Solvent-dependent gating motions of an extremophilic lipase from pseudomonas aeruginosa

Biochemistry

Volumn 51, Issue 31, 2012, Pages 6238-6245

  Johnson, Quentin R ^a,b   Nellas, Ricky B ^a,b   Shen, Tongye ^a,b  

^a UNIVERSITY OF TENNESSEE   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; COMPLEX SOLUTION; COMPLEX SOLVENT; CONFORMATIONAL DYNAMICS; CONFORMATIONAL SWITCHES; EXPLICIT SOLVENTS; INDUSTRIAL ENZYMES; MOLECULAR DYNAMICS SIMULATIONS; NON-AQUEOUS SOLVENTS; OPEN CONFORMATION; PSEUDOMONAS AERUGINOSA; SOLVENT SYSTEM; STRUCTURAL CHANGE;

BACTERIA; DYNAMICS; ENZYMES; HEXANE; INTERFACE STATES; MOLECULAR DYNAMICS; ORGANIC SOLVENTS; PROTEINS;

SOLVENTS;

BACTERIAL ENZYME; EXTREMOPHILIC LIPASE; HEXANE; ORGANIC SOLVENT TOLERANT ENZYME; SOLVENT; TRIACYLGLYCEROL LIPASE; UNCLASSIFIED DRUG; WATER;

AQUEOUS SOLUTION; ARTICLE; CHANNEL GATING; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN STABILITY; PROTEIN STRUCTURE; PSEUDOMONAS AERUGINOSA; SIMULATION;

ENZYME ACTIVATION; HEXANES; LIPASE; MODELS, MOLECULAR; MOVEMENT; PROTEIN STRUCTURE, SECONDARY; PSEUDOMONAS AERUGINOSA; SOLVENTS; WATER;

PSEUDOMONAS AERUGINOSA;

EID: 84864678581     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi300557y     Document Type: Article

References (41)

1. Fersht, A. (1999) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, W.H. Freeman, New York.
2. Klibanov, A. (2001) Improving enzymes by using them in organic solvents Nature 409, 241-246
3. Nicolas, J. P. (2003) Molecular dynamics simulation of surfactin molecules at the water-hexane interface Biophys. J. 85, 1377-1391
4. Jaeger, K.-E. and Scheidininger, B. (1997) Bacterial lipases for biotechnological applications Mol. Catal. 3, 3-12
5. Jaeger, K.-E., Dijkstra, B. W., and Reetz, M. T. (1999) Bacterial biocatalysts: Molecular biology, structure and biotechnological applications of lipases Annu. Rev. Microbiol. 53, 315-351
6. Ogino, H. (2008) in Protein Adaptation in Extremophiles (Siddiqui, K. S. and Thomas, T., Eds.) pp 193-236, Nova Biomedical, Waltham, MA.
7. Uttatree, S., Winayanuwattikun, P., and Charoenpanich, J. (2010) Isolation and characterization of a novel thermophilic-organic solvent stable lipase from Acinetobacter baylyi Appl. Biochem. Biotechnol. 162, 1362-1376
8. Theil, F. (1995) Lipase-supported synthesis of biologically active compounds Chem. Rev. 95, 2203-2227
9. Schrag, J. D. and Cygler, M. (1997) Lipases and alpha/beta hydrolase fold Methods Enzymol. 284, 85-107
10. Jaeger, K.-E., Ransac, S., Dijkstra, B. W., Colson, C., van Heuvel, M., and Misset, O. (1994) Bacterial Lipases FEMS Microbiol. Rev. 15, 29-63
11. Eltaweel, M. A., Rahman, R. N., Salleh, A. B., and Basri, M. (2005) An organic solvent-stable lipase from Bacillus sp. strain 42 Ann. Microb. 55, 187-192
12. Nardini, M. and Dijkstra, B. W. (1999) Alpha/beta hydrolase fold enzymes: The family keeps growing Curr. Opin. Struct. Biol. 9, 732-737
13. Gilbert, E. J. (1993) Pseudomonas lipases: Biochemical properties and molecular cloning Enzyme Microb. Technol. 15, 634-645
14. Trodler, P., Schmid, R., and Pleiss, J. (2009) Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase BMC Struct. Biol. 9, 1-13
15. Uppenberg, J., Hansen, M., Shamkant, P., and Jones, T. (1994) The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica Structure 2, 293-308
16. Nardini, M., Lang, D. A., Liebeton, K., Jaeger, K., and Dijkstra, B. W. (2000) Crystal structure of Pseudomonas aeruginosa lipase in the open conformation J. Biol. Chem. 275, 31219-31225
17. Lang, D., Hofmann, B., Haalck, L., Hecht, H.-J., Spener, F., Schmid, R. D., and Schomburg, D. (1996) Crystal structure of a bacterial lipase from Chromobacterium viscosum ATCC 6918 refined at 1.6 Å J. Mol. Biol. 259, 704-717
18. Kim, K. K., Song, H. K., Shin, D. H., Hwang, K. Y., and Suh, S. W. (1997) The crystal structure of a triacylglycerol lipase from Pseudomonas cepacia reveals a highly open conformation in the absence of a bound inhibitor Structure 5, 173-185
19. Tyndall, J. D. A., Sinchaikul, S., Fothergill-Gilmore, L. A., Taylor, P., and Walkinshaw, M. D. (2002) Crystal structure of a thermostable lipase from Bacillus stearothermophilus P1 J. Mol. Biol. 323, 859-869
20. Derewenda, U., Swenson, L., Wei, Y., Green, R., Kobos, P., Joerger, R., Haas, M., and Derewenda, Z. (1994) Conformational lability of lipases observed in the absence of an oil-water interface: Crystallographic studies of enzymes from the fungi Humicola lanuginosa and Rhizopus delemar J. Lipid Res. 35, 524-534
21. Matsumura, H., Yamamoto, T., Mori, T., and Salleh, A. (2007) Novel cation-pi interaction revealed by crystal structure of thermoalkalophilic lipase Proteins 70, 592-598
22. Cherukuvada, S., Seshasayee, A., Raghunathan, K., and Pennathur, G. (2005) Evidence of a double-lid movement in Pseudomonas aeruginosa lipase: Insights from molecular dynamics simulations PLoS Comput. Biol. 1, 182-189
23. Invernizzi, G., Papaleo, E., Grandori, R., and Lotti, M. (2009) Relevance of metal ions for lipase stability: Structural rearrangements induced in the Burkholderia glumae lipase by calcium depletion J. Struct. Biol. 168, 562-570
24. Branco, R., Graber, M., Denis, V., and Pleiss, J. (2009) Molecular mechanism of the hydration of Candida antarctica lipase B in the gas phase: Water adsorption isotherms and molecular dynamics simulations ChemBioChem 10, 2913-2919
25. Barbe, S., Lafaquiere, V., and Andre, I. (2009) Insights into lid movements of Burkholderia cepacia lipase inferred from molecular dynamics simulations Proteins: Struct., Funct., Bioinf. 77, 509-523
26. Hamid, T., Rahman, R., and Basri, M. (2009) The role of lid in protein-solvent interaction of the simulated solvent stable thermostable lipase from Bacillus strain 42 in water-solvent mixtures Biotechnol. Biotechnol. EQ. 23, 1524-1530
27. Karjiban, R., Rahman, M., and Wahab, H. (2009) Molecular dynamics study of the structure, flexibility and dynamics of thermostable L1 lipase at high temperatures Protein J. 28, 14-23
28. Karjiban, R., Rahman, M., and Chor, A. (2010) On the importance of the small domain in the thermostability of thermoalkalophilic lipases from L1 and T1: Insights from molecular dynamics simulation Protein Pept. Lett. 17, 1-9
29. Peters, G., Toxvaerd, S., and Svendsen, A. (1997) Computational studies of the activation of lipases and the effect of a hydrophobic environment Protein Eng. 10, 137-147
30. Jensen, M., Jensen, T., Kjaer, K., Bjornholm, T., Mouritsen, O. G., and Peters, G. H. (2002) Orientation and conformations of a lipase at an interface studied by molecualr dynamics Biophys. J. 83, 98-111
31. Ogino, H., Katou, Y., Akagi, R., Mimitsuka, T., Hiroshima, S., Gemba, Y., Doukyu, N., Yasuda, M., Ishimi, K., and Ishikawa, H. (2007) Cloning and expression of gene, and activation of an organic solvent-stable lipase from Pseudomonas aeruginosa LST-03 Extremophiles 11, 809-17
32. Ogino, H., Nakagawa, S., Shinya, K., Muto, T., Fujimura, N., Yasuda, M., and Ishikawa, H. (2000) Purification and characterization of organic solvent-stable lipase from organic solvent-tolerant Pseudomonas aeruginosa LST-03 J. Biosci. Bioeng. 89, 451-457
33. Case, D. A., Darden, T. A., Cheatham, T. E. I., Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Crowly, M., Walker, R. C., Zhang, W., Merz, K. M., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kolossvry, I., Wong, K. F., Pasani, F., Vanicek, J., Wu, X., Brozell, S. R., Steinbrecher, T., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Mathews, D. H., Seetin, M. G., Sagui, C., Babin, V., and Kollman, P. A. (2008) Amber molecular dymnamics package, AMBER 10 University of California, San Francisco.
34. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79, 926-935
35. Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L., and Schulten, K. (2005) Scalable molecular dynamics with NAMD J. Comput. Chem. 26, 1781-1802
36. Smart, O., Neduvelil, J., Wang, X., Wallace, B., and Sansom, M. (1996) HOLE: A program for the analysis of the pore dimensions of ion channel structural models J. Mol. Graphics 14, 354-360
37. Lee, P. and Helms, V. (2012) Identifying continuous pores in protein structures with propores by computational repositioning of gating residues Proteins: Struct., Funct., Bioinformatics 80, 421-432
38. Xin, Y., Gadda, G., and Hamelberg, D. (2009) The cluster of hydrophobic residues controls the entrance to the active site of choline oxidase Biochemistry 48, 9599-9605
39. Johnson, Q., Doshi, U., Shen, T., and Hamelberg, D. (2010) Water's contribution to the energetic roughness from peptide dynamics J. Chem. Theory Comput. 6, 2591-2597
40. Yennawar, N. H., Yennawar, H. P., and Farber, G. K. (1994) X-ray crystal structure of gamma-chymotrypsin in hexane Biochemistry 33, 7326-7336
41. Breslow, R. (1991) Hydrophobic effects on simple organic reactions in water Acc. Chem. Res. 24, 159-164