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Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

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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...
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Enzyme Kinetics01:19

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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.
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Catalytically Perfect Enzymes01:07

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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.
 
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Introduction to Enzyme Kinetics01:19

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Enzymes02:34

Enzymes

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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.
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Catalysis02:50

Catalysis

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The presence of a catalyst affects the rate of a chemical reaction. A catalyst is a substance that can increase the reaction rate without being consumed during the process. A basic comprehension of a catalysts’ role during chemical reactions can be understood from the concept of reaction mechanisms and energy diagrams.
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Related Experiment Video

Updated: Dec 31, 2025

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

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Elucidating Enzymatic Catalysis Using Fast Quantum Chemical Descriptors.

Igor Barden Grillo1, Gabriel A Urquiza-Carvalho2, José Fernando Ruggiero Bachega3

  • 1Department of Chemistry , Federal University of Paraíba , Cidade Universitária, João Pessoa , Paraíba 58051-085 , Brazil.

Journal of Chemical Information and Modeling
|January 3, 2020
PubMed
Summary

This study introduces reactivity descriptors to analyze enzymatic catalysis using low-level computational methods. These descriptors reveal how enzymes participate as reactants, aiding in predicting new catalytic mechanisms.

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Area of Science:

  • Computational chemistry
  • Biochemistry
  • Enzymology

Background:

  • Computational simulations of enzymatic catalysis typically require high-level methods for accurate energy values.
  • Existing methods focus on thermodynamic and structural aspects, complementing experimental studies.

Purpose of the Study:

  • To propose and validate the use of reactivity descriptors for characterizing enzymatic catalysis.
  • To outline enzymatic reaction profiles using low-level computational methods.
  • To explore enzyme participation as a reactant in catalysis.

Main Methods:

  • Calculation of reactivity descriptors from electronic structure using semiempirical Hamiltonians.
  • Simulation of three enzymatic reaction paths, including one with two reaction coordinates.
  • Analysis of local hardness, electrophilicity, and nucleophilicity along reaction coordinates.

Main Results:

  • Local hardness of the active site and stabilizing amino acid residues remained largely unchanged.
  • Abrupt changes in atomic electrophilicity and nucleophilicity were observed along reaction coordinates.
  • Findings support the role of the electrostatic environment in lowering activation energy.

Conclusions:

  • Reactivity descriptors provide a low-cost method to characterize enzymatic catalysis.
  • Enzymes actively participate as reactants in catalyzed reactions.
  • This approach facilitates the prediction of novel catalytic mechanisms and enzyme active site characterization.