Structural ensemble of an intrinsically disordered polypeptide.

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Intrinsically disordered proteins (IDPs) lack stable structures in solution, playing vital roles in cellular signaling and regulation.
• The mechanism by which IDPs achieve ordered structures upon ligand binding is debated: ligand-induced folding versus binding to pre-existing conformers.
• Understanding IDP conformational dynamics is crucial for deciphering their regulatory functions.

Purpose of the Study:

• To investigate the conformational ensemble of a p53 intrinsically disordered protein fragment.
• To determine if the p53 fragment populates structures resembling its ligand-bound state in solution.
• To explore the role of pre-existing conformers in IDP-ligand interactions.

Main Methods:

• Replica exchange molecular dynamics (REMD) simulations using a fully atomistic, explicit solvent protein model.
• Clustering analysis based on structural similarity to identify populated conformer states.
• Experimental validation of simulation-derived structural insights.

Main Results:

• The 15-residue p53 TAD fragment (wild-type and P27L mutant) populates an ensemble of conformations in solution.
• Simulated solution structures of the p53 fragment closely resemble the experimentally determined MDM2-bound conformation.
• The conformational free-energy landscape of the p53 fragment is relatively flat in the absence of its ligand.

Conclusions:

• The p53 intrinsically disordered protein fragment populates solution structures that mimic its ligand-bound state.
• This suggests that IDPs may bind ligands by recognizing and stabilizing pre-existing conformers rather than undergoing complete ligand-induced folding.
• Molecular simulations provide valuable insights into the dynamic conformational ensembles of IDPs.