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, Yoshihiro Kawahara, Atsuko Ochi, Shigeru Muta, Shunsuke Kawamura, Takao Torikata, Satoru Kuhara

Research output: Contribution to journalArticle

3 Citations (Scopus)

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, Glyl02, 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.

Original languageEnglish
Pages (from-to)221-227
Number of pages7
JournalJournal of biochemistry
Volume140
Issue number2
DOIs
Publication statusPublished - Aug 1 2006

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Egg White
Acetylglucosamine
Molecular Dynamics Simulation
Muramidase
Oligomers
Molecular dynamics
Amino Acids
Computer simulation
Substrates
Enzymes
hen egg lysozyme

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology

Cite this

Construction of enzyme-substrate complexes between hen egg-white lysozyme and N-acetyl-D-glucosamine hexamer by systematic conformational search and molecular dynamics simulation. / Hirakawa, Hideki; Kawahara, Yoshihiro; Ochi, Atsuko; Muta, Shigeru; Kawamura, Shunsuke; Torikata, Takao; Kuhara, Satoru.

In: Journal of biochemistry, Vol. 140, No. 2, 01.08.2006, p. 221-227.

Research output: Contribution to journalArticle

Hirakawa, Hideki ; Kawahara, Yoshihiro ; Ochi, Atsuko ; Muta, Shigeru ; Kawamura, Shunsuke ; Torikata, Takao ; Kuhara, Satoru. / Construction of enzyme-substrate complexes between hen egg-white lysozyme and N-acetyl-D-glucosamine hexamer by systematic conformational search and molecular dynamics simulation. In: Journal of biochemistry. 2006 ; Vol. 140, No. 2. pp. 221-227.
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AU - Ochi, Atsuko

AU - Muta, Shigeru

AU - Kawamura, Shunsuke

AU - Torikata, Takao

AU - Kuhara, Satoru

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