Situating the Phosphonated Calixarene–Cytochrome C Association by Molecular Dynamics Simulations.

Abstract

Protein-calixarenes binding plays an increasing, central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational ap- proaches such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit- solvent molecular dynamics simulations to capture the electrostatically-driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the X-ray struc- ture, the association has a larger structural impact in the protein dynamics. Our simulations, then, allow a direct comparison with analogous calixarenes, namely sulfonato, similarly re- ported as “molecular glue”. Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding.

One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics

“…Binding site search onto the protein surfaces follows a computational protocol recently exploited. [42][43][44]50 Ubiquitin monomer structure with 76 residues was taken from an unpublished, high-resolution PDB provided by Dr E. Girard IBS, Grenoble. Protonation states of ubiquitin residues were assigned using the H++ server 48 at pH 6.5.…”