CDK5-p25 Inhibitor p5 Peptide Samples Intrinsically Disordered Ensemble, Informing Selectivity.

The CDK5-p25 complex is a pathological driver in Alzheimer's disease and other neurodegenerative disorders, contributing to neuronal dysfunction and death. While the 24-residue p5 peptide selectively inhibits this complex, the precise structural basis for its specificity has remained elusive. Understanding p5's unbound conformational landscape is critical to elucidating its mechanism and designing more effective therapeutic inhibitors.

Researchers performed extensive replica exchange with solute tempering (REST2) molecular dynamics simulations on the p5 peptide in explicit solvent over 350 ns. Using the CHARMM36m force field at physiological temperature, they characterized its conformational landscape. Gaussian Mixture Variational Autoencoder (GMVAE) clustering was then applied to identify dominant conformational states, providing a detailed structural analysis of the unbound peptide.

The p5 peptide exists as an intrinsically disordered ensemble, rapidly interconverting between three dominant states: a compact disordered state, an extended disordered state, and a partially β-structured state featuring a transient antiparallel β-hairpin between residues 5-8 (WDRC) and 16-19 (SSKM).

Small free energy differences (ΔΔG < 0.35 kcal/mol) between these states enable rapid nanosecond-time scale interconversion, consistent with the hallmarks of an intrinsically disordered peptide. Temperature-dependent free energy profiles confirmed the low-energy conformational basin's robustness across a wide temperature range, validating physiological relevance. The absence of stable helical structure in the unbound state, coupled with backbone flexibility and transient β-strand propensity, strongly supports a coupled folding-and-binding mechanism upon CDK5 engagement.