Enhancing the stability and solubility of TEV protease using in silico design

Protein Science

Volumn 16, Issue 11, 2007, Pages 2360-2367

  Cabrita, Lisa D ^a   Gilis, Dimitri ^b   Robertson, Amy L ^a   Dehouck, Yves ^b   Rooman, Marianne ^b   Bottomley, Stephen P ^a  

^a MONASH UNIVERSITY   (Australia)

^b FREE UNIVERSITY OF BRUSSELS   (Belgium)

Author keywords

In silico design; Protein engineering; Protein purification; Stability; TEV protease

Indexed keywords

PROTEIN TOBACCO ETCH VIRUS; RECOMBINANT PROTEIN; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ARTICLE; CELL NUCLEUS INCLUSION BODY; COMPUTER MODEL; ENZYME STABILITY; MEDICAL RESEARCH; PRIORITY JOURNAL; PROTEIN PURIFICATION; SITE DIRECTED MUTAGENESIS; SOLUBILITY;

ENDOPEPTIDASES; GUANIDINE; KINETICS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MUTATION; PROTEIN DENATURATION; PROTEIN ENGINEERING; RECOMBINANT PROTEINS; SOLUBILITY; TEMPERATURE; THERMODYNAMICS;

TOBACCO ETCH VIRUS;

EID: 35648952843     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.072822507     Document Type: Article

References (26)

1. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242. doi: 10.1002/047001153X.g406303.
2. Cabrita, L.D. and Bottomley, S.P. 2004. Protein expression and refolding - A practical guide to getting the most out of inclusion bodies. Biotechnol. Annu. Rev. 10: 31-50.
3. Cabrita, L.D., Dai, W., and Bottomley, S.P. 2006. A family of E. coli expression vectors for laboratory scale and high-throughput soluble protein production. BMC Biotechnol. 6: 12. doi: 10.1186/1472-6750-6-12.
4. Calloni, G., Zoffoli, S., Stefani, M., Dobson, C.M., and Chiti, F. 2005. Investigating the effects of mutations on protein aggregation in the cell. J. Biol. Chem. 280: 10607-10613.
5. Chow, M.K., Amin, A.A., Fulton, K.F., Whisstock, J.C., Buckle, A.M., and Bottomley, S.P. 2006. REFOLD: An analytical database of protein refolding methods. Protein Expr. Purif. 46: 166-171.
6. Eisenberg, D., Schwarz, E., Komaromy, M., and Wall, R. 1984. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol. 179: 125-142.
7. Fauchere, J.L. and Pliska, V. 1983. Hydrophobic parameters - π of amino-acid side-chains from the partitioning of N-acetyl-amino-acid amides. Eur. J. Med. Chem. 18: 369-375.
8. Gilis, D. and Rooman, M. 1996. Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J. Mol. Biol. 257: 1112-1126.
9. Gilis, D. and Rooman, M. 1997. Predicting protein stability changes upon mutation using database-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence. J. Mol. Biol. 272: 276-290.
10. Gilis, D. and Rooman, M. 2000. PoPMuSiC, an algorithm for predicting protein mutant stability changes: Application to prion proteins. Protein Eng. 13: 849-856.
11. Gilis, D., McLennan, H.R., Dehouck, Y., Cabrita, L.D., Rooman, M., and Bottomley, S.P. 2003. In vitro and in silico design of α1-antitrypsin mutants with different conformational stabilities. J. Mol. Biol. 325: 581-589.
12. Hobohm, U., Scharf, M., Schneider, R., and Sander, C. 1992. Selection of representative protein data sets. Protein Sci. 1: 409-417.
13. Kapust, R.B. and Waugh, D.S. 1999. Escherichia coli maltose-binding protein is uncommonly effective at promoting the solubility of polypeptides to which it is fused. Protein Sci. 8: 1668-1674.
14. Kapust, R.B., Tozser, J., Fox, J.D., Anderson, D.E., Cherry, S., Copeland, T.D., and Waugh, D.S. 2001. Tobacco etch virus protease: Mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng. 14: 993-1000.
15. Kapust, R.B., Tozser, J., Copeland, T.D., and Waugh, D.S. 2002. The P1′ specificity of tobacco etch virus protease. Biochem. Biophys. Res. Commun. 294: 949-955.
16. Kocher, J.P., Rooman, M.J., and Wodak, S.J. 1994. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235: 1598-1613.
17. Kwasigroch, J.M., Gilis, D., Dehouck, Y., and Rooman, M. 2002. PoPMuSiC, rationally designing point mutations in protein structures. Bioinformatics 18: 1701-1702.
18. Nishimura, C., Uversky, V.N., and Fink, A.L. 2001. Effect of salts on the stability and folding of staphylococcal nuclease. Biochemistry 40: 2113-2128.
19. Parks, T.D., Howard, E.D., Wolpert, T.J., Arp, D.J., and Dougherty, W.G. 1995. Expression and purification of a recombinant tobacco etch virus NIa proteinase: Biochemical analyses of the full-length and a naturally occurring truncated proteinase form. Virology 210: 194-201.
20. Phan, J., Zdanov, A., Evdokimov, A.G., Tropea, J.E., PetersIII, H.K., Kapust, R.B., Li, M., Wlodawer, A., and Waugh, D.S. 2002. Structural basis for the substrate specificity of tobacco etch virus protease. J. Biol. Chem. 277: 50564-50572.
21. Roodveldt, C., Aharoni, A., and Tawfik, D.S. 2005. Directed evolution of proteins for heterologous expression and stability. Curr. Opin. Struct. Biol. 15: 50-56.
22. Tew, D.J. and Bottomley, S.P. 2001. Probing the equilibrium denaturation of the serpin α(1)-antitrypsin with single tryptophan mutants; evidence for structure in the urea unfolded state. J. Mol. Biol. 313: 1161-1169.
23. van den Berg, S., Lofdahl, P.A., Hard, T., and Berglund, H. 2006. Improved solubility of TEV protease by directed evolution. J. Biotechnol. 121: 291-298.
24. Wimley, W.C. and White, S.H. 1996. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat. Struct. Biol. 3: 842-848.
25. Wintjens, R.T., Rooman, M.J., and Wodak, S.J. 1996. Automatic classification and analysis of α α-turn motifs in proteins. J. Mol. Biol. 255: 235-253.
26. Zhang, Y.B., Howitt, J., McCorkle, S., Lawrence, P., Springer, K., and Freimuth, P. 2004. Protein aggregation during overexpression limited by peptide extensions with large net negative charge. Protein Expr. Purif. 36: 207-216. Protein Science (2007), 16:2368-2377.