Fig. 2: Binder design models and biophysical characterization.
From: Improved protein binder design using β-pairing targeted RFdiffusion
a Design models of binding complexes for each target. Left: Entire complex design models with binders indicated in green/gold and targets in teal/cyan. β-strand interface conditioned scaffold design yielded binders with interfacial β-strands (gold) forming strand-pairing hydrogen bonding interactions with target edge β-strands (cyan). Middle: Close up view of design model backbone hydrogen-bond interactions with putative hydrogen bonds shown in white. Right: schematic representation of strand pairing interactions showcase the diversity of sequence-independent β-strand pairing interactions. b Circular dichroism thermal melts. Full spectrum analyses (left) performed at 25 °C (cyan), 75 °C (green), and 95 °C (gold) assess the overall binder fold at these three temperatures, while single wavelength thermal melts (right) were measured at 217 nM to calculate binder Tm values. c SPR measurement (pink) of binding kinetics at 600pM, 4 nM, 30 nM, 200 nM, 1.5 μM, and 10 μM (association phases 1-6 on the X-axis). Fits for Kd determination (green) excluded the 10 μM data excluded due to signal aberrations at this high binder concentration. Binders were reproduced and similar SPR kinetics were fitted with n ≥ 2 for each binding protein. Source data are provided as a Source Data file.
