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Related Concept Videos

Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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...
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...
Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild...

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Steady-state, Pre-steady-state, and Single-turnover Kinetic Measurement for DNA Glycosylase Activity
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Published on: August 19, 2013

Cooperativity and specificity in enzyme kinetics: a single-molecule time-based perspective.

Hong Qian1

  • 1Department of Applied Mathematics, University of Washington, Seattle, Washington, USA. qian@amath.washington.edu

Biophysical Journal
|April 29, 2008
PubMed
Summary

This study introduces a novel theoretical framework for enzyme kinetics, focusing on a "time perspective" crucial for single-molecule enzymology. It explains cooperative substrate binding in enzymes by considering stochastic pathways over time.

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Steady-state, Pre-steady-state, and Single-turnover Kinetic Measurement for DNA Glycosylase Activity
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Published on: August 19, 2013

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Area of Science:

  • Biochemistry
  • Chemical Kinetics
  • Single-Molecule Biophysics

Background:

  • Traditional enzyme kinetics primarily uses a rate perspective.
  • Understanding enzyme behavior at the single-molecule level requires new theoretical approaches.
  • Cellular enzymatic reactions involve small enzyme copy numbers and nonequilibrium steady states.

Purpose of the Study:

  • To present an alternative theoretical approach to enzyme kinetics applicable to single-molecule enzymology.
  • To reframe enzyme kinetics from a
  • time perspective
  • emphasizing nonequilibrium steady states and small enzyme copy numbers.
  • To explain sigmoidal cooperative substrate binding in monomeric enzymes.

Main Methods:

  • Development of a theoretical framework based on a
  • time perspective
  • for enzyme kinetics.
  • Analysis of stochastic pathways and passage times for enzyme-substrate interactions.
  • Integration of dynamic cooperativity and kinetic proofreading mechanisms.

Main Results:

  • The new theory explains sigmoidal cooperative substrate binding through low-probability, long-passage-time pathways.
  • It highlights that single enzymes traverse pathways sequentially rather than in parallel.
  • The approach unifies dynamic cooperativity and kinetic proofreading for enhanced specificity.

Conclusions:

  • The
  • time perspective
  • offers a valuable alternative for understanding enzyme kinetics, especially in single-molecule studies.
  • This framework accounts for phenomena like sigmoidal binding that are overlooked by traditional rate-based models.
  • The theory provides a unified view of cooperativity and specificity amplification in enzymatic reactions.