Phylogenetic analysis, homology modelling, molecular dynamics and docking studies of caffeoyl-CoA-O- methyl transferase (CCoAOMT 1 and 2) isoforms isolated from subabul (Leucaena leucocephala)

Journal of Molecular Modeling

Volumn 15, Issue 2, 2009, Pages 203-221

  Sekhar Pagadala, Nataraj ^a   Arha, Manish ^b   Reddy, P S ^a   Kumar, Ranadheer ^a   Sirisha, V L ^a   Prashant, S ^a   Janardhan Reddy, K ^a   Khan, Bashir ^b   Rawal, S K ^b   Kavi Kishor, P B ^a  

^a OSMANIA UNIVERSITY   (India)

^b NATIONAL CHEMICAL LABORATORY   (India)

Author keywords

Caffeoyl CoA 3 O methyl transferase; Docking; Modelling; S adenosyl homocysteine

Indexed keywords

5 HYDROXYFERUOYL COENZYME A; ARGININE; ASPARAGINE; ASPARTIC ACID; CAFFEOYL COENZYME A; CAFFEOYL COENZYME A O METHYLTRANSFERASE; CAFFEOYL COENZYME A O METHYLTRANSFERASE 1; CAFFEOYL COENZYME A O METHYLTRANSFERASE 2; CATECHOL METHYLTRANSFERASE; COENZYME A; FERUOYL COENZYME A; GLUTAMINE; GLYCINE; LIGNIN; METHIONINE; METHYLTRANSFERASE; S ADENOSYLHOMOCYSTEINE; S ADENOSYLMETHIONINE; SERINE; SINAPYL COENZYME A; THREONINE; UNCLASSIFIED DRUG; VALINE;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; BINDING AFFINITY; BINDING SITE; BIOSYNTHESIS; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME SUBSTRATE COMPLEX; HIGHER PLANT; LEUCAENA LEUCOCEPHALA; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN BINDING; SEQUENCE HOMOLOGY; SOLVENT EFFECT;

AMINO ACID SEQUENCE; CATALYTIC DOMAIN; COENZYME A; COMPUTER SIMULATION; FABACEAE; ISOENZYMES; METHYLTRANSFERASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT PROTEINS; PROTEIN STRUCTURE, SECONDARY; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN; SUBSTRATE SPECIFICITY;

LEUCAENA LEUCOCEPHALA; PUFFINUS AURICULARIS;

EID: 58549095050     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-008-0395-8     Document Type: Article

References (45)

1. Higuchi T (1998) Kung S-D, Yang S-F (eds) Discoveries in plant biology. World Scientific, Singapore, 233-269
2. Grima-Pettenati J, Goffner D (1999) Plant Sci 145:51-65
3. Meyer K, Sirley AM, Cusumano JC, Bell D Lelong A, Chappel C (1998) Proc Natl Acad Sci USA 95:6619-6623
4. Tsai CJ, Mielke MR, Hu WJ, Podila GK, Chiang VL (1998) Plant Physiol 117:101-112
5. Zhong R, Morrison WH, Negrel J, Ye ZH (1998) Plant Cell 10:2033-2045
6. Ye ZH, Kneusel RE, Matern U, Varner JE (1994) Plant Cell 6:1427-1439
7. Ye ZH, Varner JE (1995) Plant Physiol 108:459-467
8. Ye ZH (1997) Plant Physiol 115:1341-1350
9. Inoue K, Vincent JH, Sewalt G, Balance MNIW, Sturzer C, Dixon RA (1998) Plant Physiol 117:761-770
10. Martz F, Maury S, Pincon G, Legrand M (1998) Plant Mol Biol 36:427-437
11. Kersey R, Inoue K, Schubert KR, Dixon RA (1999) Protoplasma 209:46-57
12. Li L, Osakabe K, Joshi CP, Chiang VL (1999) Plant Mol Biol 40:555-565
13. Meng H, Campbell WH (1998) Plant Mol Biol 38:513-520
14. Maury S, Geoffroy P, Legrand M (1999) Plant Physiol 121:215-224
15. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DJ (1997) Nucleic Acids Res 24:4876-4882
16. Nicholas KB, Nicholas HB (1997) http://www.psc.edu/biomed/genedoc [Online.]
17. Page RDM (1996) Comput Appl Biosci 12:357-358
18. Perrieère G, Gouy M (1996) Biochimie 78:364-369
19. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) J Mol Biol 215:403-410
20. Ferrer J, Zubeita C, Dixon RA, Noel JP (2005) Plant Physiol 137:1009-1017
21. Needleman SB, Wunsch CD (1970) J Mol Biol 48:443-453
22. Sali A, Blundell TL (1993) J Mol Biol 234:779-815
23. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck J, Field M, Fischer JS, Gao J, Guo H, Ha S (1998) J Phys Chem B 102:3586-3616
24. Sali A, Overington JP (1994) Protein Sci 3:1582-1596
25. Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K (1999) J Comput Phys 151:283
26. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck J, Field M, Fischer JS, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1992) FASEB J 6:A143-A143
27. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck J, Field M, Fischer JS, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher IWE, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998a) J Phys Chem B 102:3586-3616
28. Schlenkrich M, Brickmann J, MacKerell AD Jr, Karplus M (1996) A molecular perspective from computation and experiment. In: Merz KM, Roux B (eds) Birkhauser, Boston MA, pp 31-81
29. Jorgensen WL, Chandresekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926-935
30. Grubmuller H, Heller H, Windemuth A, Schulten K (1991) Mol Sim 6:121-142
31. Schlick T, Skeel R, Brunger A, Kale L, Board JA Jr, Hermans J, Schulten K (1999) Algorithmic challenges in computational molecular biophysics. J Comput Phys 151:9-48
32. Brunger (1992) X-PLOR, Version 3.1: Yale University New Haven CT
33. MacKerell AD Jr, Brooks B, Brooks CL III, Nilsson L, Roux B, Won Y, Karplus M (1998b) In: Schleyer P (ed) The encyclopedia of computational chemistry. John Wiley & Sons, Chichester, UK, pp 271-277
34. Ryckaert J-P, Ciccotti G, Berendsen HJC (1977) J Comput Phys 23:327-341
35. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) J Chem Phys 103:8577
36. Laskoswki RA, MacArthur MW, Moss DS, Thorton JM (1993) J Appl Cryst 26:283-291
37. Colovos K, Yeates TO (1993) Protein Sci 2:1511-1519
38. Vriend G (1990) J Mol Graph 8:52-56
39. Hooft RWW, Vriend G, Sander C, Abola EE (1996) Nature 381:272
40. Guex N, Peitsch MC (1997) Electrophoresis 18:2714-2723
41. Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J (2006) Nucleic Acids Res 34:W116-W118
42. Schulz-Gasch T, Stahl M (2003) J Mol Model 9:47-57
43. Rossmann MG, Moras D, Olsen KW (1974) Nature 250:194-199
44. Zhong RW, Morrison H III, Himmelsbach DS, Poole FL II, Ye ZH (2000) Plant Physiol 124:563-577
45. Hoffmann L, Maury S, Bergdoll M, Thion L, Erard M, Legrand M (2001) J Biol Chem 276:36831-36838