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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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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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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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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.
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The Equilibrium Binding Constant and Binding Strength02:18

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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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Different Single-Enzyme Conformational Dynamics upon Binding Hydrolyzable or Nonhydrolyzable Ligands.

Sung Oh Woo1, Myungkeun Oh2, Lina Alhalhooly1

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Summary

Single-molecule studies reveal how lysozyme protein dynamics change with different ligands. Ligand type dictates whether lysozyme reaches its fully closed, catalytic state or stops at an intermediate conformation, impacting enzyme specificity.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Enzymology

Background:

  • Protein dynamics are crucial for understanding enzyme function, including ligand binding and catalysis.
  • Single-molecule measurements offer high resolution to study these dynamic processes.

Purpose of the Study:

  • To investigate conformational dynamics and transitions of lysozyme interacting with peptidoglycan, chitin analogue, and indole inhibitors using single-molecule nanocircuit techniques.
  • To elucidate the enzyme-ligand interplay governing molecular recognition, enzyme specificity, and catalysis.

Main Methods:

  • High-resolution single-molecule nanocircuit measurements.
  • Analysis of lysozyme conformational dynamics and transitions upon interaction with various ligands.

Main Results:

  • Lysozyme exhibits distinct conformational pathways depending on the ligand: a concerted or nonconcerted mechanism for peptidoglycan hydrolysis.
  • With chitin or indole inhibitors, lysozyme is blocked from reaching the fully closed catalytic conformation, stopping at intermediate 'excited' states.
  • Indole inhibition is a single-step process, while chitin interaction involves hidden intermediates similar to the nonconcerted peptidoglycan mechanism, suggesting accommodation of imperfect substrates.

Conclusions:

  • Enzyme-ligand interactions precisely control protein conformational dynamics, influencing catalytic activity and specificity.
  • The study provides detailed insights into the molecular recognition mechanisms underlying enzyme function.
  • Single-molecule techniques are powerful tools for dissecting complex enzymatic processes at the molecular level.