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Study on the enantioselectivity inhibition mechanism of acetyl-coenzyme A carboxylase toward haloxyfop by homology modeling and MM-PBSA analysis

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Abstract

Acetyl-coenzyme A carboxylase (ACCase) has been identified as one of the most important targets of herbicide Aryloxyphenoxypropionates (APPs). ACCase shows different enantioselectivity toward APPs, and only (R)-enantiomers of APPs have the herbicidal activity. In order to deeply understand the enantioselective recognition mechanism of ACCase, (R)-haloxyfop, which is a typical commercial herbicide from APPs, is selected and the relative binding free energy between ACCase and (R)-haloxyfop is investigated and compared with that between ACCase and (S)-haloxyfop by homology modeling and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method. Further free energy analysis reveals that the preference of ACCase toward (R)-haloxyfop is mainly driven by Van der Waals interaction. The analysis of the interaction between the active site residues of ACCase CT domain and (R)-haloxyfop shows the van der Waals interactions have a close relationship with the addition effect of each residue. An understanding of the enantioselective recognition mechanism between ACCase and haloxyfop is desirable to discover novel chiral herbicides.

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References

  1. Wakil SJ, Stoops JK, Joshi VC (1983) Fatty acid synthesis and its regulation. Ann Rev Biochem 52:537–579

    Article  CAS  Google Scholar 

  2. Harwood JL (1988) Fatty acid metabolism. Ann Rev Plant Physiol 39:101–138

    Article  CAS  Google Scholar 

  3. Nikolau BJ, Ohlrogge JB, Wurtele ES (2003) Plant biotin-containing carboxylases. Arch Biochem Biophys 414:211–222

    Article  CAS  Google Scholar 

  4. Davis MS, Solbiati J, Cronan JE Jr (2000) Overproduction of acetyl-CoA carboxylase activity increases the rate of fatty acid biosynthesis in Escherichia coli. J Biol Chem 275:28593–28598

    Article  CAS  Google Scholar 

  5. Sasaki Y, Konishi T, Nagano Y (1985) The compartmentation of acetylcoenzyme A carboxylase in plants. Plant Physiol 108:445–449

    Google Scholar 

  6. Post-Beittenmiller D (1996) Biochemistry and molecular biology of wax production in plants. Plant Mol Biol 47:405–430

    Article  CAS  Google Scholar 

  7. Konishi T, Shinohara K, Yamada K, Sasaki Y (1996) Acetyl-CoA carboxylase in higher plants: Most plants other than gramineae have both the prokaryotic and the eukaryotic forms of this enzyme. Plant Cell Physiol 37:117–122

    Article  CAS  Google Scholar 

  8. Zhang H, Yang Z, Shen Y, Tong L (2003) Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase. Science 299:2064–2067

    Article  CAS  Google Scholar 

  9. Sasaki Y, Nagano Y (2004) Plant acetyl CoA carboxylase structure, biosynthesis, regulation, and gene mainpulation for plant breeding. Biosci Biotechnol Biochem 68:1175–1184

    Article  CAS  Google Scholar 

  10. Tong L (2005) Acetyl-coenzyme A carboxylase: crucial metabolic enzyme and attractive targer for drug discovery. Cell Mol Life Sci 62:1784–1803

    Article  CAS  Google Scholar 

  11. Konishi T, Sasaki Y (1994) Compartmentalization of two forms of acetyl-CoA carboxylase in plants and the origin of their tolerance toward herbicides. Proc Natl Acad Sci 91:3598–3601

    Article  CAS  Google Scholar 

  12. Devine MD, Shukla A (2000) Altered target sites as a mechanism of herbicide resistance. Crop Prot 19:881–889

    Article  CAS  Google Scholar 

  13. Rendina AR, Craig-Kennard AC, Beaudoi JDK, Breen M (1990) Inhibition of acetyl-coenzyme A carboxylase by two classes of grassselective herbicides. J Agric Food Chem 38:1282–1287

    Article  CAS  Google Scholar 

  14. Alban C, Baldet P, Douce R (1994) Localization and characterization of two structurally different forms of acetyl-CoA carboxylase in young pea leaves, of which one is sensitive to aryloxyphenoxypropionate herbicides. Biochem J 300:557–565

    CAS  Google Scholar 

  15. Zhang H, Tweet B, Tong L (2004) Molecular basis for the inhibition of the carboxyltransferase domain of acetyl-coenzyme-A carboxylase by haloxyfop and diclofop. Proc Natl Acad Sci 101:5910–5915

    Article  CAS  Google Scholar 

  16. Tao J, Zhao B, Tian XM, Zheng LY, Cao SG (2010) Analysis of a critical residue determining herbicide efficiency sensitivity in carboxyltransferase domain of acetyl-CoA carboxylase from poaceae by homology modeling and free energy simulation. Chem Res Chin Univ 26:816–821

    CAS  Google Scholar 

  17. Zhu XL, Zhang L, Chen Q, Wan J, Yang GF (2006) Interactions of aryloxyphenoxypropionic acids with sensitive and resistant acetyl-coenzyme a carboxylase by homology modeling and molecular dynamic simulations. J Chem Inf Model 46:1819–1826

    Article  CAS  Google Scholar 

  18. Zhu XL, Hao GF, Zhan CG, Yang GF (2009) Computational simulations of the interactions between acetyl-coenzyme-a carboxylase and clodinafop: resistance mechanism due to active and nonactive site mutations. J Chem Inf Model 49:1936–1943

    Article  CAS  Google Scholar 

  19. Zhu XL, Yang WC, Yu NX, Yang SG, Yang GF (2011) Computational simulations of structural role of the active-site W374C mutation of acetyl-coenzyme-A carboxylase: multi-drug resistance mechanism. J Mol Model 17:495–503

    Article  CAS  Google Scholar 

  20. Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779–815

    Article  CAS  Google Scholar 

  21. Fiser A, Do RK, Sali A (2000) Modeling of loops in protein structures. Protein Sci 9:1753–1773

    Article  CAS  Google Scholar 

  22. Marti-Renom MA, Stuart A, Fiser A, Melo F, Sali A (2000) Comparative protein structure modeling of genes and genomes. Ann Rev Biophys Biomol Struct 29:291–325

    Article  CAS  Google Scholar 

  23. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283–291

    Article  CAS  Google Scholar 

  24. Vriend G, Sander C (1993) Quality control of protein models: Directional atomic contact analysis. J Appl Cryst 26:47–60

    Article  CAS  Google Scholar 

  25. Eisenberg D, Lüthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzym 277:396–404

    Article  CAS  Google Scholar 

  26. Dauber-Osguthorpe P, Roberts VA, Osguthorpe DJ, Wolff J, Genest M, Hagler AT (1988) Structure and energetics of ligand binding to proteins: E. coli dihydrofolate reductase-trimethoprim, a drug-receptor system. Proteins Struct Funct Genet 4:31–47

    Article  CAS  Google Scholar 

  27. Case DA, Darden TA, Cheatham TE, Darden T, Paesani F (2006) Amber 9. University of California, San Francisco

    Google Scholar 

  28. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24:1999–2012

    Article  CAS  Google Scholar 

  29. Lee MC, Duan Y (2004) 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 55:620–634

    Article  CAS  Google Scholar 

  30. Wang J, Wolf RM, Caldwell JW, Kollamn PA, Case DA (2004) Development and testing of a general Amber force field. J Comput Chem 25:1157–1174

    Article  CAS  Google Scholar 

  31. Jakalian A, Bush BL, Jack DB, Bayly CI (2000) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method. J Comput Chem 21:132–146

    Article  CAS  Google Scholar 

  32. Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and Validation. J Comput Chem 23:1623–1641

    Article  CAS  Google Scholar 

  33. Hawkins GD, Cramer CJ, Truhlar DG (1995) Pairwise solute descreening of solute charges from a dielectric medium. Chem Phys Lett 246:122–129

    Article  CAS  Google Scholar 

  34. Hawkins GD, Cramer CJ, Truhlar DG (1996) Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J Phys Chem 100:19824–19839

    Article  CAS  Google Scholar 

  35. Tsui V, Case DA (2001) Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers (Nucl Acid Sci) 56:275–291

    Article  CAS  Google Scholar 

  36. Jorgensen WL, Chandrasekhar J, Madura J, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935

    Article  CAS  Google Scholar 

  37. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N log-(N) method for Ewald sums in large sysytem. J Chem Phys 98:10089–10092

    Article  CAS  Google Scholar 

  38. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical intergration of the Cartesian equations of motion of a system with constraints: molecular synamics of n-alkanes. J Comput Phys 23:327–341

    Article  CAS  Google Scholar 

  39. Pastor RW, Brooks BR, Szabo A (1988) An analysis of the accuracy of Langevin and molecular dynamics algorithms. Mol Phys 65:1409–1419

    Article  Google Scholar 

  40. Loncharich RJ, Brooks BR, Pastor RW (1992) Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-actylananyl-N’-methylamide. Biopolymers 32:523–535

    Article  CAS  Google Scholar 

  41. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Comput Phys 81:3684–3690

    CAS  Google Scholar 

  42. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889–897

    Article  CAS  Google Scholar 

  43. Wang JM, Morin P, Wang W, Kollman PA (2001) Use of MM-PBSA in reproducing the binding free energies to hiv-1 rt of tibo derivatives and predicting the binding mode to hiv-1 rt of efavirenz by docking and MM-PBSA. J Am Chem Soc 123:5521–5230

    Google Scholar 

  44. Huey R, Morris GM, Olson AJ, Goodsell DS (2007) A semiempirical free energy force field with charge-based desolvation. J Comput Chem 28:1145–1152

    Article  CAS  Google Scholar 

  45. Turner JA, Pernich DJ (2002) Origin of enantiomeric selectivity in the aryloxyphenoxypropionic acid class of herbicidal acetyl coenzyme A carboxylase (ACCase) inhibitors. J Agric Food Chem 50:4554–4566

    Article  CAS  Google Scholar 

  46. Délye C, Zhang XQ, Michel S, Matéjicek A, Powles SB (2005) Molecular bases for sensitivity to acetyl-coenzyme A carboxylase inhibitors in black-grass. Plant Physiol 137:794–806

    Article  Google Scholar 

Download references

Acknowledgments

The authors are grateful for the financial support from National Natural Science Foundation of China (no. 20802025, 30870539, 20432010 and 20672045), Jilin Provincial Science &Technology Sustentation Program (no.20110436), Basic operating expenses of Jilin University and 985 Project of Jilin University. The authors acknowledge Professor Yan Feng for the usage of soft Amber 9.

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Authors and Affiliations

  1. Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, 130012, People’s Republic of China

    Jin Tao, Aijun Zhang, Liangyu Zheng & Shugui Cao

  2. College of Life Science, Jilin University, Changchun, 130012, People’s Republic of China

    Guirong Zhang

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  1. Jin Tao
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  2. Guirong Zhang
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  3. Aijun Zhang
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  5. Shugui Cao
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Correspondence to Liangyu Zheng or Shugui Cao.

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Tao, J., Zhang, G., Zhang, A. et al. Study on the enantioselectivity inhibition mechanism of acetyl-coenzyme A carboxylase toward haloxyfop by homology modeling and MM-PBSA analysis. J Mol Model 18, 3783–3792 (2012). https://doi.org/10.1007/s00894-012-1387-2

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