Molecular Dynamics Approach for Capturing Calixarenes-Proteins Interactions: The Case of Cytochrome C
Résumé
Functionalized supramolecular cages are of growing importance in biology and biochemistry. They have recently been proposed as efficient auxiliaries to obtain high-resolution cocrystallized proteins. Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonated calix-[8]-arenes to cytochrome c starting from initially distant protein and ligands. We characterize two main binding sites for the sulfonated calixarene on the cytochrome c surface which are in perfect agreement with the previous experiments with regard to the structure (comparison with the X-ray structure PDB 6GD8) and the binding free energies (comparison between the molecular mechanics Poisson-Boltzmann surface 1 area (MM-PBSA) analysis and the isothermal titration calorimetry (ITC) measurements). The per-residue decomposition of the interaction energies reveals the detailed picture of this electrostatically-driven association and notably the role of the arginine R13 as a bridging residue between the two main anchoring sites. In addition, the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of an hydrogen bond network far from the binding sites, increasing the rigidity of the protein. This study paves the way towards an automated procedure to predict the supramolecular protein-cages association, with the possibility of a computational screening of new promising derivatives for controlled protein assembly and protein surface recognition processes.
Domaines
Chimie théorique et/ou physique
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