Protein-protein interactions affect alpha helix stability in crowded environments

The dense, heterogeneous cellular environment is known to affect protein stability through interactions with other biomacromolecules. The effect of excluded volume due to these biomolecules, also known as crowding agents, on a protein of interest, or test protein, has long been known to increase the stability of a test protein. Recently, it has been recognized that attractive protein-crowder interactions play an important role. These interactions affect protein stability and can destabilize the test protein. However, most computational work investigating the role of attractive interactions has used spherical crowding agents and has neglected the specific roles of crowding agent hydrophobicity and hydrogen bonding. Here we use multicanonical molecular dynamics and a coarse-grained protein model to study the folding thermodynamics of a small helical test protein in the presence of crowding agents that are themselves proteins. Our results show that the stability of the test protein depends on the hydrophobicity of the crowding agents. For low values of crowding agent hydrophobicity, the excluded volume effect is dominant, and the test protein is stabilized relative to the dilute solution. For intermediate values of the crowding agent hydrophobicity, the test protein is destabilized by favorable side chain-side chain interactions stabilizing the unfolded states. For high values of the crowding agent hydrophobicity, the native state is stabilized by the strong intermolecular attractions, causing the formation of a packed structure that increases the stability of the test protein through favorable side chain-side chain interactions. In addition, increasing crowding agent hydrophobicity increases the "foldability" of the test protein and alters the potential energy landscape by simultaneously deepening the basins corresponding to the folded and unfolded states and increasing the energy barrier between them.