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Related Concept Videos

Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
Enzyme Kinetics01:19

Enzyme Kinetics

Enzymes speed up reactions by lowering the activation energy of the reactants. The speed at which the enzyme turns reactants into products is called the rate of reaction. Several factors impact the rate of reaction, including the number of available reactants. Enzyme kinetics is the study of how an enzyme changes the rate of a reaction.
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...
Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
Catalytically Perfect Enzymes01:07

Catalytically Perfect Enzymes

The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Nonlinear Pharmacokinetics: Michaelis-Menten Equation01:18

Nonlinear Pharmacokinetics: Michaelis-Menten Equation

The Michaelis–Menten equation is a fundamental model for describing capacity-limited kinetics in drug metabolism. It offers insights into the rate of decline of plasma drug concentration Cp over time, with Vmax and KM as pivotal parameters.
Vmax represents the maximum achievable process rate, while KM, known as the Michaelis constant, signifies the drug concentration at which the process rate reaches half its maximum. This relationship between Vmax, KM, and Cp gives rise to three distinct...

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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
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Published on: January 16, 2016

Mesoscopic dynamics of diffusion-influenced enzyme kinetics.

Jiang-Xing Chen1, Raymond Kapral

  • 1Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada. jchen@chem.utoronto.ca

The Journal of Chemical Physics
|February 2, 2011
PubMed
Summary

This study introduces a particle-based model for enzyme kinetics, revealing how diffusion impacts reaction dynamics and species concentrations through power-law behaviors. The findings illuminate enzyme cooperative effects and substrate rebinding, crucial for understanding complex biological processes.

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Area of Science:

  • Biophysics
  • Chemical Kinetics
  • Computational Biology

Background:

  • Enzyme kinetics are fundamental to biological processes.
  • Understanding the influence of diffusion and hydrodynamic interactions on enzyme activity is crucial.
  • Existing models often simplify or neglect these complex dynamic effects.

Purpose of the Study:

  • To develop a particle-based mesoscopic model for enzyme kinetics.
  • To investigate the impact of diffusion on reactive dynamics and species concentration evolution.
  • To explore cooperative effects and substrate rebinding phenomena.

Main Methods:

  • A hybrid molecular dynamics-multiparticle collision dynamics (MD-MPCD) scheme was employed.
  • Enzymes and complexes modeled as soft spherical particles; others as point particles.
  • Model ensures conservation laws and detailed balance for reversible reactions.

Main Results:

  • Diffusion leads to power-law behaviors in species concentrations (e.g., t(-1/2), t(-3/2)).
  • Observed monotonic and nonmonotonic product production rates.
  • Cooperative effects influence kinetics at high enzyme concentrations.
  • Substrate rebinding exhibits power-law or exponential lifetime distributions.

Conclusions:

  • The developed model accurately captures diffusion-influenced enzyme kinetics.
  • Findings highlight the significant role of hydrodynamic interactions and concentration effects.
  • The model provides a versatile platform for further investigations into enzyme dynamics.