Rational design to control the trade-off between receptor affinity and cooperativity

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• Cooperativity in biomolecular receptors enhances responsiveness but often reduces affinity.
• A trade-off exists between cooperativity and affinity, limiting receptor design.
• Additional binding sites can overcome this trade-off by providing extra binding energy.

Purpose of the Study:

• To design and investigate cooperative, multi-site receptors using an intrinsic disorder mechanism.
• To explore how binding energy landscapes influence the balance between cooperativity and affinity.
• To create novel doxorubicin-binding aptamers with enhanced cooperative binding properties.

Main Methods:

• Utilized an intrinsic disorder mechanism to engineer receptors from a noncooperative aptamer.
• Designed two distinct three-binding-site receptors with different binding energy landscapes.
• Analyzed the impact of binding energy partitioning on cooperativity (Hill coefficient) and affinity.

Main Results:

• Achieved a Hill coefficient of 1.9 in the first receptor, favoring affinity with minimal loss compared to the parent aptamer.
• Achieved a Hill coefficient of 2.3 in the second receptor, prioritizing cooperativity at the cost of 4-fold reduced affinity.
• Identified the second binding event's affinity as a key determinant for balancing cooperativity and affinity.

Conclusions:

• Demonstrated the ability to engineer cooperative receptors with tunable affinity using intrinsic disorder.
• Showcased how manipulating binding energy landscapes can control the cooperativity-affinity trade-off.
• The second binding event acts as an allosteric gatekeeper, directing the receptor's behavior towards higher cooperativity or affinity.