Molecular modeling and its experimental verification for the catalytic mechanism of Candida antartica lipase B

Cheong Hoon Kwon, Dae Young Shin, Jong H. Lee, Seung Wook Kim, Jeong Won Kang

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Quantum mechanical and molecular dynamics simulation analysis has been performed on the model system for CALB (Candida antarctica lipase B) with esters to study the reaction mechanism and conformational preference of catalytic hydrolysis and the esterification reaction. Using quantum mechanical analysis, the ping-pong bi-bi mechanism was applied and energies and 3-dimensional binding configurations of the whole reaction pathways were calculated. Further molecular dynamics simulation analysis was performed on the basis of the transition state obtained from quantum mechanical study to observe the effect of structures of the substrates. Calculation results using substrates of different chain length and chiral configurations were compared for conformational preference. The calculated results showed very small influence on chain length, whereas chiral conformation showed big differences. Calculated results from molecular modeling studies have been compared qualitatively with the experimental data using racemic mixtures of (±)-cis-4-acetamido-cyclopent-2-ene-1-ethyl acetate as substrates.

Original languageEnglish
Pages (from-to)1098-1105
Number of pages8
JournalJournal of Microbiology and Biotechnology
Volume17
Issue number7
Publication statusPublished - 2007 Jul 1

Fingerprint

Molecular modeling
Candida
Lipases
Molecular Dynamics Simulation
Lipase
Chain length
Molecular dynamics
Esterification
Substrates
Esters
Hydrolysis
Computer simulation
Conformations
ethyl acetate
Candida antarctica lipase B
cyclodrine

Keywords

  • Candida antartica lipase B
  • Enantiomer
  • Molecular dynamics simulation
  • Molecular modeling
  • Quantum mechanics
  • Reaction mechanism

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Microbiology

Cite this

Molecular modeling and its experimental verification for the catalytic mechanism of Candida antartica lipase B. / Kwon, Cheong Hoon; Shin, Dae Young; Lee, Jong H.; Kim, Seung Wook; Kang, Jeong Won.

In: Journal of Microbiology and Biotechnology, Vol. 17, No. 7, 01.07.2007, p. 1098-1105.

Research output: Contribution to journalArticle

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AU - Kang, Jeong Won

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AB - Quantum mechanical and molecular dynamics simulation analysis has been performed on the model system for CALB (Candida antarctica lipase B) with esters to study the reaction mechanism and conformational preference of catalytic hydrolysis and the esterification reaction. Using quantum mechanical analysis, the ping-pong bi-bi mechanism was applied and energies and 3-dimensional binding configurations of the whole reaction pathways were calculated. Further molecular dynamics simulation analysis was performed on the basis of the transition state obtained from quantum mechanical study to observe the effect of structures of the substrates. Calculation results using substrates of different chain length and chiral configurations were compared for conformational preference. The calculated results showed very small influence on chain length, whereas chiral conformation showed big differences. Calculated results from molecular modeling studies have been compared qualitatively with the experimental data using racemic mixtures of (±)-cis-4-acetamido-cyclopent-2-ene-1-ethyl acetate as substrates.

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