On 3LEZ, a Deep-sea halophilic protein with in vitro class-A β-lactamase activity: Molecular-dynamics, docking, and reactivity simulations

Chemistry and Biodiversity

Volumn 9, Issue 12, 2012, Pages 2659-2684

  Pietra, Francesco ^a  

^a Accademia Lucchese di Scienze   (Italy)

Author keywords

Deep sea; Hydrostatic pressure; Marine proteins; Molecular dynamics calculations; Lactamases

Indexed keywords

4',6 DIAMIDINO 2 PHENYLINDOLE; 6 [2 (1,2,3,4 TETRAHYDRO 1 ISOPROPYL 2 METHYL 7 ISOQUINOLINYL)CYCLOPROPYL] 2 NAPHTHALENECARBOXAMIDINE; AMILORIDE; BETA LACTAMASE; CARBENOXOLONE; CEFALOTIN; CEFTAZIDIME; CEPHAMYCIN C; CLAVULANIC ACID; CONGOCIDINE; DICLOFENAC; DIMINAZENE; IBUPROFEN; IMIDOCARB; NAFAMSTAT; PENICILLIN G; PENICILLIN V; PENTAMIDINE; PROTEIN; PROTEIN 3LEZ; SARCODICTYIN A; SULBACTAM; SULFAZECIN; SURAMIN; THIENAMYCIN; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; ENZYME ACTIVE SITE; ENZYME ACTIVITY; HALOPHILE; HYDROSTATIC PRESSURE; IN VITRO STUDY; MICHAELIS MENTEN KINETICS; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SEA; THERMODYNAMICS; X RAY DIFFRACTION;

EID: 84872971425     PISSN: 16121872     EISSN: 16121880     Source Type: Journal    
DOI: 10.1002/cbdv.201200331     Document Type: Article

References (35)

1. G. M. Sharma, M. K. Sahni, in 'Marine Biotechnology, Vol. 1, Pharmaceutical and Bioactive Natural Products', Eds. D. H. Attaway, O. R. Zaborski, Plenum Press, New York, 1993.
2. F. Pietra, 'Biodiversity and Natural Product Diversity', Tetrahedron Organic Chemistry Series, Elsevier, Oxford, 2002.
3. A. Aneiros, A. Garateix, J. Chromatogr. B 2004, 803, 41.
4. J. Lu, Y. Nogi, H. Takami, FEMS Microbiol. Lett. 2001, 205, 291.
5. M. Toth, C. Smith, H. Frase, S. Mobashery, S. Vakulenko, J. Am. Chem. Soc. 2010, 132, 816
6. R. P. Ambler, A. F.W. Coulson, J. M. Frere, J. M. Ghuysen, B. Joris,M. Forsman, R. C. Levesque, G. Tiraby, S. G. Waley, Biochem. J. 1991, 276, 269.
7. C. J. López, S. Oga, W. L. Hubbell, Biochemistry 2012, 51, 6568.
8. T. Nagae, T. Kawamura, L. M. G. Chavas, K. Niwa, M. Hasegawa, C. Kato, N. Watanabe, Acta Crystallogr., Sect. D 2012, 78, 300.
9. T. Imai, S. Ohyama, A. Kovalenko, F. Hirata, Protein Sci. 2007, 16, 1927.
10. S. M. Drawz, R. A. Bonomo, Clin. Microbiol. Rev. 2010, 160.
11. O. Trott, A. J. Olson, J. Comput. Chem. 2010, 31, 455.
12. B. Wladkowski, J. N. Sanders, M. Krauss, W. J. Stevens, J. Am. Chem. Soc. 1997, 119, 6423.
13. H. Xu, S. Hazra, J. S. Blanchard, Biochemistry 2012, 41, 4551.
14. C. Michaux, P. Charlier, J.-M. Frère, J. Wouters, J. Am. Chem. Soc. 2005, 127, 3262.
15. H. Frase, C. A. Smith, M. Toth, M. M. Champion, S. Mobashery, S. B. Vakulenko, J. Biol. Chem. 2011, 286, 14396.
16. P. Swarén, L. Maveyraud, V. Guillet, J.-M. Masson, L. Monrey, J.-P. Sanama, Structure 1995, 3, 603.
17. G. L. Patrick, 'An Introduction to Medicinal Chemistry', University Press, Oxford, 1995, p. 190.
18. E. Vanquelef, S. Simon, G. Marquant, E. Garcia, G. Klimerak, J. C. Delepine, P. Cieplak, F.-Y. Dupradeau, Nucleic Acids Res. 2011, 39, W511.
19. A. G. Brown, Pure Appl. Chem. 1987, 59, 475.
20. R. A. Powers, F. Morandi, B. K. Shoichet, Structure 2002, 10, 1013.
21. F. Pietra, Chem. Biodiversity 2012, 9, 331.
22. M. D'Ambrosio, A. Guerriero, M. Ripamonti, C. Debitus, J. Waikedre, F. Pietra, Helv. Chim. Acta 1996, 79, 727.
23. D.-H. Li, S.-X.Cai, L. Tian , Z.-J. Lin, T.-J. Zhu, Y.-C. Fang, P.-P. Liu, Q.-Q. Gu, W.-M. Zhu, Arch. Pharmacal Res. 2007, 30, 1051.
24. D. Li, F. Wang, X. Zeng, Q.-Q. Gu, W. Zhu, Arch. Pharmacal Res. 2007, 30, 552.
25. M. D'Ambrosio, A. Guerriero, F. Pietra, Helv. Chim. Acta 1987, 70, 2019.
26. C. Battistini, M. Ciomei, F. Pietra, M. D-Ambrosio, A. Guerriero, to Pharmacia & Upjohn, PPC Italy, Nerviano, US Pat. 5,869,514, February 9, 1999; priority GB 9509888.5, May 16, 1995.
27. 'Frontiers in Marine Biotechnology', Eds. P. Proksch,W. E. G. Müller, Horizon Bioscience, Norfolk, 2006.
28. W. Fenical, Planta Med. 2012, 78, IL14.
29. C.-F. Kim, S. K. Y. Lee, J. Price, R.W. Jack, G. Turner, R. Y. C. Kong, Appl. Environ. Microbiol. 2003, 69, 1308.
30. D. A. Case, T. E. Cheatham III, T. Darden, H. Gohlke, R. Luo, K. M. Merz Jr., A. Onufriev, C. Simmerling, B. Wang, R. Woods, J. Comput. Chem. 2005, 26, 1668.
31. G. M. Bradbrook, T. Gleichmann, S. J. Harrop, J. Habash, J. Raftery, J. Kalb (Gilboa), J. Yariv, I. H. Hillier, J. R. Helliwell, J. Chem. Soc., Faraday Trans. 1998, 94, 1603.
32. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kalé, K. Schulten, J. Comput. Chem. 2005, 26,1781.
33. W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graphics 1996, 14, 33.
34. K. Gilbert, PCMODEL, Molecular Modeling Software, Version 9.1, Serena Software, Bloomington, USA, 2006.
35. E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, T. E. Ferrin, J. Comput. Chem. 2004, 25, 1605.