Salts modulate the behavior of intrinsically disordered proteins (IDPs) and influence the formation of membraneless organelles through liquid−liquid phase separation (LLPS). In low ionic strength solutions, IDP conformations are perturbed by the screening of electrostatic interactions, independent of the salt identity. In this regime, insight into the IDP behavior can be obtained using the theory for salt-induced transitions in charged polymers. However, salt-specific interactions with the charged and uncharged residues, known as the Hofmeister effect, influence IDP behavior in high ionic strength solutions. There is a lack of reliable theoretical models in high salt concentration regimes to predict the salt effect on IDPs. We propose a simulation methodology using a coarse-grained IDP model and experimentally measured water to salt solution transfer free energies of various chemical groups that allowed us to study the saltspecific transitions induced in the IDPs conformational ensemble. We probed the effect of three different monovalent salts on five IDPs belonging to various polymer classes based on charged residue content. We demonstrate that all of the IDPs of different polymer classes behave as self-avoiding walks (SAWs) at physiological salt concentration. In high salt concentrations, the transitions observed in the IDP conformational ensembles are dependent on the salt used and the IDP sequence and composition. Changing the anion with the cation fixed can result in the IDP transition from a SAW-like behavior to a collapsed globule. An important implication of these results is that a suitable salt can be identified to induce condensation of an IDP through LLPS.

Salts modulate the behavior of intrinsically disordered proteins (IDPs). In low ionic strength solutions, IDP conformations are primarily perturbed by the screening of electrostatic interactions, independent of the identity of the salt. In this regime, insight into the IDP behavior can be obtained using the theory for salt-induced transitions in charged polymers. However, in high ionic strength solutions, salt-specific interactions with the charged and uncharged residues, known as the Hofmeister effect, influence IDP behavior. There is a lack of reliable theoretical models in high salt concentration regimes to predict the salt effect on IDPs. Using a coarse-grained simulation model for the IDPs and experimentally measured water to salt solution transfer free-energies of various chemical groups, we studied the salt-specific transitions induced in the IDPs conformational ensemble. We probed the effect of three different salts, ranging from protective osmolyte to denaturant, on five IDPs belonging to various polymer classes classified based on charge content. The transitions observed in the IDP conformational ensembles are dependent on the salt used and the IDP polymer class. An important implication of these results is that a suitable salt can be identified to induce condensation of an IDP through liquid-liquid phase separation.

Aggregation of intrinsically disordered proteins (IDPs) can lead to neurodegenerative diseases. Although there is experimental evidence that acidic pH promotes IDP monomer compaction leading to aggregation, the general mechanism is unclear. We studied the pH effect on the conformational ensemble of prothymosin-α (proTα), which is involved in multiple essential functions, and probed its role in aggregation using computer simulations. We show that compaction in the proTα dimension at low pH is due to the protein's collapse in the intermediate region (E41−D80) rich in glutamic acid residues, enhancing its β-sheet content. We observed by performing dimer simulations that the conformations with high β-sheet content could act as aggregation-prone (N*) states and nucleate the aggregation process. The simulations initiated using N* states form dimers within a microsecond time scale, whereas the non-N* states do not form dimers within this time scale. This study contributes to understanding the general principles of pH-induced IDP aggregation.

Aggregation of intrinsically disordered proteins (IDPs) is the cause of various neu-rodegenerative diseases. Changes in solution pH can trigger IDP aggregation due to a shift in the IDP monomer population with a high aggregation propensity. Al-though there is experimental evidence that acidic pH promotes the compaction of IDP monomers, which subsequently leads to aggregation, the general mechanism is not clear. Using the IDP prothymosin-α(proTα), which is involved in multiple essential functions as a model system, we studied the pH effect on the conformational ensemble of proTαand probed its role in aggregation using a coarse-grained IDP model and molecular dynamics simulations. We show that compaction in the proTαdimension at low pH is due to the protein’s collapse in the intermediate region (E41 - D80) rich in glutamic acid residues. Further, theβ-sheet content increases in this region upon pH change from neutral to acidic. We hypothesized that the conformations with highβ-sheet content could act as aggregation-prone (N∗) states and nucleate the aggregation process. We validated our hypothesis by performing dimer simulations starting fromN∗and non-N∗states. We show that simulations initiated usingN∗states as initial conformations form dimers within 1.5μs, whereas the non-N∗states do not form dimers within this timescale. This study contributes to understanding the general principles of pH-induced IDP aggregation. The main result upon pH change from neutral to acidic, the intermediate region of proTαis responsible for aggregation due to an increase in itsβ-sheet forming propensity and forms the fibril core can be verified by experiments.Graphical TOC Entry

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