Interactions between a protein and large nearby molecules produce repulsive forces at distances that can be as large as the protein itself. The group modeled the energetic effects of these interactions on folding of a WW domain and found that it folds faster and has a more stable folded state in a crowded environment. The more spread out the protein, the more likely it is to experience unfavorable interactions with macromolecules. Compaction, in contrast, promotes its isolation.
Folding rates reach a maximum when 10% of the solution volume is taken up by other large molecules, but even at high densities the folding rates were still well above that in dilute solution. Approximately 40% of a bacterial cell is occupied by macromolecules. Thirumalai suggests that crowding effects may relieve some of the evolutionary pressure to produce rapidly folding sequences. “An optimal design may not be necessary,” he says. “Maybe in fact moderately well-designed amino acid sequences are good enough.”
The influence of crowding was also mimicked by folding proteins in a confined spherical space. These calculations were simpler than those done using crowding agents. Confinement may thus prove useful for future studies, including determining whether so-called natively unfolded proteins are actually at least partially structured in vivo.