297
Views
12
CrossRef citations to date
0
Altmetric
Original Articles

Computer-Aided Design of the Stability of Pyruvate Formate-Lyase from Escherichia coli by Site-Directed Mutagenesis

, &
Pages 746-753 | Received 19 Oct 2006, Accepted 27 Nov 2006, Published online: 22 May 2014

  • 1) Georgiou, G., and DeWitt, N., Enzyme beauty. Nat. Biotechnol., 17, 1161–1162 (1999).
  • 2) Igarashi, K., Ozawa, T., Ikawakitayama, K., Hayashi, Y., Araki, H., Endo, K., Hagihara, H., Ozaki, K., Kawai, S., and Ito, S., Thermostabilization by proline substitution in an alkaline, liquefying alpha-amylase from Bacillus sp. strain KSM-1378. Biosci. Biotechnol. Biochem., 63, 1535–1540 (1999).
  • 3) Ueda, T., Masumoto, K., Ishibashi, R., So, T., and Imoto, T., Remarkable thermal stability of doubly intramolecularly cross-linked hen lysozyme. Protein Eng., 13, 193–196 (2000).
  • 4) Zhu, G. P., Xu, C., Teng, M. K., Tao, L. M., Zhu, X. Y., Wu, C. J., Hang, J., Niu, L. W., and Wang, Y. Z., Increasing the thermostability of D-xylose isomerase by introduction of a proline into the turn of a random coil. Protein Eng., 12, 635–638 (1999).
  • 5) Bastian, S., Rekowski, M. J., Witte, K., Heckmann-Pohl, D. M., and Giffhorn, F., Engineering of pyranose 2-oxidase from Peniophora gigantea towards improved thermostability and catalytic efficiency. Appl. Microbiol. Biotechnol., 67, 654–663 (2005).
  • 6) Khan, I. H., Kim, H., Ashida, H., Ishikawa, T., Shibata, H., and Sawa, Y., Altering the substrate specificity of glutamate dehydrogenase from Bacillus subtilis by site-directed mutagenesis. Biosci. Biotechnol. Biochem., 69, 1802–1805 (2005).
  • 7) Asano, Y., Kira, I., and Yokozeki, K., Alteration of substrate specificity of aspartase by directed evolution. Biomol. Eng., 22, 95–101 (2005).
  • 8) Labrou, N. E., Kotzia, G. A., and Clonis, Y. D., Engineering the xenobiotic substrate specificity of maize glutathione S-transferase I. Protein Eng. Des. Sel., 17, 741–748 (2004).
  • 9) Bocanegra, J. A., Scrutton, N. S., and Perham, R. N., Creation of an NADP-dependent pyruvate dehydrogenase multienzyme complex by protein engineering. Biochemistry, 32, 2737–2740 (1993).
  • 10) Scrutton, N. S., Berry, A., and Perham, R. N., Redesign of the coenzyme specificity of a dehydrogenase by protein engineering. Nature, 343, 38–43 (1990).
  • 11) Yu, G. X., Park, B. H., Chandramohan, P., Munavalli, R., Geist, A., and Samatova, N. F., In silico discovery of enzyme-substrate specificity-determining residue clusters. J. Mol. Biol., 352, 1105–1117 (2005).
  • 12) Ahn, N. G., and Resing, K. A., Lessons in rational drug design for protein kinases. Science, 308, 1266–1267 (2005).
  • 13) Toscano, M. D., Stewart, K. A., Coggins, J. R., Lapthorn, A. J., and Abell, C., Rational design of new bifunctional inhibitors of type II dehydroquinase. Org. Biomol. Chem., 3, 3102–3104 (2005).
  • 14) Plescia, J., Salz, W., Xia, F., Pennati, M., Zaffaroni, N., Daidone, M. G., Meli, M., Dohi, T., Fortugno, P., Nefedova, Y., Gabrilovich, D. I., Colombo, G., and Altieri, D. C., Rational design of shepherdin, a novel anticancer agent. Cancer Cell, 7, 457–468 (2005).
  • 15) Lehtio, L., and Goldman, A., The pyruvate formate lyase family: sequences, structures and activation. Protein Eng. Des. Sel., 17, 545–552 (2004).
  • 16) Becker, A., and Kabsch, W., X-ray structure of pyruvate formate-lyase in complex with pyruvate and CoA: how the enzyme uses the Cys-418 thiyl radical for pyruvate cleavage. J. Biol. Chem., 277, 40036–40042 (2002).
  • 17) Wagner, A. F., Frey, M., Neugebauer, F. A., Schafer, W., and Knappe, J., The free radical in pyruvate formate-lyase is located on glycine-734. Proc. Natl. Acad. Sci., 89, 996–1000 (1992).
  • 18) Asanuma, N., and Hino, T., Effects of pH and energy supply on activity and amount of pyruvate formate-lyase in Streptococcus bovis. Appl. Environ. Microbiol., 66, 3773–3777 (2000).
  • 19) Bohac, M., Nagata, Y., Prokop, Z., Prokop, M., Monincova, M., Tsuda, M., Koca, J., and Damborsky, J., Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis. Biochemistry, 41, 14272–14280 (2002).
  • 20) Sambrook, J. W., and Russell, D., “Molecular Cloning, a Laboratory Manual” 3rd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor (2001).
  • 21) Takahashi-Abbe, S., Abbe, K., and Takahashi, N., Biochemical and functional properties of a pyruvate formate-lyase (PFL)-activating system in Streptococcus mutans. Oral Microbiol. Immunol., 18, 293–297 (2003).
  • 22) Gilis, D., and Rooman, M., PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins. Protein Eng., 13, 849–856 (2000).
  • 23) Kwasigroch, J. M., Gilis, D., Dehouck, Y., and Rooman, M., PoPMuSiC, rationally designing point mutations in protein structures. Bioinformatics, 18, 1701–1702 (2002).
  • 24) Gilis, D., and Rooman, M., Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J. Mol. Biol., 257, 1112–1126 (1996).
  • 25) Gilis, D., and Rooman, M., 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 (1997).
  • 26) Gilis, D., and Rooman, M., Prediction of stability changes upon single-site mutations using database-derived potentials. Theor. Chem. Acc., 101, 46–50 (1999).
  • 27) Pikkemaat, M. G., Linssen, A. B., Berendsen, H. J., and Janssen, D. B., Molecular dynamics simulations as a tool for improving protein stability. Protein Eng., 15, 185–192 (2002).
  • 28) Hao, H. J., Jiang, Y. Q., Zheng, Y. L., Ma, R., and Yu, D. W., Improved stability and yield of Fv targeted superantigen by introducing both linker and disulfide bond into the targeting moiety. Biochimie, 87, 661–667 (2005).
  • 29) Zhou, S., Causey, T. B., Hasona, A., Shanmugam, K. T., and Ingram, L. O., Production of optically pure D-lactic acid in mineral salt medium by metabolically engineered Escherichia coli W3110. Appl. Environ. Microbiol., 69, 399–407 (2005).
  • 30) Sriprapundh, D., Vieille, C., and Zeikus, J. G., Molecular determinants of xylose isomerase thermal stability and activity: analysis of thermozymes by site-directed mutagenesis. Protein Eng., 13, 259–265 (2000).
  • 31) Akanuma, S., Yamagishi, A., Tanaka, N., and Oshima, T., Further improvement of the thermal stability of a partially stabilized Bacillus subtilis 3-isopropylmalate dehydrogenase variant by random and site-directed mutagenesis. Eur. J. Biochem., 260, 499–504 (1999).
  • 32) Yang, S. J., Huh, J. W., Hong, H. N., Kim, T. U., and Cho, S. W., Important role of Ser443 in different thermal stability of human glutamate dehydrogenase isozymes. FEBS Lett., 562, 59–64 (2004).
  • 33) Li, Y., Reilly, P., and Ford, C., Effect of introducing proline residues on the stability of Aspergillus awamori. Protein Eng., 10, 1199–1204 (1997).
  • 34) Van der Sloot, A. M., Mullally, M. M., Fernandez-Ballester, G., Serrano, L., and Quax, W. J., Stabilization of TRAIL, an all-beta-sheet multimeric protein, using computational redesign. Protein Eng. Des. Sel., 17, 673–680 (2004).
  • 35) Ventura, S., Vega, M. C., Lacroix, E., Angrand, I., Spagnolo, L., and Serrano, L., Conformational strain in the hydrophobic core and its implications for protein folding and design. Nat. Struct. Biol., 9, 485–493 (2002).
  • 36) Luo, P., Hayes, R. J., Chan, C., Stark, D. M., Hwang, M. Y., Jacinto, J. M., Juvvadi, P., Chung, H. S., Kundu, A., Ary, M. L., and Dahiyat, B. I., Development of a cytokine analog with enhanced stability using computational ultrahigh throughput screening. Protein Sci., 11, 1218–1226 (2002).
  • 37) Filikov, A. V., Hayes, R. J., Luo, P., Stark, D. M., Chan, C., Kundu, A., and Dahiyat, B. I., Computational stabilization of human growth hormone. Protein Sci., 11, 1452–1461 (2002).

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.