Internal Diffusion-Controlled Enzyme Reaction: The Acetylcholinesterase Kinetics.

Area of Science:

• Biochemistry
• Enzymology
• Computational Biology

Background:

• Acetylcholinesterase is a crucial enzyme with a high turnover rate, responsible for hydrolyzing the neurotransmitter acetylcholine at the synapse.
• Understanding the precise mechanisms governing enzyme kinetics, especially at the active site, is vital for drug development and biological research.

Purpose of the Study:

• To investigate the kinetics of acetylcholinesterase by calculating the substrate diffusion rate within the enzyme's active site channel.
• To determine if internal substrate diffusion is a rate-limiting step in acetylcholinesterase catalysis, particularly at low substrate concentrations.

Main Methods:

• Atomic-level molecular dynamics simulations were employed to model the enzyme-substrate interactions.
• The diffusion rate of the substrate molecule along the active site channel was calculated.

Main Results:

• Internal substrate diffusion was identified as the rate-determining factor for acetylcholinesterase kinetics in the low substrate concentration regime.
• The calculated bimolecular reaction rate constant closely matched experimental values.
• The model provided explanations for observed effects of solution ionic strength and surface residue mutations on enzyme activity.

Conclusions:

• Substrate diffusion within the enzyme's active site channel plays a critical role in determining acetylcholinesterase kinetics.
• This finding challenges previous assumptions and highlights the importance of internal molecular transport in enzyme catalysis.
• The study suggests that internal diffusion is a key factor for understanding similar enzymes.