Calixarenes are hallmark molecules in supramolecular chemistry as guest cages for small ligands. They have also conversely proved their interest as auxiliary ligands toward assisted co-crystallization of proteins. These functionalized macromolecular cages target positively-charges residues, and notably surface-exposed lysines, with a site-selectivity finely characterized experimentally, but that remains to be assessed. Relying on a tailored molecular dynamics simulations protocol, we explore the association of para-sulfonato-calixarenes with an antifungal protein, as a small yet most competitive system with 13 surface-exposed lysines. Our computational approach probe "de novo" the electrostatically-driven interaction, ruled out by a competition with salt bridges, not only corroborating the main binding site probed by X-ray, but also characterizing a second binding site that can act as a transient hub spot. The attach-pull-release (APR) method provides a very good assessment of the overall binding free energy measured experimentally (-6.42+-0.5 vs -5.45 kcal.mol-1 by isothermal titration calorimetry). This work also probes dynamical allosteric modifications upon ligand binding, and our computational protocol could be generalized to situate the supramolecular forces ruling out the calixarene-assisted co-crystallization of proteins.
Supporting Information: Probing the dynamical interaction of para-sulfonato-calixarene with an antifungal protein
Computational Methods, MMPBSA, cluster analysis, Binding Affinity