Insight into substrate preference of two chimeric esterases by combining experiment and molecular simulation

Abstract

Better understanding of the relationship between the substrate preference and structural module of esterases is helpful to novel enzyme development. For this purpose, two chimeric esterases AAM7 and PAR, constructed via domain swapping between two ancient thermophilic esterases, were investigated on their molecular simulation(including homology modeling, substrates docking and substrate binding affinity validation) and enzymatic assay(specific activities and activation energies calculating). Our results indicate that the factors contributing to the substrate preference of many enzymes especially the broad-specificity enzymes like esterases are multiple and complicated, the substrate binding domains or binding pockets are important but not the only factor for substrate preference.

Keywords

Substrate preference / Docking / Chimeric enzyme / Thermophilic esterase

References

[1] Bornscheuer U T. Curr. Opin. Biotechnol., 2002, 13: 543.

[2] Panda T, Gowrishankar B S. Appl. Micorbiol. Biotechnol., 2005, 67: 160.

[3] Osterlund T. Eur. J. Biochem., 2001, 268: 1899.

[4] Bornscheuer U T, Bessler C, Srinivas R, Krishna S H. Trends Biotechnol., 2002, 20: 433.

[5] Nardini M, Dijkstra B W. Curr. Opin. Struct. Biol., 1999, 9: 732.

[6] Holmquist M. Curr. Protein Pept. Sci., 2000, 1: 209.

[7] Manco G, Giosuè E, D’Auria S, Herman P, Carrea G, Rossi M. Arch. Biochem. Biophys., 2000, 373: 182.

[8] Gao R, Feng Y, Ishikawa K, Ishida H, Ando S, Kosugi Y, Cao S. J. Mol. Catal. B, Enzym., 2003, 24: 1.

[9] de Simone G, Menchise V, Manco G, Mandrich L, Sorrentino N, Lang D, Rossi M, Pedone C. J. Mol. Biol., 2001, 314: 507.

[10] Bartlam M, Wang G, Yang H, Gao R, Zhao X, Xie G, Cao S, Feng Y, Rao Z. Structure, 2004, 12: 1481.

[11] Tao J, Zhao B, Tian X, Zheng L, Cao S. Chem. Res. Chinese Universities, 2010, 26(5): 816.

[12] Thompson J D, Higgins D G, Gibson T J. Nucleic Acids Res., 1994, 22: 4673.

[13] DeLano W L. The PyMOL Molecular Graphics System (Version 1.5.0.4 Schrodinger, LLC), 2002.

[14] Eswar N, Webb B, Marti-Renom M A, Madhusudhan M S, Eramian D, Shen M Y, Pieper U, Sali A. Curr. Protoc. Protein Sci., Chapter 2, Unit 2.9, 2007, New York: John Wiley & Sons, Inc.

[15] Laskowski R A, MacArthur M W, Moss D S, Thornton J M. J. App. Cryst., 1993, 26: 283.

[16] Wang Y, Wang Y, Han W, Feng Y. Chem. Res. Chinese Universities, 2012, 28(4): 707.

[17] Huey R, Morris G M, Olson A J, Goodsell D S. J. Comput. Chem., 2007, 28: 1145.

[18] Morris G M, Huey R, Lindstrom W, Sanner M F, Belew R K, Goodsell D S, Olson A J. J. Comput. Chem., 2009, 30: 2785.

[19] Morris G M, Goodsell D S, Halliday R S, Huey R, Hart W E, Belew R K, Olson A J. J. Comput. Chem., 1998, 19: 1639.

[20] Yang G, Bai A, Gao L, Feng Y. Biochim. Biophys. Acta, 2009, 1794: 94.

[21] Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J. Nucleic Acids Res., 2006, 34: W116.

[22] Zhou X, Wang H, Zhang Y, Gao L, Feng Y. Acta Biochim. Biophys. Sin., 2012, 44: 965.