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Related Concept Videos

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...
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...
Enzymes02:34

Enzymes

Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Induced-fit Model01:13

Induced-fit Model

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...
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 Enzymes01:22

Introduction to Enzymes

The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that bind the substrates and convert them into products. Many enzymes also...

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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

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Published on: January 16, 2016

Resolving the complex role of enzyme conformational dynamics in catalytic function.

Urmi Doshi1, Lauren C McGowan, Safieh Tork Ladani

  • 1Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-4098, USA.

Proceedings of the National Academy of Sciences of the United States of America
|March 28, 2012
PubMed
Summary

Enzyme conformational dynamics (ECD) significantly impact catalysis by influencing reaction rates. This study reveals ECD alters the diffusion coefficient, affecting enzyme catalysis and confirming transition state stabilization as key to rate enhancement.

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Area of Science:

  • Biochemistry
  • Enzymology
  • Computational Chemistry

Background:

  • Enzyme conformational dynamics (ECD) are crucial for catalysis, but their precise role in reaction rates remains debated.
  • Cyclophilin A (CypA), a peptidyl-prolyl cis-trans isomerase, serves as a model for studying enzyme-substrate interactions and catalytic mechanisms.

Purpose of the Study:

  • To characterize enzyme conformational dynamics (ECD) in Cyclophilin A (CypA).
  • To elucidate how ECD influences the chemical step and reaction rates during isomerization.
  • To provide an atomistic perspective on the role of ECD in enzyme catalysis.

Main Methods:

  • Atomistic molecular dynamics simulations (normal and accelerated) were employed to study ECD in CypA.
  • Kinetics and free energy landscapes of isomerization were explored in solution and enzyme environments.
  • Kramers' rate theory was applied to analyze the impact of ECD on reaction dynamics.

Main Results:

  • Reaction dynamics are intricately coupled to enzymatic motions across multiple timescales.
  • Enzyme modes are selected based on the energy barrier of the chemical step.
  • ECD slows the effective diffusion coefficient by approximately tenfold in the enzyme compared to solution, impacting the preexponential factor.

Conclusions:

  • Enzyme conformational dynamics (ECD) play a significant role in modulating catalytic rates by altering the diffusion coefficient.
  • Transition state stabilization is confirmed as a primary mechanism for catalytic rate enhancement.
  • This study offers a unified, atomistic view of ECD's contribution to enzyme catalysis, aligning with experimental observations.