Structure and dynamics of cold-adapted enzymes as investigated by FT-IR spectroscopy and MD. the case of an esterase from Pseudoalteromonas haloplanktis

Journal of Physical Chemistry B

Volumn 113, Issue 22, 2009, Pages 7753-7761

  Aurilia, Vincenzo ^a   Rioux Dubé, Jean François ^b   Marabotti, Anna ^c   Pézolet, Michel ^b   D'Auria, Sabato ^a  

^a INSTITUTE OF PROTEIN BIOCHEMISTRY   (Italy)

^b UNIVERSITÉ LAVAL   (Canada)

^c CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSTS; DYNAMICS; FOURIER TRANSFORM INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; SPECTROSCOPIC ANALYSIS;

ACTIVE SITE; CATALYTIC EFFICIENCIES; DIMERIC STRUCTURE; ENZYME STABILITY; FTIR SPECTROSCOPY; LOW TEMPERATURES; MOLECULAR DYNAMICS SIMULATIONS; PROTEIN FUNCTIONS; PROTEIN SEGMENTS; PSEUDOALTEROMONAS HALOPLANKTIS; STRUCTURAL ELEMENTS; STRUCTURE AND DYNAMICS;

ENZYMES;

EID: 66549117516     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp901921r     Document Type: Article

References (40)

1. Stetter, K. O.; Fiala, G.; Huber, R.; Huber, A.; Segerer, A. FEMS Microbiol. Lett. 1990, 75, 117.
2. Van den Burg, B.; Vriend, G.; Veltman, O. R.; Venema, G.; Eijsink, V. G. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 2056.
3. Kraut, J. Science 1988, 242, 533.
4. Goldman., A. Structure 1995, 3, 1277.
5. Yip, K. S.; Stillman, T. J.; Britton, K. L.; Artymiuk, P. J.; Baker, P. J.; Sedelnikova, S. E.; Engel, P. C.; Pasquo, A.; Chiaraluce, R.; Consalvi, V.; Scandurra, R.; Rice, D. W. Strucutre 1995, 3, 1147.
6. Tang, K. E.; Dill, K. A. J. Biomol. Struct. Dyn. 1998, 16, 397.
7. Aurilia, V.; Parracino, A.; Saviano, M.; Rossi, M.; D'Auria, S. Gene 2007, 397, 51.
8. Médigue, C.; et al. Genome Res. 2005, 15, 1325.
9. Griffiths, P. R.; Pariente. G. L. Typids Anal. Chem. 1986. 5, 209.
10. Sali, A.; Blundell, T. L. J. Mol. Biol. 1993, 234, 779.
11. Legler, P. M.; Kumaran, D.; Swaminathan, S.; Studier, F. W.; Millard, C. B. 2008, 47, 9592.
12. Berman, H.; Henrick, K.; Nakamura, H.; Markley, J. L. Nucleic Acids Res. 2007, 35 (Database Issue), D301.
13. Altschul, S. F.; Madden, T. L.; Schaffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Nucleic Acids Res. 1997, 25, 3389.
14. Karplus, K.; Karchin, R.; Draper, J.; Casper, J.; Mandel-Gutfreund, Y.; Diekhans, M.; Hughey, R. Proteins 2003, 53 (Suppl. 6), 491.
15. Shi, J.; Blundell, T. L.; Mizuguchi, K. J. Mol. Biol. 2001, 310, 243.
16. The UniProt Consortium. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res. 2009, 37 (Database Issue), D169.
17. Notredame, C.; Higgins, D. G.; Higgins, J. J. Mol. Biol. 2000, 302, 205.
18. Rost, B.; Yachdav, G.; Liu, J. Nucleic Acids Res. 2004, 32 (Web Server Issue), W321.
19. Kabsch, W.; Sander, C. Biopolymersers 1983, 22, 2577.
20. Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. J. Appl. Crystallogr. 1993, 26, 283.
21. Sippl, M. Proteins 1993, 17, 355.
22. Lindahl, E.; Hess, B.; van. der Spoel, D. J. Mol. Model. 2001, 7, 306.
23. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. J. Comput. Chem. 2005, 26, 170.1.
24. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hunenberger, P. H.; Kruger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; vdf Hochschulverlag AG an der ETH Zurich;: Zurich, Switzerland, 1996; p 1042.
25. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Interaction models for water in relation to protein hydration. In lntermolecular Forces; Pullman, B., Ed.; D. Reidel Publishing Company: Dordrecht, The Netherlands, 1981; p 331.
26. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463.
27. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Di Nola, A.; Haak, J. R. Chem. Phys. 1984, 81, 3684.
28. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
29. McDonald, I. K.; Thornton, J. M. J. Mol. Biol, 1994, 238, 111.
30. Kumar, S.; Nussinov, R. J. Mol. Biol. 1999, 293, 1241.
31. Krimm, S.; Bandekar, J. ¿¿p. Protein Chem. 1986, 38, 181.
32. Byler, D. M.; Susi, H. Biopolymers 1986, 25, 469.
33. Surewicz. W. K.; Mantsch, H. H. Biochim. Biophys. Acta 1988, 952, 115.
34. Goormaghtigh, E.; Cabiaux, V.; Ruysschaeit, J. M. Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy. III. Secondary structures. In Physicochemical Methods in the Study of Biomembranes; Subcellular Biochemistry Series; Hilderson, H. J., Ralstion, G. B., Eds.; Plenum Press: New York, 1994; Vol. 23, p 450.
35. Alterio, V.; Aurilia, V.; Parracino, A.; Saviano, M.; Pedone, C.; Rossi, M.; D'Auria, S.; De Simone, G.Presented at the First Meeting of the Italian and Spanish Crystallographic Associations (MISCA) Copanello di Stalettì, Italy, Sep 24-28, 2006.
36. Aurilia, V.; Parracino, A.; D'Auria, S. Gene 2008, 410, 234.
37. Timasheff, S. N.; Susi, H.; Stevens, L. J. Biol. Chem. 1967, 242, 5467.
38. Clark, A. H.; Saunderson, D. H.; Suggett, A. Int. J. Pept. Protein Res. 1981, 17, 353.
39. Muga, A.; Surewicz, W. K.; Wong, P. T.; Mantsch, H. H. Biochemistry 1990, 29, 2925.
40. Jackson, M.; Mantsch, H. H. Biochim. Phys. Acta 1992, 1118, 139.