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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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Updated: Dec 13, 2025

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
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On Monomeric and Multimeric Structures-Based Protein-Ligand Interactions.

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    Quaternary structure (QS) modeling reveals more accurate protein-ligand interactions than monomeric structure (MS). QS modeling is recommended for improved binding free energy and ligand conformations in drug discovery.

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    Area of Science:

    • Biochemistry
    • Structural Biology
    • Computational Chemistry

    Background:

    • Protein-ligand interactions are crucial for biological processes.
    • Template-based modeling often uses monomeric structures (MS), potentially missing quaternary structure (QS) binding information.

    Purpose of the Study:

    • To systematically compare protein-ligand interactions using both monomeric structure (MS) and quaternary structure (QS).
    • To evaluate the impact of using MS versus QS on binding free energy and docking accuracy.

    Main Methods:

    • Large-scale comparison of protein-ligand complexes.
    • Molecular docking experiments.
    • Binding free energy estimations.

    Main Results:

    • 18.6% of ligands interact with multiple protein chains in QS.
    • QS consistently shows lower binding free energy than MS for multi-chain interactions (95% of cases).
    • QS docking yields more accurate ligand conformations than MS in over 70% of multi-chain pocket complexes.

    Conclusions:

    • Quaternary structure (QS) provides more complete information for protein-ligand interaction studies than monomeric structure (MS).
    • Utilizing QS in modeling is encouraged for enhanced accuracy in predicting binding and conformations.
    • This study highlights the limitations of MS and advocates for QS-based approaches in drug discovery and structural biology.