Salt-Dependent Conformational Changes of Intrinsically Disordered Proteins.

Area of Science:

• Biophysics
• Computational Biology
• Protein Science

Background:

• Intrinsically disordered proteins (IDPs) possess flexible structures sensitive to environmental factors like salt concentration.
• While electrostatic screening is recognized, the impact of the salting-out effect on uncharged residues in IDPs is often underestimated.
• Understanding salt-dependent conformational changes is crucial for IDP function and behavior, including liquid-liquid phase separation (LLPS).

Purpose of the Study:

• To develop and validate a coarse-grained model that incorporates the salting-out effect for intrinsically disordered proteins.
• To assess the contribution of the salting-out effect to IDP behavior across varying salt concentrations.
• To evaluate the model's accuracy in predicting experimental salt-dependent LLPS of diverse protein sequences.

Main Methods:

• Parametrization of the salting-out effect into a coarse-grained model using Förster resonance energy transfer (FRET) data.
• Validation of the model against experimental salt-dependent liquid-liquid phase separation (LLPS) data for 17 different proteins.
• Computational survey of over 500 intrinsically disordered protein sequences to assess the prevalence of salting-out effects.

Main Results:

• The refined coarse-grained model successfully captured the salt-dependent behavior of 13 out of 17 tested protein sequences, an improvement of 6 sequences over previous models.
• The study demonstrated that the salting-out effect is a significant factor influencing IDP conformations, particularly for sequences with moderate charge.
• The model's predictions align well with experimental observations of salt-dependent LLPS, highlighting the importance of the salting-out contribution.

Conclusions:

• The salting-out effect plays a more critical role than previously assumed for intrinsically disordered proteins, especially at physiological salt concentrations.
• The developed computational scheme effectively models salt-dependent IDP conformations and LLPS, offering a valuable tool for biophysical studies.
• This approach is broadly applicable to enhance other computational models for predicting salt-induced changes in IDP behavior.