Phosphonated Calixarene as a “Molecular Glue” for Protein Crystallization

Abstract

Protein crystallization remains a serious bottleneck to structure determination by X-ray diffraction methods. Compounds acting as “molecular glue” provide a promising strategy to overcome this bottleneck. Such molecules interact via noncovalent bonds with two or more protein surfaces to promote lattice formation. Here, we report a 1.5 Å resolution crystal structure of lysine-rich cytochrome c complexed with p-phosphonatomethyl-calix[4]arene (pmclx4). Evidence for complex formation in solution was provided by NMR studies. Similar to p-sulfonato-calix[4]arene (sclx4), the cavity of pmclx4 entrapped a single lysine side chain. Interesting features of protein recognition by the phosphonate substituents were identified in the crystal structure. A new calixarene binding site was identified at Lys54. The electron density at this site indicated two distinct calixarene conformers, suggesting a degree of ligand mobility. The role of pmclx4 in protein crystal packing (molecular glue and patchy particle model) as well as differences in protein-binding with respect to sclx4 are discussed.