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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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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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Solvents01:12

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A solvent is a substance, most often a liquid, that can dissolve other substances. Here, the substance being dissolved is called a solute. When a solvent and a solute combine, they form a solution - a homogenous mixture of both the solvent and the solute. Water is a universal biological solvent. Its polar structure allows it to dissolve many other polar compounds. The ability of water to dissolve is governed by a balance between water molecules binding to each other and binding to the solute.
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Switching of BJT01:22

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Switching behavior in Bipolar Junction Transistors (BJTs) is a fundamental aspect utilized in various electronic circuits, particularly for digital logic applications like switches and amplifiers. In a typical switching circuit, a BJT alternates between cut-off and saturation modes, corresponding to the "off" and "on" states, respectively, thus behaving like an ideal switch.
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Related Experiment Video

Updated: Jan 29, 2026

A Kinetic Fluorescence-based Ca2+ Mobilization Assay to Identify G Protein-coupled Receptor Agonists, Antagonists, and Allosteric Modulators
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Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling.

Justin R Porter1, Katelyn E Moeder1, Carrie A Sibbald1

  • 1Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri.

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|February 13, 2019
PubMed
Summary

A new method identifies functional protein changes by analyzing shifts in residue solvent exposure, termed exposons. This approach successfully predicts allosteric sites in antibiotic resistance enzymes.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Proteins exist in dynamic conformational states, but low populations hinder structural and functional analysis.
  • Computer simulations aid in identifying functionally relevant protein states, yet analyzing large datasets remains challenging.

Purpose of the Study:

  • To develop a method for identifying functionally relevant protein conformational changes from simulation data.
  • To prioritize conformational changes based on cooperative alterations in residue solvent exposure.

Main Methods:

  • Introduced a method to segment protein structures into clusters of residues with cooperative changes in solvent exposure (exposons).
  • Analyzed the hierarchy of interactions between these exposon clusters.
  • Applied the method to model systems and beta-lactamase enzymes.

Main Results:

  • The exposon method identified experimentally validated conformational changes, including switches, allosteric coupling, and cryptic pockets.
  • Key functional sites were found to be hubs in the exposon network.
  • Predicted and experimentally confirmed cryptic allosteric sites in CTX-M-9 and TEM-1 beta-lactamases, with one site showing potent allosteric control.

Conclusions:

  • Exposons provide a powerful way to identify functionally significant protein dynamics and allosteric sites.
  • The method has significant implications for understanding protein function and discovering novel drug targets, particularly in antibiotic resistance.