Keywords

IDR, Intrinsically Disordered Proteins, Structural Bias, FRET, Polymer Physics, Biophysics

Reference

DOI: https://doi.org/10.1038/s41594-023-01148-8

Abstract

Intrinsically disordered proteins (IDPs) form a large part of the proteome and perform essential cellular roles. Unlike folded proteins, IDPs exist as dynamic ensembles, but sequence-dependent intramolecular interactions create structural biases that shape these ensembles.
Although typically studied in vitro, whether these biases persist in cells has been unclear. This study shows that structural biases measured in vitro are largely recapitulated in human-derived cells and that environmental changes can modulate IDP ensembles in a sequence-dependent manner. These findings highlight how IDP ensemble sensitivity may serve as a mechanism for regulation, signaling, or disease and could inspire disorder-based biosensor design.

Notes

1. Big Questions

  • To what extent are IDP structural biases observed in vitro preserved in the cell?
  • How do IDP structural biases respond to changes in the intracellular environment?

2. Methods

  • Ensemble FRET, SEC-SAXS, solution space scanning, all-atom molecular simulations.
  • GS (Glycine-Serine) repeats used as model-free, unbiased standards to benchmark naturally occurring IDPs.

3. Cool Findings

A. GS Repeats as a Universal IDP Model

  • GS repeats:
    • Lack hydrophobicity, charge, and aromaticity — easy to express and highly soluble.
    • No local or long-range structural biases — behave as ideal Gaussian chains.
  • FRET-based E_app measurements for GS repeats show linear dependence on length in dilute buffers.
  • SEC-SAXS and simulations confirm ideal polymer behavior.
  • GS repeats serve as a length-dependent benchmark to assess deviations in natural IDPs.

B. Structural Biases in Naturally Occurring IDPs

  • PUMA: More compact than GS repeats — intramolecular structural bias present.
  • PUMA Scrambles: Disruption of sequence order removes biases but retains amino acid composition.
  • Structural biases exist even without residual helicity, but PUMA WT is uniquely more compact and sensitive.
  • Amino acid sequence, not just composition, dictates structural bias.

C. In-Cell vs. In Vitro Comparisons

  • Live-cell FRET measurements in HEK293T cells recapitulate in vitro GS results, suggesting minimal perturbation by cellular context.
  • Structural biases for PUMA and other IDPs persist in live cells, even without helicity.
  • IDP structural biases are encoded in sequence and remain in cellular environments.

D. Response to Cellular Environmental Changes

  • Hyperosmotic challenge (osmotic stress) induces compaction in GS constructs, proportional to length.
  • Solution space scanning shows different IDPs respond variably to solutes, even when GS remains consistent.
  • Structural bias response to environmental changes is sequence-dependent and tunable.

4. Structural Bias in Other IDPs

  • IDPs studied:
    • PUMA (BH3 domain) — compact.
    • FUS (low-complexity domain) — compact, but expanded in nucleus (possibly RNA interaction).
    • E1A (adenovirus hub protein) — compact, but unusual expansion in cells.
    • p53 (N-terminal domain) — similar to GS repeats.
    • Ash1 (C-terminal domain) — similar to GS repeats.
  • Conclusion:
    • Some IDPs (PUMA, FUS, E1A) show compaction relative to GS.
    • Others (p53, Ash1) behave like unbiased polymers.
  • Structural biases are common but vary widely among IDPs — not all IDPs are highly compact.

5. Broader Implications

  • IDP ensembles are shaped by sequence-encoded structural biases, which remain intact inside cells.
  • Structural bias can be modulated by:
    • Subcellular localization.
    • Intracellular milieu.
    • Interaction with folded domains.
  • These biases may be evolutionarily selected to act as sensors/actuators in response to cellular conditions.
  • Perturbation of IDP biases could contribute to disease, especially under conditions like cancer or viral infection, where intracellular environments shift.