Intrinsically disordered proteins are characterized by a low content of hydrophobic amino acids and a high net charge of the sequence. Given the lack of persistent structure, their conformations are expected to be very sensitive to the local environment in the cell. Important factors include not only the presence of specific cellular ligands, but also pH, salt concentration, and macromolecular crowding.
Single-molecule Förster Resonance Energy Transfer (FRET) is a powerful tool to quantitatively access the distance distributions of the disordered ensemble.
Role of electrostatic interactions
In contrast to the compact unfolded conformations that have been observed for many proteins at low denaturant concentration, IDPs can exhibit a prominent expansion at low ionic strength that correlates with their net charge. Charge-balanced polypeptides, however, can exhibit an additional collapse at low ionic strength, as predicted by polyampholyte theory, due to the attraction between opposite charges in the chain. We are interested in understanding how the patterning of charges and the electrostatic screening mediated by different types of salts lead to a further modulation of chain dimensions and protein interactions.
Role of macromolecular crowding
Currently, it is poorly understood how the crowded cellular milieu affects the structural distributions of intrinsically disordered proteins. We use biocompatible synthetic polymers to mimic the crowded interior of the cell (PEG, Dextran, PVA, PVP). We have found that macromolecular crowding induces compaction of the disordered states of ProTα, ACTR and IN despite the strong electrostatic repulsion within the IDP. The extent of compaction depends on crowder and protein size and has its maximum for crowders of similar size comparable to or larger than the protein.Polymer theories provide a quantitative framework where we can understand the single-molecule FRET observations.