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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...
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...
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...
Evolutionary Processes in Microbes01:26

Evolutionary Processes in Microbes

Microbial evolution occurs rapidly due to short generation times and a variety of genetic processes, including horizontal gene transfer, mutation, recombination, and genetic drift. These mechanisms collectively enable microbes to adapt swiftly to changing environments.Horizontal gene transfer (HGT) allows genes to move between different species and occurs through three main mechanisms: conjugation, transformation, and transduction. Conjugation involves direct cell-to-cell contact for DNA...
Pharmacodynamic Models: Emax Drug–Concentration Effect Model01:18

Pharmacodynamic Models: Emax Drug–Concentration Effect Model

The Emax drug-concentration effect model is central to pharmacodynamics in drug discovery and development. This model is predicated on the receptor occupancy theory, which posits that the effect of a drug is directly related to the number of receptors occupied by the drug and the resultant complex formation.The model describes the reversible interaction between a drug (C) and a receptor (R) to form a drug-receptor complex (RC). The kinetics of this interaction are quantified by an equation that...

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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Modeling the complex dynamics of enzyme-pathway coevolution.

Moritz Schütte1, Alexander Skupin, Daniel Segrè

  • 1Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.

Chaos (Woodbury, N.Y.)
|January 5, 2011
PubMed
Summary
This summary is machine-generated.

This study models the coevolution of metabolic networks and enzyme genes. It reveals that enzymes evolve in bursts, not gradually, suggesting a punctuated equilibrium in biochemical evolution.

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Area of Science:

  • Biochemistry
  • Evolutionary Biology
  • Computational Biology

Background:

  • Metabolic pathways and enzyme gene sequences coevolve.
  • The evolutionary interplay between metabolic networks and genomes is not well understood.

Purpose of the Study:

  • To present a computational model for simulating the evolutionary dynamics of metabolic networks.
  • To investigate the patterns of enzyme and organism appearance during chemical evolution.

Main Methods:

  • Developed a computational model simulating parallel evolution of metabolic reactions and enzymes.
  • Expanded metabolic networks iteratively based on enzyme sequence similarity.
  • Monitored the appearance of metabolites, enzymes, and organisms over simulated time.

Main Results:

  • New enzymes appear in clusters corresponding to enzyme classes, not gradually.
  • The model exhibits biased random walks with long-range correlations, akin to punctuated equilibrium.
  • Detected a correlation between enzyme appearance time and enzyme repertoire size.

Conclusions:

  • A quantitative molecular principle may drive punctuated equilibrium in enzyme evolution.
  • The model provides insights into the rise of biochemical and genomic complexity.
  • Simulated evolutionary trends offer a putative timeline for enzyme and organism emergence.