Keywords

IDP, Preformed Structure, Protein Interaction, Folding upon Binding, Partner Recognition

Reference

DOI: 10.1016/j.jmb.2004.03.017

Abstract

Intrinsically unstructured proteins (IUPs) lack extensive structural order but often exhibit local residual structure. This paper proposes that preformed structural elements are crucial for their interactions with structured partners, serving as initial recognition elements that guide final binding conformation.

A database of 24 IUPs with known 3D structures in their bound state was analyzed, revealing high coil content and disallowed backbone torsion angles, even when bound. Secondary structure prediction indicates that IUP sequences have inherent structural preferences, especially helices, marking regions involved in binding, while flexible linkers connect them. These preformed elements facilitate faster, energetically favorable binding, highlighting a functional advantage of residual structure in IUPs.

Notes

1. General Background

  • IUPs (IDPs) are dynamic, flexible proteins without stable folded structures but contain residual structural elements.
  • Traditionally thought to be random coils, but they retain local structure, enabling induced folding upon binding.
  • Hierarchical folding model suggested: stable secondary structures form first, guiding further folding.
  • Binding characterized by high association/dissociation rates — fast, reversible interactions.
  • Even in harsh conditions, IDPs are never truly random coils.

2. Functional Mechanisms and Models

  • Two models for IUP binding:
    1. Hydrophobic-collapse model — random contacts serve as initial folding centers.
    2. Framework model — pre-existing structural elements guide binding (supported here).
  • IUPs may combine both models, like globular proteins being “in-between”.
  • Flexible linkers connect stable segments, enabling fast recognition and binding with minimal entropic cost.
  • Binding often involves induced folding — disorder-to-order transitions essential for function.

3. Findings

3.1 Structural Analysis

  • IUPs vs globular proteins:
    • Similar helical content, but only 50% of β-structure content compared to globular proteins.
    • Higher proportion of coil and disallowed torsion angles, especially at charged residues.
    • Indicates incomplete ordering even when bound.

3.2 Sequence-Based Secondary Structure Prediction

  • Predicted secondary structure matches bound state better than random sequences — indicates intrinsic preference.
  • Helices dominate the preformed structures; β-structures less common (likely due to lack of stable core).

4. Discussion (Amazing Section!)

  • Excessive stabilization of secondary structure hinders binding, as seen in p27.
  • Binding as a special case of folding — binding ≈ folding with a partner as a template.
  • IDPs are “mixtures” of strong and weak secondary structure segments — modular architecture.
  • Nucleation-condensation model:
    • Preformed elements serve as nucleation sites for folding upon partner interaction.
    • Facilitates fast, efficient, specific binding.
  • Enthalpy-entropy compensation:
    • Binding is driven by favorable enthalpic interactions that compensate for loss of flexibility.
    • Allows binding despite disorder, critical for biological function.
  • Hierarchical folding model applied to IDPs:
    • Preformed segments engage first, followed by adaptation of flexible regions.
    • Reduces search space, accelerating complex formation.

5. Additional Insights

  • Binding site flexibility enhances ligand diversity — adaptive recognition.
  • Flexibility in linker regions allows reversible interactions, fine-tuned signaling.
  • Globular proteins share some characteristics but with more rigid internal cores.
  • Reduced β-content in IDPs reflects absence of internal hydrophobic core necessary to stabilize sheets.

6. Interesting Concepts

  • Enthalpy-entropy compensation enables energetically balanced binding.
  • Hierarchical folding explains how local structure leads to global interaction.
  • Flexible linkers as entropic springs between structured recognition motifs.

Take-home Messages

  • IUPs/IDPs are not purely random coils — they harbor preformed elements essential for partner recognition.
  • Preformed helices serve as initial contact points, guiding disorder-to-order transitions.
  • Flexible linkers between preformed segments allow rapid, specific interactions.
  • Binding involves hierarchical folding, combining pre-formed nucleation and induced fit.
  • Functional advantage: Energetically efficient, highly specific, and reversible binding, key to signaling and regulation.