354
Views
17
CrossRef citations to date
0
Altmetric
Articles

Modeling stability and flexibility of α-Chymotrypsin in room temperature ionic liquids

, , , &
Pages 1263-1273 | Received 14 Mar 2013, Accepted 06 Jun 2013, Published online: 11 Jul 2013

References

  • Appel, W. (1986). Chymotrypsin: Molecular and catalytic properties. Clinical Biochemistry, 19, 317–322.
  • Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81, 3684–3690.
  • Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Section 9.1, proteases: Facilitating a difficult reaction. Biochemistry (5th ed.). New York, NY: W. H. Freeman.
  • Broos, J., Visser, A. J. W. G., Engbersen, J. F. J., Verboom, W., Hoek van, A., & Reinhoudt, D. N. (1995). Flexibility of enzymes suspended in organic solvents probed by time-resolved fluorescence anisotropy. Evidence that enzyme activity and enantioselectivity are directly related to enzyme flexibility. Journal of American Chemical Society, 117, 12657–12663.
  • Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. Journal of Chemical Physics, 126, 1–7.
  • Craik, C. S., Roczniak, S., Largman, C., & Rutter, W. J. (1987). The catalytic role of the active site aspartic acid in serine proteases. Science, 237, 909–913.
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. Journal of Chemical Physics, 98, 10089–10092.
  • Dordick, J. S. (1992). Designing enzymes for use in organic solvents. Biotechnology Progress, 8, 259–267.
  • Eckstein, M., Sesing, M., Kragl, U., & Adlercreutz, P. (2002). At low water activity α-Chymotrypsin is more active in an ionic liquid than in non-ionic organic solvents. Biotechnology Letters, 24, 867–872.
  • Gu, Z., & Brennecke, J. F. (2002). Volume expansivities and isothermal compressibilities of imidazolium and pyridinium-based ionic liquids. Journal of Chemical & Engineering Data, 47, 339–345.
  • Hartsough, D. S., & Merz, K. M., Jr (1992). Protein flexibility in aqueous and nonaqueous solutions. Journal of American Chemical Society, 114, 10113–10116.
  • Herńandez-Ferńandez, F. J., de los Rìos, A. P., Tomas-Alonso, F., Gómez, D., & Vìllora, G. (2009). Stability of hydrolase enzymes in ionic liquids. The Canadian Journal of Chemical Engineering, 87, 910–914.
  • Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18, 1463–1472.
  • Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435–447.
  • Howells, R. D., & McCown, J. D. (1977). Trifluoromethanesulfonic acid and derivatives. Chemical Reviews, 77, 69–92.
  • Huddleston, J. G., Visser, A. E., Reichert, W. M., Willauer, H. D., Broker, G. A., & Rogers, R. D. (2001). Characterization and comparison of hydrophilic and hydrophobic room temperature ionic liquids incorporating the imidazolium cation. Green Chemistry, 3, 156–164.
  • Irimescu, R., & Kato, K. (2004). Investigation of ionic liquids as reaction media for enzymatic enantioselective acylation of amines. Journal of Molecular Catalysis B: Enzymatic, 30, 189–194.
  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79, 926–935.
  • Kaar, J. L., Jesionowski, A. M., Berberich, J. A., Moulton, R., & Russell, A. J. (2003). Impact of ionic liquid physical properties on lipase activity and stability. Journal of American Chemical Society, 125, 4125–4131.
  • Kim, K.-W., Song, B., Choi, M.-Y., & Kim, M.-J. (2001). Biocatalysis in ionic liquids: Markedly enhanced enantioselectivity of lipase. Organic Letters, 3, 1507–1509.
  • Klähn, M., Lim, G. S., & Wu, P. (2011). How ion properties determine the stability of a lipase enzyme in ionic liquids: A molecular dynamics study. Physical Chemistry Chemical Physics, 13, 18647–18660.
  • Klibanov, A. M. (1989). Enzymatic catalysis in anhydrous organic solvents. Trends in Biochemical Sciences, 14, 141–144.
  • Klibanov, A. M. (1997). Why are enzymes less active in organic solvents than in water? Trends in Biotechnology, 15, 97–101.
  • Laszlo, J. A., & Compton, D. L. (2001). α-Chymotrypsin catalysis in imidazolium-based ionic liquids. Biotechnology and Bioengineering, 75, 181–186.
  • Lau, R. M., van Rantwijk, F., Seddon, K. R., & Sheldon, R. A. (2000). Lipase-catalyzed reactions in ionic liquids. Organic Letters, 2, 4189–4191.
  • Lee, S. H., Ha, S. H., Lee, S. B., & Koo, Y.-M. (2006). Adverse effect of chloride impurities on lipase-catalyzed transesterifications in ionic liquids. Biotechnology Letters, 28, 1335–1339.
  • Lee, S. H., Koo, Y.-M., & Ha, S. H. (2008). Influence of ionic liquids under controlled water activity and low halide content on lipase activity. Korean Journal of Chemical Engineering, 25, 1456–1462.
  • Lopes, J. N. C., & Pádua, A. A. H. (2004). Molecular force field for ionic liquids composed of triflate or bistriflylimide anions. Journal Physical Chemistry B, 108, 16893–16898.
  • Lopes, J. N. C., & Pádua, A. A. H. (2006). Molecular force field for ionic liquids III: Imidazolium, pyridinium, and phosphonium cations; chloride, bromide, and dicyanamide anions. Journal Physical Chemistry B, 110, 19586–19592.
  • Lopes, J. N. C., Pádua, A. A. H., & Shimizu, K. (2008). Molecular force field for ionic liquids IV: Trialkylimidazolium and alkoxycarbonyl-imidazolium cations; alkylsulfonate and alkylsulfate anions. Journal Physical Chemistry B, 112, 5039–5046.
  • Lozano, P., de Diego, T., Carrié, D., Vaultier, M., & Iborra, J. L. (2003). Enzymatic ester synthesis in ionic liquids. Journal of Molecular Catalysis B: Enzymatic, 21, 9–13.
  • Lozano, P., de Diego, T., Guegan, J.-P., Vaultier, M., & Iborra, J. L. (2001). Stabilization of α-Chymotrypsin by ionic liquids in transesterification reactions. Biotechnology and Bioengineering, 75, 563–569.
  • Martínez, L., Andrade, R., Birgin, E. G., & Martínez, J. M. (2009). PACKMOL: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30, 2157–2164.
  • Micaêlo, N. M., & Soares, C. M. (2007). Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents. FEBS Journal, 274, 2424–2436.
  • Micaêlo, N. M., & Soares, C. M. (2008). Protein structure and dynamics in ionic liquids. Insights from molecular dynamics simulation studies. Journal Physical Chemistry B, 112, 2566–2572.
  • Micaelo, N. M., Teixeira, V. H., Baptista, A. M., & Soares, C. M. (2005). Water dependent properties of cutinase in nonaqueous solvents: A computational study of enantioselectivity. Biophysical Journal, 89, 999–1008.
  • Noritomi, H., Suzuki, K., Kikuta, M., & Kato, S. (2009). Catalytic activity of α-Chymotrypsin in enzymatic peptide synthesis in ionic liquids. Biochemical Engineering Journal, 47, 27–30.
  • Olivier-Bourbigou, H., & Magna, L. (2002). Ionic liquids: Perspectives for organic and catalytic reactions. Journal of Molecular Catalysis A: Chemical, 182–183, 419–437.
  • Paljevac, M., Habulin, M., & Knez, Ž. (2006). Ionic liquids as (co)solvents for enzymatic reactions. Chemical Industry and Chemical Engineering Quarterly, 12, 181–186.
  • Park, S., & Kazlauskas, R. J. (2003). Biocatalysis in ionic liquids – advantages beyond green technology. Current Opinion in Biotechnology, 14, 432–437.
  • Peter, W., & Wilhelm, K. (2000). Ionic liquids – new “solutions” for transition metal catalysis. Angewandte Chemie International Edition, 39, 3772–3789.
  • Poole, C. F. (2004). Chromatographic and spectroscopic methods for the determination of solvent properties of room temperature ionic liquids. Journal of Chromatography A, 1037, 49–82.
  • Seddon, K. R., Stark, A., & Torres, M.-J. (2000). Influence of chloride, water, and organic solvents on the physical properties of ionic liquids. Pure Applied Chemistry, 72, 2275–2287.
  • Sheldon, R. A., Lau, R. M., Sorgedrager, M. J., van Rantwijk, F., & Seddon, K. R. (2002). Biocatalysis in ionic liquids. Green Chemistry, 4, 147–151.
  • Trodler, P., & Pleiss, J. (2008). Modeling structure and flexibility of Candida antarctica lipase B in organic solvents. BMC Structural Biology, 8, 9–18.
  • Tsuzuki, S., Shinoda, W., Saito, H., Mikami, M., Tokuda, H., & Watanabe, M. (2009). Molecular dynamics simulations of ionic liquids: Cation and anion dependence of self-diffusion coefficients of ions. Journal Physical Chemistry B, 113, 10641–10649.
  • Turner, M. B., Spear, S. K., Huddleston, J. G., Holbrey, J. D., & Rogers, R. D. (2003). Ionic liquid salt-induced inactivation and unfolding of cellulase from Trichoderma reesei. Green Chemistry, 5, 443–447.
  • van Rantwijk, F., Secundo, F., & Sheldon, R. A. (2006). Structure and activity of Candida antarctica lipase B in ionic liquids. Green Chemistry, 8, 282–286.
  • Wang, D., Bode, W., & Huber, R. (1985). Bovine chymotrypsinogen a X-ray crystal structure analysis and refinement of a new crystal form at 1.8 Å resolution. Journal of Molecular Biology, 185, 595–624.
  • Yang, Z., & Pan, W. (2005). Ionic liquids: Green solvents for nonaqueous biocatalysis. Enzyme and Microbial Technology, 37, 19–28.
  • Yang, Z., Yue, Y.-J., Huang, W.-C., Zhuang, X.-M., Chen, Z.-T., & Xing, M. (2009). Importance of the ionic nature of ionic liquids in affecting enzyme performance. Journal of Biochemistry, 145, 355–364.
  • Zaks, A., & Klibanov, A. M. (1988). The effect of water on enzyme action in organic media. Journal of Biological Chemistry, 263, 8017–8021.
  • Zhang, S., Sun, N., He, X., Lu, X., & Zhang, X. (2006). Physical properties of ionic liquids: Database and evaluation. Journal of Physical Chemistry Reference Data, 35, 1475–1517.
  • Zhao, H. (2010). Methods for stabilizing and activating enzymes in ionic liquids – a review. Journal of Chemical Technology and Biotechnology, 85, 891–907.
  • Zhao, H., Olubajo, O., Song, Z., Sims, A. L., Person, T. E., Lawal, R. A., & Holley, L. A. (2006). Effect of kosmotropicity of ionic liquids on the enzyme stability in aqueous solutions. Bioorganic Chemistry, 34, 15–25.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.