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Journal of Biochemistry Advance Access published online on July 6, 2006
Journal of Biochemistry, doi:10.1093/jb/mvj142
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© 2006 The Japanese Biochemical Society.
Received May 11, 2006
Accepted June 7, 2006

Regular Paper

Construction of Enzyme-Substrate Complexes between Hen Egg-White Lysozyme and N-Acetyl-D-Glucosamine Hexamer by Systematic Conformational Search and Molecular Dynamics Simulation

Hideki Hirakawa 1, Yoshihiro Kawahara 2, Atsuko Ochi 2, Shigeru Muta 2, Shunsuke Kawamura 3, Takao Torikata 3, and Satoru Kuhara 4 *

1 Graduate School of Systems Life Sciences, Kyushu University, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
2 Graduate School of Genetic Resource Technology, Kyushu University, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
3 Department of Bioscience, School of Agriculture, Kyushu Tokai University, Aso, Kumamoto 869-1404, Japan
4 Graduate School of Systems Life Sciences, Kyushu University, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan; Graduate School of Genetic Resource Technology, Kyushu University, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan

* To whom correspondence should be addressed.
Satoru Kuhara, E-mail: kuhara{at}grt.kyushu-u.ac.jp


  Abstract

We constructed the complexes between HEWL and (GlcNAc)6 oligomer in order to investigate the amino acid residues related to substrate binding in the productive and nonproductive complexes, and the relationship between the distortion of the GlcNAc residue D and the formation of the productive complexes.

We obtained 49 HEWL-(GlcNAc)6 complexes by a systematic conformational search and classified the each one to the three binding modes; left side, center, or right side. Furthermore we performed the molecular dynamics simulation against 20 HEWL-(GlcNAc)6 complexes (8: chair model, 12: half-chair model) selected from the 49 complexes to investigate the interaction between HEWL and (GlcNAc)6. As results, we confirmed that it is necessary for GlcNAc residue D to be half-chaired form to bind toward the right side to form productive complexes. We found newly that eight amino acid residues interact with the (GlcNAc)6 oligomer, as follows, Arg73, Gly102, Asn103 for GlcNAc residue A; Asn103 for GlcNAc residues B and C; Leu56, Ala107, Val109 for GlcNAc residue D; Ala110 for GlcNAc residue E; and Lys33 for GlcNAc residue F. We also indicated that GlcNAc residue F does not interact with Thr47 and rarely interacts with Phe34 and Asn37.

Keywords: lysozyme; docking; structure of complex; systematic conformational search; molecular dynamics (MD) simulation.
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H. Hirakawa, A. Ochi, Y. Kawahara, S. Kawamura, T. Torikata, and S. Kuhara
Catalytic Reaction Mechanism of Goose Egg-white Lysozyme by Molecular Modelling of Enzyme-Substrate Complex
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[Abstract] [Full Text] [PDF]


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