1,793
Views
12
CrossRef citations to date
0
Altmetric
Research Article

Mechanism of the plant cytochrome P450 for herbicide resistance: a modelling study

, , , , , , , & show all
Pages 1182-1191 | Received 16 Jan 2012, Accepted 05 Aug 2012, Published online: 11 Oct 2012

References

  • Dill GM. Glyphosate-resistant crops: history, status and future. Pest Manag Sci 2005;61:219–224.
  • Yuan JS, Tranel PJ, Stewart CN Jr. Non-target-site herbicide resistance: a family business. Trends Plant Sci 2007;12:6–13.
  • Heinrich S Jr.. Molecular ecotoxicology of plants. Trends Plant Sci 2004;9:406–413.
  • de Groot MJ. Designing better drugs: predicting cytochrome P450 metabolism. Drug Discov Today 2006;11:601–606.
  • Werck-Reichhart D, Hehn A, Didierjean L. Cytochromes P450 for engineering herbicide tolerance. Trends Plant Sci 2000;5:116–123.
  • Schuler MA, Werck-Reichhart D. Functional genomics of P450s. Annu Rev Plant Biol 2003;54:629–667.
  • Yun MS, Yogo Y, Miura R, Yamasue Y, Fischer AJ. Cytochrome P-450 monooxygenase activity in herbicide-resistant and -susceptible late watergrass (Echinochloa phyllopogon). Pestic Biochem Phys 2005;83:107–114.
  • Holt JS, Powles SB, Holtum JAM. Mechanisms and agronomic aspects of herbicide resistance. Plant Mol Biol 1993;44:203–229.
  • De Prado RA, Franco AR. Cross-resistance and herbicide metabolism in grass weeds in Europe: biochemical and physiological aspects. Weed Sci 2004;52:441–447.
  • Kemp Malcolm S, Moss Stephen R, Thomas Tudor H. Herbicide resistance in Alopecurus myosuroides. In: Managing Resistance to Agrochemicals. American Chemical Society 1990;421:376–393.
  • Robineau T, Batard Y, Nedelkina S, Cabello-Hurtado F, LeRet M, Sorokine O et al. The chemically inducible plant cytochrome P450 CYP76B1 actively mebalolizes phenylureas and other xenobiontics. Plant Physiol 1998;118:1049–1056.
  • Didierjean L, Gondet L, Perkins R, Lau SM, Schaller H, O’Keefe DP et al. Engineering herbicide metabolism in tobacco and Arabidopsis with CYP76B1, a cytochrome P450 enzyme from Jerusalem artichoke. Plant Physiol 2002;130:179–189.
  • Siminszky B, Corbin FT, Ward ER, Fleischmann TJ, Dewey RE. Expression of a soybean cytochrome P450 monooxygenase cDNA in yeast and tobacco enhances the metabolism of phenylurea herbicides. Proc Natl Acad Sci USA 1999;96:1750–1755.
  • Lamb DC, Kelly DE, Hanley SZ, Mehmood Z, Kelly SL. Glyphosate is an inhibitor of plant cytochrome P450: functional expression of Thlaspi arvensae cytochrome P45071B1/reductase fusion protein in Escherichia coli. Biochem Biophys Res Commun 1998;244:110–114.
  • Xiang W, Wang X, Ren T. Expression of a wheat cytochrome P450 monooxygenase cDNA in yeast catalyzes the metabolism of sulfonylurea herbicides. Pestic Biochem Phys 2006;85:1–6.
  • Lamb SB, Lamb DC, Kelly SL, Stuckey DC. Cytochrome P450 immobilisation as a route to bioremediation/biocatalysis. FEBS Lett 1998;431:343–346.
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882.
  • Andrej A. Comparative protein modeling by satisfaction of spatial restraints. Mol Med Today 1995;1:270–277.
  • Meng XY, Zheng QC, Zhang HX. A comparative analysis of binding sites between mouse CYP2C38 and CYP2C39 based on homology modeling, molecular dynamics simulation and docking studies. Biochim Biophys Acta 2009;1794:1066–1072.
  • Bolwell GP, Bozak K, Zimmerlin A. Plant cytochrome P450. Phytochemistry 1994;37:1491–1506.
  • Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges. Tetrahedron 1980;36:3219–3228.
  • Medina-Franco JL, López-Vallejo F, Kuck D, Lyko F. Natural products as DNA methyltransferase inhibitors: a computer-aided discovery approach. Mol Divers 2011;15:293–304.
  • Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, et al. AMBER 10 University of California, San Francisco 2008.
  • Jorgensen WL. Revised TIPS for simulations of liquid water and aqueous solutions. J Chem Phys 1982;77:4156–4163.
  • Darden T, York D, Pedersen L. Particle mesh Ewald: An N [center-dot] log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089–10092.
  • Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327–341.
  • Brünger A, Brooks Iii CL, Karplus M. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem Phys Lett 1984;105:495–500.
  • Lee MC, Duan Y. Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins 2004;55:620–634.
  • Harris DL, Park JY, Gruenke L, Waskell L. Theoretical study of the ligand-CYP2B4 complexes: effect of structure on binding free energies and heme spin state. Proteins 2004;55:895–914.
  • Li W, Ode H, Hoshino T, Liu H, Tang Y, Jiang H. Reduced catalytic activity of P450 2A6 mutants with coumarin: a computational investigation. J Chem Theory Comput 2009;5:1411–1420.
  • Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000;33:889–897.
  • Hou T, Wang J, Li Y, Wang W. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model 2011;51:69–82.
  • Weiser J, Shenkin PS, Still WC. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem 1999;20:217–230.
  • Gilson MK, Sharp KA, Honig BH. Calculating the electrostatic potential of molecules in solution: Method and error assessment. J Comput Chem 1988;9:327–335.
  • Sitkoff D, Sharp KA, Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 1994;98:1978–1988.
  • Yano JK, Hsu MH, Griffin KJ, Stout CD, Johnson EF. Structures of human microsomal cytochrome P450 2A6 complexed with coumarin and methoxsalen. Nat Struct Mol Biol 2005;12:822–823.
  • Shimazu S, Inui H, Ohkawa H. Phytomonitoring and phytoremediation of agrochemicals and related compounds based on recombinant cytochrome P450s and aryl hydrocarbon receptors (AhRs). J Agric Food Chem 2011;59:2870–2875.
  • Graham SE, Peterson JA. How similar are P450s and what can their differences teach us? Arch Biochem Biophys 1999;369:24–29.
  • Poulos T, Johnson E. (2005). Cytochrome P450: Structure, Mechanism, and Biochemistry. In: Ortiz de Montellano PR, ed. New York: Springer US, 87–114.
  • CDS. Cytochrome P450 Conformational Diversity. Structure 2004;12:1921–1922.
  • Werck-Reichhart D, Feyereisen R. Cytochromes P450: a success story. Genome Biol 2000;1:REVIEWS3003.
  • Jensen K, Osmani SA, Hamann T, Naur P, Møller BL. Homology modeling of the three membrane proteins of the dhurrin metabolon: catalytic sites, membrane surface association and protein-protein interactions. Phytochemistry 2011;72:2113–2123.
  • Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283–291.
  • Schoch GA, Attias R, Le Ret M, Werck-Reichhart D. Key substrate recognition residues in the active site of a plant cytochrome P450, CYP73A1. Homology guided site-directed mutagenesis. Eur J Biochem 2003;270:3684–3695.
  • Saladino AC, Xu Y, Tang P. Homology modeling and molecular dynamics simulations of transmembrane domain structure of human neuronal nicotinic acetylcholine receptor. Biophys J 2005;88:1009–1017.
  • Robineau T, Batard Y, Nedelkina S, Cabello-Hurtado F, LeRet M, Sorokine Oet al. The chemically inducible plant cytochrome P450 CYP76B1 actively metabolizes phenylureas and other xenobiotics. American Society of Plant Physiologists.
  • Gotoh O. Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. J Biol Chem 1992;267:83–90.
  • Wang H, Cheng JD, Montgomery D, Cheng KC. Evaluation of the binding orientations of testosterone in the active site of homology models for CYP2C11 and CYP2C13. Biochem Pharmacol 2009;78:406–413.
  • Werck-Reichhart D, Hehn A, Didierjean L. Cytochromes P450 for engineering herbicide tolerance. Trends Plant Sci 2000;5:1360–1385.

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.