Incorporation of Hard and Soft Protein–Protein Interactions into Models for Crowding Effects in Binary and Ternary Protein Mixtures. Comparison of Approximate Analytical Solutions with Numerical Simulation
mediaposted on 25.10.2016, 00:00 by Travis Hoppe, Allen P. Minton
In order to better understand how nonspecific interactions between solutes can modulate specific biochemical reactions taking place in complex media, we introduce a simplified model aimed at elucidating general principles. In this model, solutions containing two or three species of interacting globular proteins are modeled as a fluid of spherical particles interacting through square well potentials that qualitatively capture both steric hard core repulsion and longer-ranged attraction or repulsion. The excess chemical potential, or free energy of solvation, of each particle species is calculated as a function of species concentrations, particle radii, and square well interaction range and depth. The results of analytical models incorporating two-body and three-body interactions are compared with the estimates of free energy obtained via Widom insertion into simulated equilibrium square-well fluids. The analytical models agree well with results of numeric simulations carried out for a variety of model parameters and fluid compositions up to a total particle volume fraction of ca. 0.2.
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particle volume fractionparticle speciesmodel parametersspecies concentrationsparticle radiiApproximate Analytical Solutionsnumeric simulationsinteraction rangecore repulsionfluid compositionsWidom insertionglobular proteinsNumerical SimulationCrowding Effectsequilibrium square-well fluidslonger-ranged attractionTernary Protein Mixtures