Influence of structural fluctuation on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies

Yingkai Zhang, Jeremy Kua, J. Andrew McCammon

Research output: Contribution to journalArticle

Abstract

To account for protein dynamics and to investigate the effect of different conformations on the enzyme reaction energy barrier, we have studied the initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE) with a multiple QM/MM reaction path approach. The approach consists of two main components: generating enzyme-substrate conformations with classical molecular dynamics simulation and mapping out the minimum reaction energy path for each conformational snapshot with combined quantum mechanical/ molecular mechanical (QM/MM) calculations. It is found that enzyme-substrate conformation fluctuations lead to significant differences in the calculated reaction energy barrier; however, the qualitative picture of the role of the catalytic triad and oxyanion hole in AChE catalysis is very consistent. Our results emphasize the importance of employing multiple starting structures in the QM/MM study of enzyme reactions and indicate that structural fluctuation is an integral part of the enzyme reaction process.

Original languageEnglish (US)
Pages (from-to)4459-4463
Number of pages5
JournalJournal of Physical Chemistry B
Volume107
Issue number18
StatePublished - May 8 2003

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Energy barriers
enzymes
Enzymes
Conformations
Acetylcholinesterase
energy
Acylation
Substrates
Catalysis
acylation
Molecular dynamics
Proteins
catalysis
Computer simulation
molecular dynamics
proteins

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Influence of structural fluctuation on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies. / Zhang, Yingkai; Kua, Jeremy; McCammon, J. Andrew.

In: Journal of Physical Chemistry B, Vol. 107, No. 18, 08.05.2003, p. 4459-4463.

Research output: Contribution to journalArticle

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