Effect of Macromolecular Crowding on the Electrostatic Interaction of Barnase-Barstar: Initial Steps Using an Explicit Solvent Model

Proteins that bind intracellularly are surrounded by other macromolecules. Macromolecular crowding has been shown to impact protein folding and binding, but its effects on the electrostatics of protein binding have not been thoroughly studied. Two ways crowding can affect binding are via loss of water mobility and water depletion. Crowding causes loss of water mobility because more water molecules will be organized into solvation shells around the crowding agents, instead of being in bulk form; waters in solvation shells are less mobile. Water is depleted because the crowders occupy volume that would have held water. We are interested in the effect of loss of water mobility, but it is difficult to separate the effects of loss of water mobility and water depletion. We had previously used implicit solvent to study the effect of water depletion due to crowding. An explicit solvent model will show both loss of water mobility and water depletion effects. In combination with the results from the implicit solvent study, we can then assess the effect of loss of water mobility. In this study, we used free energy perturbation and component analysis in explicit water to begin to examine the binding of barnase and barstar. Specifically, we evaluated the contribution of the charge of a particular residue, barstar’s aspartic acid 35, to the binding free energy of the barnase-barstar complex. In the future, we will introduce crowders into the system, so we may see how the contribution of the charge of a residue to the binding free energy changes in the presence of crowders.