Confinement and Catalysis within De Novo Designed Peptide Barrels

Area of Science:

• Supramolecular chemistry
• Protein engineering
• Biophysical chemistry

Background:

• De novo protein design enables predictable generation of peptide assemblies and protein structures.
• Integrating functions like small-molecule binding and catalysis into designed proteins is a key challenge.
• Controlling the binding and orientation of multiple small molecules is crucial for directing chemical reactions.

Purpose of the Study:

• To design, characterize, and apply small-molecule:peptide ternary complexes in aqueous solution.
• To utilize alpha-helical barrel (αHB) peptide assemblies as adaptable molecular scaffolds.
• To demonstrate the controlled binding of multiple small molecules within designed protein structures.

Main Methods:

• Design and construction of alpha-helical barrel (αHB) peptide assemblies with tunable channel properties.
• Utilizing Förster resonance energy transfer (FRET) to monitor the proximity of bound molecules.
• Employing specific organic dyes (1,6-diphenyl-1,3,5-hexatriene, Nile red) and anthracene as model small molecules.

Main Results:

• Demonstrated that specific αHBs can co-locate two different organic dyes (1,6-diphenyl-1,3,5-hexatriene and Nile red) using FRET.
• Showed that two anthracene molecules can be accommodated within an αHB to promote photodimerization.
• Observed that not all ternary complexes yield productive energy transfer or photodimerization, indicating design-dependent control.

Conclusions:

• Alpha-helical barrel (αHB) peptide assemblies can function as programmable molecular flasks for accommodating multiple small molecules.
• The design of αHBs allows for predictable control over the binding and proximity of small molecules.
• This work paves the way for developing novel protein-based systems for catalysis and other functions requiring precise molecular organization.