Interactions of aryloxyphenoxypropionic acids with sensitive and resistant acetyl-coenzyme a carboxylase by homology modeling and molecular dynamic simulations

Journal of Chemical Information and Modeling

Volumn 46, Issue 4, 2006, Pages 1819-1826

  Zhu, Xiao Lei ^a   Zhang, Li ^a   Chen, Qiong ^a   Wan, Jian ^a   Yang, Guang Fu ^a  

^a CENTRAL CHINA NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONS; CRYSTAL STRUCTURE; ENZYMES; HYDROGEN BONDS; MOLECULAR DYNAMICS; STRUCTURE (COMPOSITION);

ARYLOXYPHENOXYPROPIONIC ACIDS; CARBOXYL-TRANSFERASE (CT); ENZYME - LIGAND COMPLEX; HOMOLOGY MODELING; RESISTANT ACETYL-COENZYME;

CARBOXYLIC ACIDS;

ACETYL COENZYME A CARBOXYLASE; PROPIONIC ACID; PROPIONIC ACID DERIVATIVE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM;

ACETYL-COA CARBOXYLASE; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROPIONIC ACIDS;

EID: 33746914363     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci0600307     Document Type: Article

References (41)

1. Burton, J. D.; Gronwald, J. W.; Keith, R. A.; Somers, D. A.; Gengenbach, B. G.; Wyse, D. L. Kinetics of inhibition of acetylcoenzyme A carboxylase by sethoxydim and haloxyfop. Pestic. Biochem. Physiol. 1991, 39, 100-109.
2. Rendina, A. R.; Felts, J. M. Cyclohexandione herbicides are selective and potent inhibitors of acetyl-CoA carboxylase from grasses. Plant Physiol. 1988, 86, 983-986.
3. Egli, M. A.; Gengenbach, B. G.; Gronwald, J. W.; Somers, D. A.; Wyse, D. L. Characterization of maize acetyl-coenzyme A carboxylase. Plant Physiol. 1993, 101, 499-506.
4. Nikolau, B. J.; Ohlrogge, J. B.; Wurtel, E. S. Plant biotin-containing carboxylase. Arch. Biochem. Biophys. 2003, 414, 211-222.
5. Sasaki, Y.; Konishi, T.; Nagano, Y. The compartmentation of acetyl-coenzyme A carboxylase in plants. Plant Physiol. 1995, 108, 445-449.
6. Post-Beittenmiller, D. Biochemistry and molecular biology of wax production in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 1996, 47, 405-430.
7. Konishi, T.; Shinohara, K.; Yamada, K.; Sasaki, Y. Acetyl-CoA carboxylase in higher plants: Most plants other than gramineae have both the prokaryotic and eukaryotic forms of this enzyme. Plant Cell. Physiol. 1996, 37, 117-122.
8. Steve, R. W.; Christopher Hall, J. Monoclonal-based elisa for the identification of herbicidal cyclohexanedione analogues that inhibit graminaceous acetyl coenzyme-A carboxylase. J. Agric. Food Chem. 2000, 48, 1210-1218.
9. Hernánde, M.; Río, A.; Esteve, T.; Prat, S.; Pla, M. A rapeseed-specific gene, Acetyl-CoA carboxylase, can be used as a reference for qualitative and real-time quantitative PCR detection of transgenes from mixed food samples. J. Agric. Food Chem. 2001, 49, 3622-3627.
10. Rendina, A. R.; Craig-Kennard, A. C.; Beaudion, J. D.; Breen, M. K. Inhibition of acetyl coenzyme-A carboxylase by two classes of grass-selective herbicides. J. Agric. Food Chem. 1990, 38, 1282-1287.
11. Zhang, H.; Yang, Z. R.; Shen, Y.; Tong, L. Crystal structure of the carboxylase domain of acetyl coenzyme-A carboxylase. Science 2003, 299, 2064-2067.
12. Rendina, A. R.; Campopiano, O.; Marsili, E.; Hixon, M.; Chi, H.; Taylor, W. S.; Hagenah, J. A. Overlap between herbicidal inhibitors of acetyl coenzyme-A carboxylase: Enhanced binding of cyclic triketones, a novel triketones, a novel class of graminicide. Pestic. Sci. 1995, 43, 368-371.
13. Nick, M.; Stephen, B. P.; Christopher, P. Mechanisms of resistance to acetyl-coenzyme A carboxylase-inhibiting herbicides in a Hordeum ieporinum population. Pest Manage. Sci. 2000, 56, 441-447.
14. Kay, M. C.; David, S. N.; Julian, O. C.; Stephen, R. M. Resistance to ACCase-inhibiting herbicides and isoproturon in UK populations of Lolium multiflorum: Mechanisms of resistance and implications for control. Pest Manage. Sci. 2001, 57, 587-597.
15. Stephen, R. M.; Kay, M. C.; Amanda, C. B.; Linda, H.; Linda, M. F. Characterisation of target-site resistance to ACCase-inhibiting herbicides in the weed Alopecurus myosuroides (black-grass). Pest Manage. Sci. 2003, 59, 190-201.
16. Volenberg, D.; Stoltenberg, D. Altered acetyl-coenzyme A carboxylase confers resistance to clethodim, fluazifop and sethoxydim in Setaria faberi and Digitaria sanguinalis. Weed Res. 2002, 42, 342-350.
17. Incledon, B. J.; Christopher Hall, J. Inhibition of ACCase220 and ACCase240 isozymes from sethoxydim-resistant and -susceptible maize hybrids. J. Agric. Food Chem. 1999, 47, 299-304.
18. Shukla, A.; Nycholat, C.; Mani, V. S.; Richard, J. A.; Malaolm, D. D. Use of resistant ACCase mutants to screen for novel inhibitors against resistant and susceptible forms of ACCase from grass weeds. J. Agric. Food Chem. 2004, 52, 5144-5150.
19. Zhang, H.; Tweet, B.; Tong, L. Molecular basis for the inhibiton of the carboxyltransferase domain of acetyl coenzyme-A carboxylase by haloxyfop and diclofop. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 5910-5915.
20. Zhao, H. J.; Wang, J. H.; Gao, P.; Zhang, J. Q.; Wang, T. Y.; Wang, G. Y. Cloning of plastid acetyl-CoA carboxylase cDNA from Setariaitlica and sequence analysis graminicide target site. Acta Biontaica Sinica 2004, 46, 751-756.
21. National Center for Biotechnology Information. http://www.nchi.nlm.nih. gov (accessed May 2005).
22. Schwede, T.; Kopp, J.; Guex, N.; Peitsch, M. C. SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res. 2003, 31, 3381-3385.
23. Zhang, H. L.; Benjiamin, T.; Jiang, L.; Liang, T. Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with CP-640186. Structure 2004, 12, 1683-1691.
24. Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993, 26, 283-291.
25. Rullmann, J. A. C. AQUA; Utrecht University: Utrecht, The Netherlands, 1996.
26. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III; Wang, J.; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Tsui, V.; Gohlke, H.; Radmer, R. J.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 7; University of California, San Francisco, CA, 2002.
27. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
28. Darden, T.; York, D. L. Pedersen, Particle mesh Ewald: An N log-(N) method for Ewald sums in large sysytem. J. Chem. Phys. 1993, 98, 10089-10092.
29. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical intergration of the Cartesian equations of motion of a system with constraints: Molecular synamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
30. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath. J. Comput. Phys. 1984, 81, 3684-3690.
31. Sippl, M. J. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J. Comput.-Aided Mol. Des. 1993, 7, 473-501.
32. Zagnitko, O.; Jelenska, J.; Tevzadze, G.; Haselkon, R.; Gornicki, P. An isoleucine/leucine residue in the carboxyltransferase domain if acetyl-CoA carboxylase is critical for interaction with aryloxyphenoxypropionate and cyclohexanedione. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 6617-6622.
33. Nikolskaya, T.; Zagnitko, O.; Tevzadze, G.; Haselkon, R.; Gornicki, P. Herbicide sensitivity determinant of wheat plastid acetyl-Coa carboxylase is located in a 400-amino acid fragment of the carboxyltransferase domain. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14647-14651.
34. Délye, C.; Zhang, X. Q.; Claire, C.; Michel, S.; Powles, S. B. An isoleucine residue within the carboxyltransferase domain of multidomain acetyl-CoA carboxylase is a major determinant of sensitivity to aryloxyphenoxypropionate but not to cyclohexanedione. Plant Physiol. 2003, 132, 1716-1723.
35. Délye, C.; Michel, S. 'Universal' primers for PCR-sequenceing of grass chloroplastic acetyl-CoA carboxylase domains involved in resistance to herbicides. Weed Res. 2005, 45, 323-330.
36. Herbert, D.; Pricel, J.; Alban, C.; Dehaye, L.; Job, J.; Pallett, K. E.; Harwood, J. L. Kinetic studies on two isoforms of acetyl-CoA carboxylase from maize leaves. Biochem. J. 1996, 318, 997-1006.
37. Anna, M.; Angelo, M. F. Homology modeling studies on human galactose-1-phosphate uridylytransferase and on its galactosemia-related mutant Q188R provide an explanation of molecular effects of the mutation on homo- and heterodimers. J. Med. Chem. 2005, 48, 773-779.
38. Mcfadden, J. J.; Frear, D. S.; Magasager, E. R. Aryl hydroxylation of diclofop by a cytochrom P450 dependent monoxygenase from wheat. Pestic. Biochem. Physiol. 1989, 34, 92-100.
39. Donald, W. W.; Shimabukuro, R. H. Selectivity of diclofopmethyl between wheat and wild oat: Growth and herbicide metabolism. Physiol Plant 1980, 49, 459-464.
40. Steve, R. W.; Christopher Hall, J. Development and evaluation of an immumologocal approach for the identification of novel acetyl coenzyme-A carboxylase inhibitors: Assay optimization and pilot screen results. J. Agric. Food. Chem. 2000, 48, 1219-1228.
41. James, A. T.; Daniel, J. P. Origin of enantiomeric selectivity in the aryloxyphenoxypropionic acid class of herbicidal acetyl coenzyme A carboxylase (ACCase) inhibitors. J. Agric. Food. Chem. 2002, 50, 4554-4566.