Prediction of the solvent affecting site and the computational design of stable Candida antarctica lipase B in a hydrophilic organic solvent

Journal of Biotechnology

Volumn 163, Issue 3, 2013, Pages 346-352

  Park, Hyun June ^a   Joo, Jeong Chan ^a   Park, Kyungmoon ^b   Kim, Yong Hwan ^c   Yoo, Young Je ^a  

^a Seoul National University   (South Korea)

^b Hong Ik University   (South Korea)

^c Kwangwoon University   (South Korea)

Author keywords

Candida antarctica lipase B; Enzyme engineering; Molecular dynamics; Organic solvent stability

Indexed keywords

CANDIDA ANTARCTICA LIPASE B; COMPUTATIONAL DESIGN; COSOLVENTS; ENZYME ENGINEERING; ENZYME REACTION; INDUSTRIAL ENZYMES; INDUSTRIAL POTENTIALS; MD SIMULATION; METHANOL CONCENTRATION; MOLECULAR DYNAMICS SIMULATIONS; ORGANIC SYNTHESIS; ROOT MEAN SQUARE DEVIATIONS; SITE DIRECTED MUTAGENESIS; SOLVENT MOLECULES; SOLVENT STABILITY; STRUCTURAL MOTION; SURFACE RESIDUES;

ENZYMES; HYDROPHILICITY; ISOMERS; METHANOL; MOLECULAR DYNAMICS; REACTION KINETICS; SOLVENTS; STABILITY;

ORGANIC SOLVENTS;

LIPASE B; ORGANIC SOLVENT;

ARTICLE; CANDIDA ANTARCTICA; ENZYME STABILITY; HUMAN; HYDROPHILICITY; MOLECULAR DYNAMICS; MUTAGENESIS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN INTERACTION; SIMULATION;

CANDIDA; ENZYME STABILITY; FUNGAL PROTEINS; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LIPASE; METHANOL; MOLECULAR DYNAMICS SIMULATION; MUTAGENESIS, SITE-DIRECTED; SOLVENTS; WATER;

EID: 84873856468     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2012.11.006     Document Type: Article

References (27)

1. Anderson E.M., Larsson K.M., Kirk O. One biocatalyst-many applications: the use of Candida antarctica B-lipase in organic synthesis. Biocatalysis and Biotransformation 1998, 16:181-204.
2. Castro G.R., Knubovets T. Homogeneous biocatalysis in organic solvents and water-organic mixtures. Critical Reviews in Biotechnology 2003, 23:195-231.
3. Chen K., Robinson A.C., Van Dam M.E., Martinez P., Economou C., Arnold F.H. Enzyme engineering for nonaqueous solvents II. Additive effects of mutations on the stability and activity of subtilisin E in polar organic media. Biotechnology Progress 1991, 7:125-129.
4. Colombo G., Merz K.M. Stability and activity of mesophilic subtilisin E and its thermophilic homolog: insights from molecular dynamics simulations. Journal of the American Chemical Society 1999, 121:6895-6903.
5. Dordick J.S. Enzymatic catalysis in monophasic organic solvents. Enzyme and Microbial Technology 1989, 11:194-211.
6. Gorman L.A.S, Dordick J.S. Organic solvents strip water off enzymes. Biotechnology and Bioengineering 1992, 39:392-397.
7. Hu X., Kuhlman B. Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences. Proteins: Structure, Function and Genetics 2006, 62:739-748.
8. Joo J.C., Pack S.P., Kim Y.H., Yoo Y.J. Thermostabilization of Bacillus circulans xylanase: computational optimization of unstable residues based on thermal fluctuation analysis. Journal of Biotechnology 2011, 151:56-65.
9. Joo J.C., Pohkrel S., Pack S.P., Yoo Y.J. Thermostabilization of Bacillus circulans xylanase via computational design of a flexible surface cavity. Journal of Biotechnology 2010, 146:31-39.
10. Kawata T., Ogino H. Amino acid residues involved in organic solvent-stability of the LST-03 lipase. Biochemical and Biophysical Research Communications 2010, 400:384-388.
11. Khmnelnitsky Y.L., Levashov A.V., Klyachko N.L., Martinek K. Engineering biocatalytic systems in organic media with low water content. Enzyme and Microbial Technology 1988, 10:710-724.
12. Li C., Tan T., Zhang H., Feng W. Analysis of the conformational stability and activity of Candida antarctica lipase B in organic solvents: insight from molecular dynamics and quantum mechanics/simulations. Journal of Biological Chemistry 2010, 285:28434-28441.
13. Martinez P., Arnold F.H. Surface charge substitutions increase the stability of α-lytic protease in organic solvents. Journal of the American Chemical Society 1991, 113:6336-6337.
14. Meharenna Y.T., Poulos T.L. Using molecular dynamics to probe the structural basis for enhanced stability in thermal stable cytochromes P450. Biochemistry 2010, 49:6680-6686.
15. Micaêlo N.M., Soares C.M. Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents. FEBS Journal 2007, 274:2424-2436.
16. Norin M., Haeffner F., Hult K., Edholm O. Molecular dynamics simulations of an enzyme surrounded by vacuum, water, or a hydrophobic solvent. Biophysical Journal 1994, 67:548-559.
17. Ogino H., Ishikawa H. Enzymes which are stable in the presence of organic solvents. Journal of Bioscience and Bioengineering 2001, 91:109-116.
18. Pack S.P., Yoo Y.J. Packing-based difference of structural features between thermophilic and mesophilic proteins. International Journal of Biological Macromolecules 2005, 35:169-174.
19. Park H.J., Joo J.C., Park K., Yoo Y.J. Stabilization of Candida antarctica lipase B in hydrophilic organic solvent by rational design of hydrogen bond. Biotechnology and Bioprocess Engineering 2012, 17:722-728.
20. Song J.K., Rhee J.S. Enhancement of stability and activity of phospholipase A1 in organic solvents by directed evolution. Biochimica et Biophysica Acta: Protein Structure and Molecular Enzymology 2001, 1547:370-378.
21. Takahashi T., Ng K.K.S., Oyama H., Oda K. Molecular cloning of the gene encoding Vibrio metalloproteinase vimelysin and isolation of a mutant with high stability in organic solvents. Journal of Biochemistry 2005, 138:701-710.
22. Trodler P., Nieveler J., Rusnak M., Schmid R.D., Pleiss J. Rational design of a new one-step purification strategy for Candida antarctica lipase B by ion-exchange chromatography. Journal of Chromatography A 2008, 1179:161-167.
23. Trodler P., Pleiss J. Modeling structure and flexibility of Candida antarctica lipase B in organic solvents. BMC Structural Biology 2008, 8.
24. Uppenberg J., Hansen M.T., Patkar S., Jones T.A. The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica. Structure 1994, 2:293-308.
25. Yang L., Dordick J.S., Garde S. Hydration of enzyme in nonaqueous media is consistent with solvent dependence of its activity. Biophysical Journal 2004, 87:812-821.
26. Yang S., Zhou L., Tang H., Pan J., Wu X., Huang H., Yuan Z. Rational design of a more stable penicillin G acylase against organic cosolvent. Journal of Molecular Catalysis B: Enzymatic 2002, 18:285-290.
27. Zumárraga M., Bulter T., Shleev S., Polaina J., Martínez-Arias A., Plou F.J., Ballesteros A., Alcalde M. In vitro evolution of a fungal laccase in high concentrations of organic cosolvents. Chemistry and Biology 2007, 14:1052-1064.