Rationalizing Diverse Binding Mechanisms to the Same Protein Fold: Insights for Ligand Recognition and Biosensor
Alison C Leonard1, Anika J Friedman1, Rachel Chayer1
1Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States.
ACS Chemical Biology
|July 17, 2024
Summary
Engineered protein biosensors can now recognize complex molecules like agrochemicals and synthetic cannabinoids. This study reveals how mutations enhance binding and provides computational methods for designing new biosensors.
Area of Science:
- Biochemistry and Molecular Biology
- Computational Biology
- Biotechnology
Background:
- Engineering novel protein-ligand interactions is crucial for developing advanced protein biosensors.
- Existing methods struggle with complex, drug-like molecules, limiting biosensor applications.
Purpose of the Study:
- To engineer and analyze PYR1-derived biosensors for recognizing specific agrochemicals and synthetic cannabinoids.
- To elucidate the mechanisms underlying protein-ligand binding and inform future biosensor design.
Main Methods:
- Quantitative deep mutational scanning experiments.
- Molecular dynamics (MD) simulations to analyze protein-ligand interactions.
- Computational design strategies for optimizing biosensor function.
Main Results:
- Mutations at specific sites enhanced protein-ligand shape complementarity for diverse molecules.
- Distinct electrostatic networks were identified for binding different ligands.
- MD simulations confirmed binding of a single, low-energy ligand conformer.
- Computational design yielded WIN55,212-2 sensors with nanomolar detection limits.
Conclusions:
- The PYR1 scaffold is versatile for engineering diverse ligand-binding biosensors.
- Computational methods for sampling ligand conformers and orientations simplify biosensor design.
- This work advances the development of protein biosensors for novel molecules.
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