Structural Ensemble of an Intrinsically Disordered Polypeptide

• Published in: The journal of physical chemistry. B Vol. 117; no. 1; pp. 118 - 124
• Main Authors: Mittal, Jeetain, Yoo, Tae Hyeon, Georgiou, George, Truskett, Thomas M
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 10.01.2013
• Subjects: Amino Acid Sequence; Binding; Biological and medical sciences; Biophysics; Circular Dichroism; Computer simulation; Fundamental and applied biological sciences. Psychology; In solution. Condensed state. Thin layers; Ligands; Mathematical models; Models, Molecular; Molecular biophysics; Molecular dynamics; Molecular Sequence Data; Molecular structure; Nuclear Magnetic Resonance, Biomolecular; Peptides; Peptides - chemistry; Physico-chemical properties of biomolecules; Protein Conformation; Proteins; Chemical solution; Phase transformation; Disordered system; Atomistic model; Molecular dynamics method; Free energy; Aminoacid polymer; Protein; Conformation
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp308984e

Intrinsically disordered proteins (IDPs), which play key roles in cell signaling and regulation, do not display specific tertiary structure when isolated in solution. Instead, they dynamically explore an ensemble of unfolded configurations, adopting more stable, ordered structures only after binding to their ligands. Whether ligands induce IDP structural changes upon binding or simply bind to pre-existing conformers that are populated within the IDP’s structural ensemble is not well understood. Molecular simulations can provide information with the spatiotemporal resolution necessary to resolve these issues. Here, we report on the conformational ensemble of a 15-residue wild-type p53 fragment from the TAD domain and its mutant (TAD-P27L) obtained by replica exchange molecular dynamics simulation using an optimized (fully atomistic, explicit solvent) protein model and the experimental validation of the simulation results. We use a clustering method based on structural similarity to identify conformer states populated by the peptides in solution from the simulated ensemble. We show that p53 populates solution structures that strongly resemble the ligand (MDM2)-bound structure, but at the same time, the conformational free-energy landscape is relatively flat in the absence of the ligand.