Volume changes of globular protein association

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

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.

Determination of reaction volumes and polymer distribution characteristics of tobacco mosaic virus coat protein

A method that allows the quantitative determination of reaction volumes from sedimentation velocity experiments in an analytical ultracentrifuge is presented. Combined with a second method for detecting pressure-induced depolymerization, general characteristics of polymer distributions may be probed. We show that it is possible to determine if a sample is in an equilibrium or metastable state of subunit association. Our approach to probe macromolecular aggregation systems by small pressure perturbations is not restricted to the use of centrifuges. This method has been applied to characterize certain aspects of the polymerization of tobacco mosaic virus coat protein (TMVP). There are at least two helical polymer conformations in RNA-free coat protein rods. The smaller, helix I, polymers are limited to sizes below about 70 subunits (four to five helical turns) and undergo some kind of cooperative conformational change before further subunits may be added indefinitely. In contrast to helix I, the larger helix II polymers occur as broader and skewed size distributions. Under moderately strong polymerization conditions, the equilibrium state can contain both types of helical rods. The reaction volume for the addition of trimers is -220 ml/mol for both types of helical polymers. These results are compared with the results of previous thermodynamic analyses of TMVP polymerization.