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Coupling Supervised Molecular Dynamics (SuMD) with Entropy Estimations To Shine Light on the Stability of Multiple Binding Sites.

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Exploring at the molecular level, all possible ligand-protein approaching pathways and, consequently, identifying the energetically favorable binding sites is considered crucial to depict a clear picture of the whole scenario… Click to show full abstract

Exploring at the molecular level, all possible ligand-protein approaching pathways and, consequently, identifying the energetically favorable binding sites is considered crucial to depict a clear picture of the whole scenario of ligand-protein binding. In fact, a ligand can recognize a protein in multiple binding sites, adopting multiple conformations in every single binding site and inducing protein modifications upon binding. In the present work, we would like to present how it is possible to couple a supervised molecular dynamics (SuMD) approach to explore, from an unbound state, the most energetically favorable recognition pathways of the ligand to its protein, with an enthalpic and entropic characterization of the most stable ligand-protein bound states, using the protein kinase CK2α as a prototype study. We identified two accessory binding pockets surrounding the ATP-binding site having a strong enthalpic contribution but a different configurational entropy contribution, suggesting that they play a different role.

Keywords: binding sites; multiple binding; ligand protein; molecular dynamics; supervised molecular; binding

Journal Title: ACS medicinal chemistry letters
Year Published: 2019

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