jp6b07736_si_003.mpg (10.29 MB)
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
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posted on 2016-10-25, 00:00 authored by Travis Hoppe, Allen P. MintonIn 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