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Capturing the Supramolecular Association of Calixarenes onto Proteins Relying on Molecular Dynamics Simulations: The Case of Cytochrome C

preprint
submitted on 26.02.2020 and posted on 27.02.2020 by Alessio Bartocci, florence szczepaniak, Tao Jiang, Natacha Gillet, Elise Dumont
Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonatedcalix-[8]-arenes to cytochrome c. The binding sites prone to interactions with sulfonated calixarenescan be identified without prior knowledge of the X-ray structure, and the binding free energiesestimated by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) post-analysis arefound to be in neat agreement with the isothermal titration calorimetry (ITC) measurements The per-residuedecomposition reveals the detailed picture of this electrostatically-driven association and notably therole of the arginine R13 as a bridge 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 theprotein.

History

Email Address of Submitting Author

natacha.gillet@ens-lyon.fr

Institution

Université de Lyon, ENS de Lyon, CNRS UMR5182

Country

France

ORCID For Submitting Author

0000-0002-7657-6861

Declaration of Conflict of Interest

no conflict of interest

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