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  3. Optimizing Stability In Dynamic Small-molecule Binding Proteins.
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  3. Optimizing Stability In Dynamic Small-molecule Binding Proteins.

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Optimizing Stability in Dynamic Small-Molecule Binding Proteins.

Marc Scherer1,2, Mark Kriegel1, Birte Höcker1

  • 1Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.

Journal of the American Chemical Society
|December 29, 2025

View abstract on PubMed

Summary
This summary is machine-generated.

Designing mutations compatible with both open and closed protein states enhances stability. This method stabilizes dynamic proteins, crucial for developing robust biosensors without compromising function.

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Area of Science:

  • Protein engineering
  • Structural biology
  • Biochemistry

Background:

  • Protein function relies on conformational stability and energy barriers between states.
  • Designing beneficial mutations is limited by unknown energy barrier details.
  • Periplasmic binding proteins (PBPs) are dynamic, switching between open and closed states upon ligand binding.

Purpose of the Study:

  • To develop a reliable protein stability design method by considering multiple conformational states.
  • To engineer stabilized variants of periplasmic binding proteins (PBPs).
  • To overcome limitations in protein design for dynamic proteins.

Main Methods:

  • Hypothesized that designing mutations compatible with distinct equilibrium conformations enables reliable stability design.
  • Focused on PBPs, constraining evolutionary and structural features of hinge and interface residues.
  • Filtered incompatible mutations and designed stabilized variants from four different PBPs.

    • Main Results:

    • Design based on a single conformation with evolutionary constraints was insufficient for wild-type binding affinity.
    • Using mutations compatible with both conformations and structural constraints enhanced thermal stability.
    • This approach mitigated trade-offs between stability and ligand binding affinity.

    Conclusions:

    • A straightforward method for one-shot stabilization of dynamic proteins was demonstrated.
    • This method provides robust starting points for thermostable and responsive biosensors.
    • Considering multiple conformations is key for successful protein stabilization design.