Dioxygenase from Aspergillus fumigatus MC8: Molecular modelling and in silico studies on enzyme-substrate interactions

Molecular Simulation

Volumn 38, Issue 2, 2012, Pages 144-151

  Roopesh, Krishnankutty ^a   Abhilash, Joseph ^b   Haridas, M ^b   Sabu, Abdulhameed ^b   Isabelle, Perraud Gaime ^a   Roussos, Sevastianos ^a   Augur, Christopher ^a  

^a INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^b KANNUR UNIVERSITY   (India)

Author keywords

dioxygenase; homology modelling; molecular docking; peptide sequencing

Indexed keywords

3D STRUCTURE; ASPERGILLUS FUMIGATUS; BIOCATALYSIS; CATALYSE; DIOXYGENASES; ENZYME-SUBSTRATE INTERACTIONS; EPICATECHIN; EXTRACELLULAR; FLAVOENZYMES; HOMOLOGY MODELLING; IN-SILICO; MECHANISTIC PROPERTIES; MOLECULAR DOCKING; MOLECULAR DOCKING SIMULATIONS; ONLINE SERVERS; OXIDATIVE MODIFICATION; OXYGENASES; PEPTIDE FRAGMENTS; PEPTIDE SEQUENCING; POTENTIAL APPLICATIONS; PROTEIN DATABASE; PROTEIN DIGESTION; PROTEIN HOMOLOGY; PROTEIN SUBSTRATE; RECOGNITION ENGINES; REGIO-SELECTIVE; SEQUENCE ANALYSIS;

ASPERGILLUS; ENZYMES; LIGANDS; MOLECULAR MODELING; OXYGENATION; PEPTIDES; PHENOLS; THREE DIMENSIONAL;

SUBSTRATES;

EID: 84856305187     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927022.2011.608672     Document Type: Article

References (31)

1. S.G. Burton, Oxidizing enzymes as biocatalysts, Trends in Biotech. 21(12) (2003), pp. 543-549. (Pubitemid 37415006)
2. Z. Li, J.B. van Beilen, A.W. Duetz, A. Schmid, A. de Raadt, H. Griengl, and B. Witholt, Oxidative biotransformations using oxygenases, Curr. Opin. Chem. Biol. 6 (2002), pp. 136-144. (Pubitemid 34251367)
3. L.P. Wackett, Mechanism and applications of Rieske non-heam iron dioxygenases, Enzyme Microb. Technol. 31 (2002), pp. 577-587. (Pubitemid 35239843)
4. H.L. Holland, Organic Synthesis with Oxidative Enzymes, VCH Publishers Inc., New York, 1992, pp. 5-40.
5. J.B. Broderick, Catechol dioxygenases, Essays Biochem. 34 (1999), pp. 173-189. (Pubitemid 129638937)
6. S. Harayama, M. Kok, and E.L. Neidle, Functional and evolutionary relationships among diverse oxygenases, Annu. Rev. Microbiol. 46 (1992), pp. 565-601.
7. Y. Noda, S. Nishikawa, K.I. Shiozuka, H. Kadokura, H. Nakajima, K. Yoda, Y. Katayama, N. Morohoshi, T. Haraguchi, and M. Yamasaki, Molecular cloning of the protocatechuate 4,5-dioxygenase genes of Pseudomonas paucimobilis, J. Bacteriol. 172 (1990), pp. 2704-2709. (Pubitemid 20141428)
8. D.I. Roper and R.A. Cooper, Subcloning and nucleotide sequence of the 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase gene from Escherichia coli C, FEBS Lett. 275 (1990), pp. 53-57. (Pubitemid 20386174)
9. M. Kabisch and P. Fortnagel, Nucleotide sequence of metapyrocatechase I (catechol 2,3-oxygenase I) gene mpcI from Alcaligenes eutrophus JMP222, Nucl. Acid. Res. 18 (1990), pp. 3405-3406. (Pubitemid 20191759)
10. S. Han, L.D. Eltis, K.N. Timmis, S.W. Muchmore, and J.T. Bolin, Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCBFIG degrading Pseudomonad, Science 270 (1995), pp. 976-980.
11. K. Lee, B. Kauppi, R.E. Parales, D.T. Gibson, and S. Ramaswany, Purification and crystallization of the oxygenase component of naphthalene dioxygenase in native and selenomethionine-derivatized forms, Biochem. Biophys. Res. Commun. 241 (1997), pp. 553-557. (Pubitemid 28020139)
12. U. Gowthaman, M. Jayakanthan, and D. Sundar, Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: Computational screening of inhibitors to HIV-1 entry, BMC Bioinform 9(Suppl. 12) (2008), p. S14.
13. K. Roopesh, S. Guyot, A. Sabu, P.G. Isabelle, S. Roussos, and C. Augur, Biotransformation of procyanidins by a purified fungal dioxygenase: Identification and characterization of the products using mass spectrometry, Proc. Biochem. 45 (2010), pp. 904-913.
14. J.D. Thompson, D.J. Higgins, and T.J. Gibson, CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice, Nucl. Acid. Res. 22 (1994), pp. 4673-4680. (Pubitemid 24354800)
15. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman, Gapped BLASTand PSI-BLAST: A new generation of protein database search programs, Nucl. Acid. Res. 25 (1997), pp. 3389-3402. (Pubitemid 27359211)
16. L.A. Kelley and M.J.E. Sternberg, Protein structure prediction on the web: A case study using the Phyre server, Nat. protoc. 4 (2009), pp. 363-371.
17. R.A. Sayle and E.J. Milner-White, RASMOL: Biomoleculer graphics for all, Trends Biochem. Sci. 20 (1995), pp. 374-376.
18. T.A. Halgren, R.B. Murphy, R.A. Friesner, H.S. Beard, L.L. Frye, W.T. Pollard, and J.L. Banks, Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening, J. Med. Chem. 47 (2004), pp. 1750-1759. (Pubitemid 38380918)
19. R.A. Friesner, J.L. Banks, R.B. Murphy, T.A. Halgren, J.J. Klicic, D.T. Mainz, M.P. Repasky, E.H. Knoll, M. Shelley, J.K. Perry, D.E. Shaw, P. Francis, and P.S. Shenkin, Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy, J. Med. Chem. 47 (2004), pp. 1739-1749. (Pubitemid 38380917)
20. W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives, Development and testing of the OPLS all-atom force field on conformational energetics of organic liquids, J. Am. Chem. Soc. 118 (1996), pp. 11225-11236. (Pubitemid 26399746)
21. R.A. Friesner, R.B. Murphy, M.P. Repasky, L.L. Frye, J.R. Greenwood, T.A. Halgren, P.C. Sanschagrin, and D.T. Mainz, Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes, J. Med. Chem. 49 (2006), pp. 6177-6196. (Pubitemid 44595196)
22. M. Ferraroni, P.M. Kolomytseva, P.I. Solyanikova, A. Scozzafava1, A.L. Golovleva, and F. Briganti, Crystal structure of 3-chlorocatechol 1,2-dioxygenase key enzyme of a new modified ortho-pathway from the gram-positive Rhodococcus opacus 1CP grown on 2-chlorophenol, J. Mol. Biol. 360 (2006), pp. 788-799. (Pubitemid 43993918)
23. M.W. Vetting and D.H. Ohlendorf, The 1.8Å crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker, Struct. Fold. Des. 8 (2000), pp. 429-440. (Pubitemid 30202903)
24. B. Sherman, T. Day, M.P. Jacobson, R.A. Friesner, and R.A. Farid, Novel procedure for modeling ligand/receptor induced fit effects, J. Med. Chem. 49 (2006), pp. 534-553. (Pubitemid 43157487)
25. R.P. Sheridan, M.D. Miller, D.J. Underwood, and S.K. Kearsley, Chemical similarity using geometric atom pair descriptors, J. Chem. Inform. Comput. Sci. 36 (1996), pp. 128-136. (Pubitemid 126579144)
26. M.D. Eldridge, C.W.Murray, T.R.Auton, G.V. Paolini, and R.P.Mee, Empirical scoring functions: The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes, J. Comput. Aided Mol. Des. 11 (1997), pp. 425-445. (Pubitemid 127505895)
27. W.C. Nierman, A. Pain, M.J. Anderson, J.R. Wortman, H.S. Kim, J. Arroyo, M. Berriman, K. Abe, D.B. Archer, C. Bermejo, J. Bennett, P. Bowyer, D. Chen, M. Collins, R. Coulsen, R. Davies, P.S. Dyer, M. Farman, N. Fedorova, N. Fedorova, T.V. Feldblyum, R. Fischer, N. Fosker, A. Fraser, J.L. García, M.J. García, A. Goble, G.H. Goldman, K. Gomi, S. Griffith-Jones, R. Gwilliam, B. Haas, H. Haas, D. Harris, H. Horiuchi, J. Huang, S. Humphray, J. Jiménez, N. Keller, H. Khouri, K. Kitamoto, T. Kobayashi, S. Konzack, R. Kulkarni, T. Kumagai, A. Lafon, J.P. Latgé, W. Li, A. Lord, C. Lu, W.H. Majoros, G.S. May, B.L. Miller, Y. Mohamoud, M. Molina, M. Monod, I. Mouyna, S. Mulligan, L. Murphy, S. O'Neil, I. Paulsen, M.A. Peñalva, M. Pertea, C. Price, B.L. Pritchard, M.A. Quail, E. Rabbinowitsch, N. Rawlins, M.A. Rajandream, U. Reichard, H. Renauld, G.D. Robson, S. Rodriguez de Córdoba, J.M. Rodríguez-Peña, C.M. Ronning, S. Rutter, S.L. Salzberg, M. Sanchez, J.C. Sánchez-Ferrero, D. Saunders, K. Seeger, R. Squares, S. Squares, M. Takeuchi, F. Tekaia, G. Turner, C.R. Vazquez de Aldana, J. Weidman, O. White, J. Woodward, J.H. Yu, C. Fraser, J.E. Galagan, K. Asai, M. Machida, N. Hall, B. Barrell, and D.W. Denning, Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus, Nature 438 (2005), pp. 1151-1156. (Pubitemid 41831684)
28. D.H. Ohlendorf, J.D. Lipscomb, and P.C. Weber, Structure and assembly of protocatechuate 3,4-dioxygenase, Nature 336 (1988), pp. 403-405.
29. M.W. Vetting, D.A. D'Argenio, L.N. Ornston, and D.H. Ohlendorf, Structure of Acinetobacter strain ADP1 protocatechuate 3,4-dioxygenase at 2.2Å resolution: Implications for the mechanism of an intradiol dioxygenase, Biochemistry 39 (2000), pp. 7943-7955. (Pubitemid 30452368)
30. 3+ ligand displacement in response to substrate binding, Biochemistry 36 (1997), pp. 10052-10066. (Pubitemid 27357713)
31. T.E. Elgren, A.M. Orville, K.A. Kelly, J.D. Lipscomb, D.H. Ohlendorf, and L. Que, Jr, Crystal structure and resonance Raman studies of protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate, Biochemistry 36 (1997), pp. 11504-11513. (Pubitemid 27408634)