engineering the thermostability of Trichoderma reesei endo-1,4-β-xylanase II by combination of disulphide bridges. Extremophiles 8 (2004) 393-400
37. Yoshida Y., Ohkuri T., Kino S., Ueda T., and Imoto T. Elucidation of the relationship between enzyme activity and internal motion using a lysozyme stabilized by cavity-filling mutations. Cell. Mol. Life Sci. 62 (2005) 1047-1055
38. Zheng L., Baumann U., and Reymond J.L. An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res. 32 (2004) e115