Rationalizing Diverse Binding Mechanisms to the Same Protein Fold: Insights for Ligand Recognition and Biosensor Design

• DOI: 10.1021/acschembio.4c00243
• Publication Date: 2024-07-17T14:53:35Z
• Authors: Alison C. Leonard; Anika J. Friedman; Rachel Chayer; Brian M. Petersen; Janty Woojuh; Zenan Xing; Sean R. Cutler; Joel L. Kaar; Michael R. Shirts; Timothy A. Whitehead

The engineering of novel protein-ligand binding interactions, particularly for complex drug-like molecules, is an unsolved problem, which could enable many practical applications protein biosensors. In this work, we analyzed two engineered biosensors, derived from the plant hormone sensor PYR1, to recognize either agrochemical mandipropamid or synthetic cannabinoid WIN55,212-2. Using a combination quantitative deep mutational scanning experiments and molecular dynamics simulations, demonstrated that mutations at common positions can promote shape complementarity revealed prominent differences in electrostatic networks needed complement diverse ligands. MD simulations indicate both PYR1 complexes bind single conformer their target ligand close lowest free-energy conformer. Computational design using fixed rigid body orientation led new WIN55,212-2 sensors with nanomolar limits detection. This work reveals mechanisms by versatile biosensor scaffold also provides computational methods sample realistic conformers alignments simplify biosensors ligands interest.