Quantification of Compactness and Local Order in the Ensemble of the Intrinsically Disordered Protein FCP1

• Published in: The journal of physical chemistry. B Vol. 120; no. 34; pp. 8960 - 8969
• Main Authors: Gibbs, Eric B, Showalter, Scott A
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 01.09.2016
• Subjects: Binding; Bridges (structures); computer simulation; Disorders; Fluctuation; Humans; Mathematical models; Molecular Dynamics Simulation; Molecular structure; Monte Carlo Method; nuclear magnetic resonance spectroscopy; Nuclear Magnetic Resonance, Biomolecular; Phosphoprotein Phosphatases - chemistry; Physical chemistry; Protein Binding; Protein Folding; protein-protein interactions; Proteins; Scattering, Small Angle; Software; X-radiation; X-Ray Diffraction
• ISSN: 1520-6106; 1520-5207; 1520-5207
• DOI: 10.1021/acs.jpcb.6b06934

Intrinsically disordered protein regions (IDRs) partially or completely lack a cooperatively folded structure under native conditions, preventing their equilibrium state from being adequately described by a single structural model. As a direct consequence of their disorder, remarkably few experimental studies have quantified the ensembles IDRs adopt in solution. Here, we conduct unbiased computer simulations of the RAP74 interaction motif from the human phosphatase FCP1 in the unbound state, which provides an ensemble in quantitative agreement with both experimental NMR chemical shift information and small-angle X-ray scattering data. The partially α-helical short linear motif found in the C-terminus of FCP1 has been the subject of extensive biophysical characterization aimed at developing a molecular description for the mechanism of coupled folding and binding and establishing the functional relevance of partial order in the unbound state. The analysis presented here yields a remarkably consistent molecular picture enumerating the diversity of structures present in a “partially formed” helix. Specific interactions, including anticorrelations in backbone dihedral angle fluctuations as well as the transient formation of a helix-stabilizing salt bridge, stabilize the preformed structure in the unbound state. The general consequences of these findings for mechanistic analysis of protein–protein interactions are discussed.