Sequence-ensemble-function relationships for disordered proteins in live cells

Abstract

Intrinsically disordered protein regions (IDRs) are ubiquitous across all kingdoms of life and play a variety of essential cellular roles. IDRs exist in a collection of structurally distinct conformers known as an ensemble. An IDR’s amino acid sequence determines its ensemble, which in turn can play an important role in dictating molecular function. Yet a clear link connecting IDR sequence, its ensemble properties, and its molecular function in living cells has not been directly established. Here, we set out to test this sequence-ensemble-function paradigm using a novel computational method (GOOSE) that enables the rational design of libraries of IDRs by systematically varying specific sequence properties. Using ensemble FRET, we measured the ensemble dimensions of a library of rationally designed IDRs in human-derived cell lines, revealing how IDR sequence influences ensemble dimensionsin situ.Furthermore, we show that the interplay between sequence and ensemble can tune an IDR’s ability to sense changes in cell volume - ade novomolecular function for these synthetic sequences. Our results establish biophysical rules for intracellular sequence-ensemble relationships, enable a new route for understanding how IDR sequences map to function in live cells, and set the ground for the design of synthetic IDRs withde novofunction.

Direct prediction of intrinsically disordered protein conformational properties from sequence

“…The overall approach for developing ALBATROSS involved several steps. First, we generated a library of synthetic disordered proteins that systematically titrated across compositional space using our artificial disordered protein design package GOOSE 33 . Next, we fine-tuned the Mpipi force field, making small changes to the previously published parameters to address minor shortcomings, leading to a version we refer to as Mpipi-GG 24 .…”

“…A systematic exploration of IDR sequence space enabled our deep-learning models to learn the complex underlying sequence-encoded conformational biases of disordered proteins. Rationally designed IDRs were generated using GOOSE, our recently developed computational package for synthetic IDR design 33 . GOOSE allowed us to titrate across a range of sequence features that impact IDR conformational behavior (Fig.…”

“…Using the IDR design package GOOSE, we assembled a library of chemically diverse synthetic disordered proteins (https://github.com/idptools/goose) 33 . The sequences varied in charge, hydropathy, charge patterning and amino acid composition and were between 10 and 750 residues long.…”

Direct prediction of intermolecular interactions driven by disordered regions

“…Disorder prediction is calculated using metapredict V2-FF ( 45 , 123 ). Rational sequence designs used for examining homopolymer vs. IDR properties were generated using GOOSE ( 124 ). Proteome-wide analysis was performed using SHEPHARD, with data obtained from UniProt ( 67 , 125 ).…”