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

Journal of Enzyme Inhibition and Medicinal Chemistry

Volumn 28, Issue 6, 2013, Pages 1182-1191

  Li, Qinfan ^a   Fang, Yupeng ^a   Li, Xiuxiu ^a   Zhang, Hong ^a   Liu, Mengmeng ^a   Yang, Huibin ^b   Kang, Zhuo ^b   Li, Yan ^c   Wang, Yonghua ^a  

^a NORTHWEST A F UNIVERSITY   (China)

^b State Key Laboratory of the Discovery and Development of Novel Pesticide   (China)

^c DALIAN UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Chlortoluron; Cytochrome P450; Homology modelling; Molecular docking; Molecular dynamics simulation

Indexed keywords

CHLORTOLURON; CYTOCHROME P450; CYTOCHROME P450 71A10; CYTOCHROME P450 71B1; CYTOCHROME P450 76B1; CYTOCHROME P450 C6V1; HEME; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CHEMICAL STRUCTURE; HERBICIDE RESISTANCE; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULAR MODEL; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

BIOCATALYSIS; CYTOCHROME P-450 ENZYME SYSTEM; HERBICIDE RESISTANCE; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PHENYLUREA COMPOUNDS; PLANTS; THERMODYNAMICS;

EID: 84887436486     PISSN: 14756366     EISSN: 14756374     Source Type: Journal    
DOI: 10.3109/14756366.2012.719505     Document Type: Article

References (49)

1. Dill GM. Glyphosate-resistant crops: History, status and future. Pest Manag Sci 2005;61:219-224
2. Yuan JS, Tranel PJ, Stewart CN Jr. Non-Target-site herbicide resistance: A family business. Trends Plant Sci 2007;12:6-13
3. Heinrich S, Jr. Molecular ecotoxicology of plants. Trends Plant Sci 2004;9:406-413
4. De Groot MJ. Designing better drugs: Predicting cytochrome P450 metabolism. Drug Discov Today 2006;11:601-606
5. Werck-Reichhart D, Hehn A, Didierjean L. Cytochromes P450 for engineering herbicide tolerance. Trends Plant Sci 2000;5:116-123
6. Schuler MA, Werck-Reichhart D. Functional genomics of P450s. Annu Rev Plant Biol 2003;54:629-667
7. 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
8. Holt JS, Powles SB, Holtum JAM. Mechanisms and agronomic aspects of herbicide resistance. Plant Mol Biol 1993;44:203-229
9. 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
10. 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
11. 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
12. 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
13. 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
14. 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
15. 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
16. Lamb SB, Lamb DC, Kelly SL, Stuckey DC. Cytochrome P450 immobilisation as a route to bioremediation/biocatalysis. FEBS Lett 1998;431:343-346
17. 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
18. Andrej A. Comparative protein modeling by satisfaction of spatial restraints. Mol Med Today 1995;1:270-277
19. 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
20. Bolwell GP, Bozak K, Zimmerlin A. Plant cytochrome P450. Phytochemistry 1994;37:1491-1506
21. Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativity-A rapid access to atomic charges. Tetrahedron 1980;36:3219-3228
22. 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
23. Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, et al. AMBER 10. University of California, San Francisco 2008
24. Jorgensen WL. Revised TIPS for simulations of liquid water and aqueous solutions. J Chem Phys 1982;77:4156-4163
25. Darden T, York D, Pedersen L. Particle mesh Ewald: An N [centerdot] log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092
26. 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
27. Brünger A, Brooks Iii CL, Karplus M. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem Phys Lett 1984;105:495-500
28. 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
29. 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
30. 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
31. 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
32. 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
33. Weiser J, Shenkin PS, Still WC. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem 1999;20:217-230
34. 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
35. Sitkoff D, Sharp KA, Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 1994;98:1978-1988
36. 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
37. 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
38. Graham SE, Peterson JA. How similar are P450s and what can their differences teach us' Arch Biochem Biophys 1999;369:24-29
39. Poulos T, Johnson E. (2005). Cytochrome P450: Structure, Mechanism, and Biochemistry. In: Ortiz De Montellano PR, ed. New York: Springer US, 87-114
40. CDS. Cytochrome P450 Conformational Diversity. Structure 2004;12:1921-1922
41. Werck-Reichhart D, Feyereisen R. Cytochromes P450: A success story. Genome Biol 2000;1:REVIEWS3003
42. 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
43. 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
44. 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
45. 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
46. Robineau T, Batard Y, Nedelkina S, Cabello-Hurtado F, LeRet M, Sorokine O et al. The chemically inducible plant cytochrome P450 CYP76B1 actively metabolizes phenylureas and other xenobiotics. American Society of Plant Physiologists
47. 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
48. 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
49. Werck-Reichhart D, Hehn A, Didierjean L. Cytochromes P450 for engineering herbicide tolerance. Trends Plant Sci 2000;5:1360-1385