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Molecular dynamics approach for capturing calixarenes--proteins interactions: the case of cytochrome c

revised on 16.09.2020, 19:47 and posted on 17.09.2020, 12:24 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.


Email Address of Submitting Author


Université de Lyon, ENS de Lyon, CNRS UMR5182



ORCID For Submitting Author


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no conflict of interest


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