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http://dx.doi.org/10.5808/GI.2011.9.2.79

Analysis of the Structure-stability Relationship of Cold-adapted Lipase PsLip1 from Homology Modeling  

Choo, Dong-Won (Department of Bioinformatics, Korea Bio-Polytechnic)
Abstract
Two initial models of cold-adapted lipase PsLip1 have been constructed, based on homology with the bacterial lipases Chromobacterium viscosum (CvLip) and Pseudomonas cepacia (PcLip), whose X-ray structures have been solved and refined to high resolution. The mature polypeptide chains of these lipases have 84% similarity. The models of Mod1 and Mod2 have been compared with the tertiary structures of CvLip and PcLip, respectively, and analyzed in terms of stabilizing interactions. Several structural aspects that are believed to contribute to protein stability have been compared: the number of conserved salt bridges, aromatic interactions, hydrogen bonds, helix capping, and disulfide bridges. The 3-dimensional structural model of PsLip1 has been constructed in order to elucidate the structural reasons for the decreased thermostability of the enzyme in comparison with its mesophilic counterparts.
Keywords
cold-adapted lipase; thermostability; homology modeling;
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1 Sambrook, J., Fritsch, E.F., and Maniatis, T.C. (1989). Molecular cloning (New York: Cold Spring Harber Laboratory Press).
2 Suzuki, T., Nakayama, T., Choo, D.W., Hirano, Y., Kurihara, T., Nishino, T., and Esaki, N. (2003). Cloning, heterologous expression, renaturation, and characterization of a cold adapted esterase with unique primary structure from a psychrotroph Pseudomonas sp. strain B11-1. Protein Expr. Purif. 30, 171-178.   DOI
3 Tutino, M.L., di Prisco, G., Marino, G., and de Pascale, D. (2009). Cold-adapted esterase and lipase: from fundmentals to application. Protein Pept. Lett. 16, 1172-1180.   DOI
4 Vriend, G. (1990). WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8, 52-56.   DOI
5 Yip, K.S.P., Stillman, T.J., Britton, K.L., Artymiuk, P.J., Baker, P.J., Sedelnikova, S.E., Engel, P.C., Pasqua, A., Chiaraluce, R., Consalvi, V., Scandurra, R., and Rice, D.W. (1995). The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion pair networks in maintaining enzyme stability at extreme temperatures. Structure 3, 1147-1158.   DOI
6 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.   DOI
7 Korndorfer, I., Steipe, B., Huber, R., Tomschy, A., and Jaenicke, R. (1995). The crystal structure of holo-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima at 2.5 ${\AA}$ resolution. J. Mol. Biol. 246, 511-521.   DOI
8 Lang, D., Hoffmann, B., Haalck, L., Hecht, H.J., Spenner, F., Shimid, R.D., and Schmburg, D. (1996). Crystal structure of a bacterial lipase from Chromobacterium viscosum ATCC 6918 refined at 1.6 angstroms resolution. J. Mol. Biol. 259, 704-717.   DOI
9 Luthy , R., Bowie, J.U., and Einsenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature 356, 83-85.   DOI
10 Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291.   DOI
11 Morita, R.Y. (1975). Psychrophilic bacteria. Bacterial. Rev. 39, 144-167.
12 Prins, R.A., de Vriji, W., Gottschal, J.C., and Hansen, T.A. (1990). Adaptation of microorganisms to extreme environments. FEMS Microbiol. Rev. 75, 103-104.   DOI
13 Rost, B. and Sander, C. (1993). Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232, 584-599.   DOI
14 Russel, N.J. (1992). In Molecular biology and biotechnology of extremophiles. Herbert, R.A. and Sharp, R.J., eds. (Blackie), pp.203-224.
15 Russel, R.J.M., Hough, D.W., Danson, M.J., and Taylor, G.L. (1994). The crystal structure of citrate synthase from the thermophilic archaeon, Thermoplasma acidophilum. Structure 2, 1157-1167.   DOI
16 Hennig, M., Darimont, B., Sterner, R., Kirschner, K., and Jansonius, J.N. (1995). 2.0 ${\AA}$ structure of indole-3-glycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus: possible determinants of protein stability. Structure 3, 1295-1306.   DOI
17 Atlas, R.M. and Bartha, R. (1987). In Microbial Ecology : Fundamentals and Applications, 2nd edition , (Menlo Park, CK: Benjamin Cummings Publ. Comp. Inc), pp.233-262.
18 Feller, G., Thiry, M., Aspigny, J.L., Mergeay, M., and Gerday, C. (1990). Lipases from psychrotropic antarctic bacteria. FEMS Microbiol. Lett. 66, 239-244.   DOI
19 Fujinaga, M., Berthed-Colominas, C., Yaremchuck, A.D., Yukalo, M.A., and Cusack, S. (1993). Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 A resolution. J. Mol. Biol. 234, 222-233.   DOI
20 Joseph B., Ramteke P.W., and Thomas G. (2008). Cold active microbial lipases: some hot issues and recent developments. Biotechnol. Adv. 26, 457-470.   DOI