Protein-protein binding spans over diverse kinds of biomolecular processes, e.g., enzyme substrate binding, signaling and so on. Proteins participating in such processes undergo small or large conformational changes upon complex formation with its cognate partners. Therefore, it is expected that the entropy change upon complex formation is an important component of binding free energy. Here, we employ a Gaussian-based model of atomic densities; it models an atom as a spherical object whose density decreases according to a Gaussian distribution while moving away from its center. In this method, we infer entropy change from energy minimized protein-protein complex structure via computing changes in mean density around atoms forming sidechain-torsions with reference to energy minimized structure of single amino acid. Entropy derived from this method in combination to energy terms: Molecular Mechanics (MM), polar solvation using Poisson Boltzmann (PB), and non-polar solvation from solvent accessible Surface Area (SA) change are used to assess the improvement in correlation of predicted/computed values against experimental binding energy values over a protein-protein dataset is estimated.

Gaussian-based method for quick estimation of entropy change upon protein-protein binding.

ACS Spring Meeting 2021

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