Residual structure within the disordered C‐terminal segment of p21^{Waf1/Cip1/Sdi1} and its implications for molecular recognition

Abstract

Probably the most unusual class of proteins in nature is the intrinsically unstructured proteins (IUPs), because they are not structured yet play essential roles in protein-protein signaling. Many IUPs can bind different proteins, and in many cases, adopt different bound conformations. The p21 protein is a small IUP (164 residues) that is ubiquitous in cellular signaling, for example, cell cycle control, apoptosis, transcription, differentiation, and so forth; it binds to approximately 25 targets. How does this small, unstructured protein recognize each of these targets with high affinity? Here, we characterize residual structural elements of the C-terminal segment of p21 encompassing residues 145-164 using a combination of NMR measurements and molecular dynamics simulations. The N-terminal half of the peptide has a significant helical propensity which is recognized by calmodulin while the C-terminal half of the peptide prefers extended conformations that facilitate binding to the proliferating cell nuclear antigen (PCNA). Our results suggest that the final bound conformations of p21 (145-164) pre-exist in the free peptide even without its binding partners. While the conformational flexibility of the p21 peptide is essential for adapting to diverse binding environments, the intrinsic structural preferences of the free peptide enable promiscuous yet high affinity binding to a diverse array of molecular targets.

Molecular simulations of protein disorderThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

“…Its structural plasticity allows it to adopt both a-helical and extended structures. Interestingly, the bound conformations of p21 were found to exist in the conformational ensemble of its unbound state, supporting a conformational selection mechanism for p21's binding promiscuity (Yoon et al 2009). …”

“…This approach is effective when the partially unfolded state represents a relatively small perturbation from the folded state, and the structure of the folded state is known (Fuentes et al 2005). Another approach that makes use of chemical shift information is the energy-minima mapping and weighting (EMW) method (Huang and Stultz 2008;Yoon et al 2009). The EMW method consists of three steps: conformational sampling, ensemble generation, and validation.…”

“…Using the library of initial conformations, EMW generates many candidate ensembles, each of which is independently consistent with a set of 13 Ca chemical shifts. Validation of the ensembles is performed using 13 CO, 15 N, and Ha chemical shifts and scalar J-couplings (Yoon et al 2009). The EMW method has been used to study the conformational ensemble of a C-terminal fragment of p21, an IDP capable of recognising and binding to at least 25 different substrates.…”

Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding–Binding Process: A Critical Assessment of the “Fly-Casting” Mechanism

“…51 Changing α values in our scheme regulates the system between coupled folding-binding and docking (Fig. 3).…”

The Stress-response protein prostate-associated gene 4, interacts with c-Jun and potentiates its transactivation

“…Thus, conformational dynamics is believed to represent a major functional advantage for the IDPs, enabling them to interact with a broad range of biological targets under normal physiological conditions where their expression is tightly regulated [15,16]. However, experimental evidence demonstrating conformational dynamics in IDPs is limited to only a few examples [17–25]. …”