Abstract Intrinsically disordered protein regions (IDRs) pervasively engage in essential molecular functions, yet they are often poorly conserved as assessed by sequence alignment. To understand the seeming paradox of how sequence variability is compatible with function, we examined the functional determinants for a poorly conserved but essential IDR. We show that IDR function depends on two distinct but related properties: sequence- and chemical specificity. While sequence-specificity works via linear binding motifs, chemical-specificity reflects the sequence-encoded chemistry of multivalent interactions through amino acids across an IDR. Unexpectedly, an apparently essential binding motif can be removed if compensatory changes to the sequence chemistry are made, highlighting the orthogonality and interoperability of both properties. Our results provide a general framework to understand the functional constraints on IDR sequence evolution. One-Sentence Summary Interactions driven by intrinsically disordered regions can be understood using a two-dimensional landscape that defines binding via motif-dependent and motif-independent contributions.

Sequence- and chemical specificity define the functional landscape of intrinsically disordered regions