Molecular modeling and dynamics studies of purine nucleoside phosphorylase from Bacteroides fragilis

Journal of Molecular Modeling

Volumn 15, Issue 8, 2009, Pages 913-922

  Pauli, Ivani ^a   Macedo Timmers, Luis Fernando Saraiva ^a   Andrade Caceres, Rafael ^a   Augusto Basso, Luiz ^a   Santiago Santos, Diógenes ^a   Filgueira de Azevedo Jr , Walter ^a  

^a PONTIFICAL CATHOLIC UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

Bacteroides fragilis; Bioinformatics; Drug design; Molecular dynamics; Molecular modeling

Indexed keywords

BACTERIAL ENZYME; PURINE NUCLEOSIDE PHOSPHORYLASE;

ALPHA HELIX; ARTICLE; BACTEROIDES FRAGILIS; BETA SHEET; BINDING AFFINITY; BINDING SITE; CRYSTALLOGRAPHY; ENZYME CONFORMATION; ENZYME STRUCTURE; HUMAN; HYDROGEN BOND; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SIMULATION; STRUCTURE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BACTEROIDES FRAGILIS; BINDING SITES; BINDING, COMPETITIVE; COMPUTER SIMULATION; ENZYME STABILITY; HUMANS; KINETICS; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PURINE-NUCLEOSIDE PHOSPHORYLASE; SEQUENCE HOMOLOGY, AMINO ACID;

BACTEROIDES FRAGILIS;

EID: 67649550153     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-008-0445-2     Document Type: Article

References (64)

1. Myers LL, Shoop DS, Stackhouse LL, Newman FS, Flaherty RJ, Letson GW, Sack RB (1987) J Clin Microbiol 12:2330-2333
2. Duerden BI, Collee JG, Brown R, Deacon AG, Holbrook WP (1980) J Med Microbiol 13:231-245
3. Border M, Feirehammer BD, Shoop DS, Myers LL (1985) J Clin Microbiol 21:472-473
4. Almeida FS, Nakano V, Avila-Campos MJ (2007) FEMS Microbiol Lett 272:15-21
5. Wu S, Shin J, Zhang G, Cohen M, Franco A, Sears CL (1984) Infect Immun 74:5382-5390
6. Salyers AA (1984) Annu Rev Microbiol 38:293-313
7. Nakano V, Avila-Campos MJ (2004) Mem Inst Oswaldo Cruz 99:319-324
8. Gupta A, Vlamakis H, Shoemarker N, Salyers AA (2003) Appl Environ Microbiol 69:6455-6463
9. Silva RG, Nunes JES, Canduri F, Borges JC, Gava LM, Moreno FB, Basso LA, Santos DS (2007) Curr Drugs Target 8:413-422
10. Caceres RA, Saraiva Timmers LF, Dias R, Basso LA, Santos DS, de Azevedo WF Jr (2008) Bioorg Med Chem 16:4984-93
11. Canduri F, Fadel V, Dias MVB, Basso LA, Palma MS, Santos DS, De Azevedo WF Jr (2005) Biochem Biophys Res Commun 326:335-338
12. De Azevedo WF, Canduri F, Santos DM, Pereira JH, Dias MVB, Silva RG, Mendes MA, Basso LA, Palma MS, Santos DS (2003) Biochem Biophys Res Commun 309:917-922
13. Kalckar HM (1947) J Biol Chem 167:429-443
14. Canduri f, Fadel V, Basso LA, Palma MS, Santos DS, de Azevedo WF Jr (2005) Biochem Biophys Res Commun 327:646-649
15. Bzowska A, Kulikowska E, Shugar D (2000) Pharmacol Ther 88:349-425
16. Pugmire MJ, Ealick SE (2002) Biochem J 361:1-25
17. Timmers LFSM, Caceres RA, Vivan AL, Gava LM, Dias R, Ducati RG, Basso LA, Santos DS, de Azevedo WF Jr (2008) Arch Biochem Biophys 479:28-38. doi: 10.1016/j.abb.2008.08.015
18. Pauli I, Caceres RA, de Azevedo WF Jr (2008) Bioorg Med Chem 16:8098-8108
19. Kroemer RT, Doughty SW, Robinson AJ, Richards WG (1996) Protein Eng 9:493-498
20. dos Santos DM, Canduri F, Pereira JH, Dias MVB, Silva RG, Mendes MA, Palma MS, Basso LA, de Azevedo WF, Santos DS (2003) Biochem Biophys Res Commun 308:553-559
21. de Azevedo WF, Canduri F, dos Santos MD, Pereira JH, Dias MVB, Silva RG, Mendes MA, Basso LA, Palma MS, Santos DS (2003) Biochem Biophys Res Commun 312:767-772
22. Silva RG, Pereira JH, Canduri F, de Azevedo WF Jr WF, Basso LA, Santos DS (2005) Arch Biochem Biophys 442:49-58
23. Canduri F, Silva RG, Dos Santos DS, Palma MS, Basso LA, Santos DS, de Azevedo WF (2005) Acta Crystallogr D 61:856-862
24. Canduri F, dos Santos DM, Silva RG, Mendes MA, Basso LA, Palma MS, de Azevedo WF Jr, Santos DS (2004) Biochem Biophys Res Comm 313:907-914
25. Hall TA (1999) Nucleic Acids Symp Ser 41:95-98
26. Uchoa HB, Jorge GE, Da Silveira NJF, Camera JC, Canduri F, de Azevedo WF (2004) Biochem Biophys Res Commun 325:1481-1486
27. Sali A, Blundell TL (1993) J Mol Biol 234:779-815
28. Canduri F, Uchoa HB, de Azevedo WF (2004) Biochem Biophys Res Commun 324:661-666
29. de Azevedo WF, Mueller-Dieckmann JH, Schulze-Gahmen U, Worland PJ, Sausville E, Kim SH (1996) Proc Natl Acad Sci USA 93:2735-2740
30. Politzer P, Murray JS, Lane P (2007) Int J Quant Chem 107:3046-3052
31. Murray S, Lane P, Clark T, Politzer P (2007) J Mol Mod 13:1033-1038
32. Wang R, Liu L, Lai L, Tang Y (1998) J Mol Mod 4:379-394
33. Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) J Appl Crystallogr 26:283-291
34. Collaborative Computation Project, Number 4 (1994) Acta Crystallogr D 50:760-763
35. Wallace AC, Laskowski RA, Thornton JM (1995) Protein Eng 8:127-134
36. van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005) J Comp Chem 26:1701-1718
37. Ooestenbrik C, Soares TA, van der Vegt NFA, van Gunsteren WF (2005) Eur Biophys J 34:273-284
38. van Aalten DMF, Bywater B, Findlay JBC, Hendlich M, Hooft RWW, Vriend GJ (1996) Comput Aided Mol Des 10:255-262
39. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su SJ, Windus TL, Dupuis M, Montgomery JAJ (1993) Comput Chem 14:1347-1363
40. Hofer TS, Randolf BR, Rode BM (2008) J Phys Chem B 48(1):85-98
41. Guex N, Peitsch MC (1997) Electrophoresis 18:2714-2723
42. Berendsen HJC, Postma JPM, Van Gunsteren WF, Hermans J (1981) In: Pullman B (ed) Intermolecular forces. Reidel, Dordrecht
43. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) J Comput Chem 18:1463
44. Miyamoto S, Kollman PA (1992) J Comput Chem 13:952
45. Chowdhuri S, Tan ML, Ichiye T (2006) J Chem Phys 125:144513
46. Darden T, York D, Pedersen LA (1993) J Chem Phys 98:10089-10092
47. De Souza ON, Ornstein RL (1999) J Biomol Struct Dyn 16:1205-1218
48. Hünenberger PH, Mark AE, Van Gunsteren WF (1995) J Mol Biol 252:492-503
49. Van Gunsteren WF, Mark AE (1998) J Chem Phys 108:6109-6116
50. Delano WL, Lam JW (2005) Abstr Pap Am Chem Soc 230:1371-1372
51. Chou PY, Fasman GD (1978) Adv Enzymol Relat Areas Mol Biol 47:45-148
52. Jones DT (1999) J Mol Biol 292:195-202
53. Azevedo WF, Canduri F, Dos Santos DM, Silva RG, Oliveira JS, Carvalho LPS, Basso LA, Mendes MA, Palma MS, Santos DS (2003) Biochem Biophys Res Commun 308:545-552
54. De Azevedo Jr. WF (2008) Curr Drug Targets 9:1030-1030
55. De Azevedo Jr. WF, Dias R (2008) Curr Drug Targets 9:1031-1039
56. Dias R, De Azevedo Jr. WF (2008) Curr Drug Targets 9:1040-1047
57. Canduri F, De Azevedo Jr. WF (2008) Curr Drug Targets 9:1048-1053
58. Pauli I, Timmers LFSM, Caceres RA, Soares MBP, De Azevedo Jr. WF (2008) Curr Drug Targets 9:1054-1061
59. Dias R, Timmers LFSM, Caceres RA, De Azevedo Jr. WF (2008) Curr Drug Targets 9:1062-1070
60. De Azevedo Jr. WF, Dias R (2008) Curr Drug Targets 9:1071-1076
61. Caceres RA, Pauli I, Timmers LFSM, De Azevedo Jr. WF (2008) Curr Drug Targets 9:1077-1083
62. Barcellos GB, Pauli I, Caceres RA, Timmers LFSM, Dias R, De Azevedo Jr. WF (2008) Curr. Drug Targets 9:1084-1091
63. Timmers LFS, Pauli I, Caceres RA De Azevedo Jr. WF (2008) Curr. Drug Targets 9:1092-1099
64. Alexander CS, Yan X, Pei T (2005) Biophys J 88:1009-1017