Beyond Stickers and Spacers: Residue-level Contact Networks Predict IDR Organization and Phosphorylation Rewiring

Abstract

Intrinsically disordered regions (IDRs) act through ensembles of interconverting conformations, and the sticker and spacer framework describes how IDR sequences encode behaviour by sorting residues into two context-dependent classes. Coarse-grained simulations cover whole proteomes, yet force fields have been compared mainly on global dimensions rather than on residue-level contacts where stickers and spacers act. Here we turn simulations of thousands of IDRs with three force fields into contact networks and describe each residue by contact degree, how densely the residue is contacted, and how often the residue bridges distant parts of the chain. We show that residue types dominating these networks follow the parameters of each force field, whereas the positions of densely contacted and bridging residues are shared between force fields, set by sequence arrangement and learned by a model whose frozen predictions track experimental ensembles in blind tests. We then show that phosphorylation rewires the network most where the electrostatic potential of the unmodified ensemble fluctuates, in two force fields and beyond sequence charge descriptors, and that simulated contact changes track NMR shift changes. Contact degree from a simple model extends the sticker and spacer framework from two classes to a predictive, residue-level description of disordered proteins.