Studies of effects of macromolecular crowding and confinement on protein folding and protein stability

In cells, proteins execute specific tasks in crowded environments; these environments influence their stability and dynamics. Similarly, for an enzyme molecule encapsulated in an inorganic cavity as in biosensors or biocatalysts, confinement or excluded volume plays an important role in its stability and dynamics. In this article we present results of our experimental and theoretical investigations of the confinement and macromolecular crowding effects on protein. On the experimental side we study the stability of encapsulated cytochrome c against unfolding induced by the presence of denaturants, such as urea. Results show that, as the pore size in which protein is trapped is reduced, protein shows higher stability against denaturant-induced unfolding. On the theoretical side, after reviewing our previous study of the confinement effects on the equilibrium and dynamic properties of protein using a minimalist (two-dimensional lattice, Monte Carlo, Brownian dynamics) model, we have extended the model so that the effects of macromolecular crowding on such properties can be studied. Our simulations show that both folding and unfolding times increase with the number of crowders in solution, however, the equilibrium constant is affected such that the equilibrium is shifted towards the folded state. Furthermore, our results show that, for a fixed number of crowders as the size of crowder (or excluded volume) increases, the average size of protein at equilibrium decreases.