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Related Concept Videos

Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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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...
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Ligand Binding and Linkage00:49

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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Introduction to Mechanisms of Enzyme Catalysis01:13

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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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Allosteric Proteins-ATCase01:19

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Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
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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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Allosteric Regulation01:08

Allosteric Regulation

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Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
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Related Experiment Video

Updated: Sep 15, 2025

Bio-layer Interferometry for Measuring Kinetics of Protein-protein Interactions and Allosteric Ligand Effects
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Substrate binding and channeling allosterically modulate the interactions within the AlkB-AlkG electron transfer

Karolina Mikulska-Ruminska1, Matthew Licht2,3, Mehmed Z Ertem4

  • 1Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, PL87100 Torun, Poland.

Biorxiv : the Preprint Server for Biology
|July 16, 2025
PubMed
Summary

This study reveals how the AlkB-AlkG enzyme complex binds and processes alkane substrates, detailing a translocation pathway and enhanced electron transfer crucial for alcohol production.

Keywords:
Alkane monooxygenasedynamics diiron centerelectron transfermolecular dynamics simulationsubstrate translocation

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Area of Science:

  • Biochemistry
  • Enzymology
  • Structural Biology

Background:

  • The AlkB-AlkG complex catalyzes alkane hydroxylation to produce alcohols.
  • A recent cryo-EM study elucidated the structure of the *Fontimonas thermophila* AlkB-AlkG complex (FtAlkBG) with a dodecane (D12) substrate.
  • The molecular mechanism of FtAlkBG remains largely unknown.

Purpose of the Study:

  • To investigate the dynamics and interactions within the FtAlkBG complex.
  • To elucidate the molecular mechanism of alkane hydroxylation by FtAlkBG.
  • To identify key sites for engineering improved AlkB variants.

Main Methods:

  • Multiscale computations, including molecular dynamics (MD) simulations.
  • Elastic network model (ENM) analysis.
  • Quantum mechanics/molecular mechanics (QM/MM) study of the catalytic site.

Main Results:

  • Dodecane (D12) remained stably bound in the active site, stabilized by hydrophobic residues.
  • A defined translocation pathway for D12 exit and re-entry was identified.
  • Substrate binding enhanced AlkB-AlkG contacts and electron transfer efficiency.
  • ENM analysis revealed allosteric regulation of substrate channeling and enzymatic activity.

Conclusions:

  • Substrate binding and channeling are critical for FtAlkBG function.
  • Key residues and interactions involved in substrate binding and electron transfer were identified.
  • The findings provide targets for developing novel AlkB variants for alkane conversion.