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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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Modulating binding affinity, specificity, and configurations by multivalent interactions.

Yunxin Deng1, Artem K Efremov1, Jie Yan2

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Multivalent interactions involving proteins with multiple domains significantly enhance binding affinity and specificity. This study reveals how these interactions regulate cellular processes like signal transduction and gene transcription.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biophysics

Background:

  • Protein functions depend on specific interactions with binding partners.
  • Multidomain proteins engage in multivalent interactions with multi-site targets.
  • The role of multivalent interactions in modulating binding affinity and specificity is established, but other effects are less explored.

Purpose of the Study:

  • To investigate the effects of multivalent interactions using a transfer-matrix formalism.
  • To analyze the binding of two-domain ligands to targets with multiple binding sites.
  • To explore how multivalent interactions influence binding affinity, specificity, and cellular processes.

Main Methods:

  • Development of a broadly applicable transfer-matrix formalism.
  • Computational investigation of two-domain ligand binding to multi-site targets.
  • Analysis of binding affinity, specificity, and concentration-dependent configurations.

Main Results:

  • Two-domain ligands significantly boost binding affinity and specificity compared to single-domain ligands.
  • Domain-domain cooperativity or nonspecific binding domains lower the working concentration range by increasing affinity without sacrificing specificity.
  • Bound ligand configuration exhibits strong concentration dependence, offering insights into cellular phase separation.

Conclusions:

  • Multivalent interactions are critical for efficient regulation of protein-target binding in cells.
  • These interactions play a key role in diverse cellular processes, including signal transduction, gene transcription, and antibody-antigen recognition.
  • The findings provide a framework for understanding the physical basis of multivalent interactions in biological systems.