Molecular Modelling and Functional Studies of the Non-Stereospecific α-Haloalkanoic Acid Dehalogenase (DehE) from Rhizobium SP. RC1 and its Association with 3-Chloropropionic Acid (β-Chlorinated Aliphatic Acid)

REFERENCES

• Allison N., Skinner A.J., Cooper R.A. (1983) J. Gen. Microbiol., 129, 1283–1293.
   Google Scholar
• Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. (1990) J. Mol. Biol., 215, 403–410.
   PubMed Web of Science ®Google Scholar
• Berry E.K.M., Allison N., Skinner A.J., Cooper R.A. (1979) J. Gen. Microbiol., 110, 39–45.
   Google Scholar
• Brokamp A., Schmidt F.R.J. (1991) Curr. Microbiol., 22, 299–306.
   Web of Science ®Google Scholar
• Brokamp A., Happe B., Schmidt F.R.J. (1996) Biodegradation, 7, 383–396.
   PubMed Web of Science ®Google Scholar
• Cairns S.S., Cornish A., Cooper R.A. (1996). Eur. J. Biochem., 235, 744–749.
   PubMedGoogle Scholar
• Combet C., Blanchet C., Geourjon C., Deléage G. (2000) Trends Biochem. Sci., 25, 147–150.
   PubMed Web of Science ®Google Scholar
• Corpet F. (1998) Nucleic Acids Res., 16, 10881–10890.
   Google Scholar
• Eisenberg D., Luthy R., Bowie J. (1997) Method. Enzymol., 277, 396–404.
   PubMed Web of Science ®Google Scholar
• Frisch C., Schreiber G., Johnson C.M., Fersht A.R. (1997) J. Mol. Biol., 267, 696–706.
   PubMedGoogle Scholar
• Furukawa K., Tomizuka N., Kamibayashi A. (1979) Appl. Environ. Microbiol., 38, 301–310.
   PubMed Web of Science ®Google Scholar
• Gasteiger E., Hoogland C., Gattiker A., Duvaud S.E., et al.. (2005) In: The Proteomics Protocols Handbook (J.M. Walker, Ed.), Humana Press, Totowa, NJ, USA, 571–607.
   Google Scholar
• Guex N., Peitsch M.C. (1997) Electrophoresis, 18, 2714–2723.
   PubMed Web of Science ®Google Scholar
• Hill K.E., Marchesi J.R., Weightman A.J. (1999) J. Bacteriol., 181, 2535–2547.
   PubMed Web of Science ®Google Scholar
• Huyop F., Nemati M. (2010) Afr. J. Microbiol. Res., 4, 2836–2847.
   Google Scholar
• Huyop F., Cooper R.A. (2011) Biotechnol. Biotech. Eq., 25, 2237–2242.
   Web of Science ®Google Scholar
• Huyop F., Yusn T.Y., Ismail M., Wahab R.A.b., Cooper R.A. (2004) As. Pac. J. Mol. Biol. Biotech., 1/2, 15–20.
   Google Scholar
• Jeong M.Y., Kim, S., Yun C.W., Choi Y.J., Cho S.G. (2007) J. Biotechnol., 127, 300–309.
   PubMedGoogle Scholar
• Kelley L.A., Sternberg M.J.E. (2009) Nat. Protocols, 4, 363–371.
   PubMed Web of Science ®Google Scholar
• Laskowski R.A., Chistyakov V.V., Thornton J.M. (2005) Nucleic Acids Res., 33, D266–D268.
   PubMed Web of Science ®Google Scholar
• Laskowski R., Rullmannn J., MacArthur M., Kaptein R., Thornton J. (1996) J. Biomol. NMR, 8, 477–486.
   PubMed Web of Science ®Google Scholar
• Laurie A.T.R., Jackson R.M. (2005) Bioinformatics, 21, 1908–1916.
   PubMed Web of Science ®Google Scholar
• Leigh J. (1986) Studies on Bacterial Dehalogenases, PhD Thesis, Nottingham Trent Polytechnic, United Kingdom.
   Google Scholar
• Leigh J., Skinner, A., Cooper R.A. (1986) FEMS Microbiol. Lett., 36, 163–166.
   Web of Science ®Google Scholar
• McGuffin L.J. (2007) BMC Bioinformatics, 8, 345.
   PubMedGoogle Scholar
• Melo F., Feytmans E. (1998) J. Mol. Biol., 277, 1141–1152.
   PubMed Web of Science ®Google Scholar
• Mesri S., Wahab R.A.b., Huyop F. (2009) Annal. Microbiol., 59, 447–451.
   Web of Science ®Google Scholar
• Morris G.M., Goodsell D.S., Halliday R.S., Huey R., et al.. (1998) J. Comput. Chem., 19, 1639–1662.
   Web of Science ®Google Scholar
• Motosugi K., Esaki N., Soda K. (1982) J. Bacteriol., 150, 522–527.
   PubMed Web of Science ®Google Scholar
• Nardi-Dei V., Kurihara T., Park C., Miyagi M., et al.. (1999) J. Biol. Chem., 274, 20977–20981.
   PubMed Web of Science ®Google Scholar
• Nardi-Dei V., Kurihara T., Park C., Esaki N., Soda K. (1997) J. Bacteriol., 179, 4232–4238.
   PubMed Web of Science ®Google Scholar
• Oh M., Joo K., Lee J. (2009) Proteins, 77, 152–156.
   PubMedGoogle Scholar
• Park C., Kurihara T., Yoshimura T., Soda K., Esaki N. (2003) J. Mol. Catal. B-Enzym., 23, 329–336.
   Google Scholar
• Petrek M., Otyepka M., Banas P., Kosinova P., et al.. (2006) BMC Bioinformatics, 7, 316.
   PubMed Web of Science ®Google Scholar
• Pries F., Kingma J., Pentenga M., van Pouderoyen G., et al.. (1994) Biochemistry, 33, 1242–1247.
   PubMed Web of Science ®Google Scholar
• Ramachandran G., Ramakrishnan C., Sasisekharan V. (1963) J. Mol. Biol., 7, 95–99.
   PubMed Web of Science ®Google Scholar
• Scheer M., Grote A., Chang A., Schomburg I., et al.. (2011) Nucleic Acids Res., 39, D670–D676.
   PubMed Web of Science ®Google Scholar
• Schmidberger J.W., Wilce J.A., Weightman A.J., Whisstock J.C., Wilce M.C. (2008) J. Mol. Biol., 378, 284–294.
   PubMed Web of Science ®Google Scholar
• Schwede T., Kopp J., Guex N., Peitsch M.C. (2003) Nucleic Acids Res., 31, 3381–3385.
   PubMed Web of Science ®Google Scholar
• Slater J.H. (1994) In: Biochemistry of Microbial Degradation (C. Ratledge, Ed.), Kluwer Academic Publishers, Dordrecht, 379–421.
   Google Scholar
• Slater J.H., Bull A.T., Hardman D.J. (1996) In: Advances in Microbial Physiology (R.K. Poole, Ed.), Academic Press, 133–176.
   Google Scholar
• Stringfellow J.M., Cairns S.S., Cornish A., Cooper R.A. (1997) Eur. J. Biochem., 250, 789–793.
   PubMedGoogle Scholar
• Topping A. (1992) An Investigation into the Transposition and Dehalogenase Functions of deh, a Mobile Genetic Element, from Pseudomonas putida strain PP3, PhD Thesis, University of Wales, United Kingdom.
   Google Scholar
• van Der Spoel D., Lindahl E., Hess B., Groenhof G., et al.. (2005) J. Comput. Chem., 26, 1701–1718.
   PubMed Web of Science ®Google Scholar
• van Gunsteren W.F., Billeter S.R., Eising A.A., Hünenberger P.H., et al.. (1996) Biomolecular Simulation: The GROMOS96 Manual and User Guide, Vdf Hochschulverlag AG an der ETH Zürich, Zürich, Switzerland, pp. 1–1042.
   Google Scholar
• Wakarchuk W.W., Campbell R.L., Sung W.L., Davoodi J., Yaguchi M. (1994) Protein Sci., 3, 467–475.
   PubMed Web of Science ®Google Scholar
• Weightman A.J., Topping A.W., Hill K.E. Lee L.L., et al.. (2002) J. Bacteriol., 184, 6581–6591.
   PubMed Web of Science ®Google Scholar
• Weightman A.J., Weightman A.L., Slater J.H. (1982) J. Gen. Microbiol., 128, 1755–1762.
   PubMedGoogle Scholar
• Yang G., Liang P.H., Dunaway-Mariano D. (1994) Biochemistry, 33, 8527–8531.
   PubMedGoogle Scholar
• Yusn T., Huyop F. (2009) Biotechnol., 8, 385–388.
   Google Scholar
• Zhang Y., Li Z.S., Wu J.Y., Sun M., et al.. (2004) Biochem. Biophys. Res. Co., 325, 414–420.
   PubMedGoogle Scholar