Conformational ensembles of the human intrinsically disordered proteome

Giulio Tesei (), Anna Ida Trolle, Nicolas Jonsson, Johannes Betz, Frederik E. Knudsen, Francesco Pesce, Kristoffer E. Johansson and Kresten Lindorff-Larsen ()
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Giulio Tesei: University of Copenhagen
Anna Ida Trolle: University of Copenhagen
Nicolas Jonsson: University of Copenhagen
Johannes Betz: University of Copenhagen
Frederik E. Knudsen: University of Copenhagen
Francesco Pesce: University of Copenhagen
Kristoffer E. Johansson: University of Copenhagen
Kresten Lindorff-Larsen: University of Copenhagen

Nature, 2024, vol. 626, issue 8000, 897-904

Abstract: Abstract Intrinsically disordered proteins and regions (collectively, IDRs) are pervasive across proteomes in all kingdoms of life, help to shape biological functions and are involved in numerous diseases. IDRs populate a diverse set of transiently formed structures and defy conventional sequence–structure–function relationships1. Developments in protein science have made it possible to predict the three-dimensional structures of folded proteins at the proteome scale2. By contrast, there is a lack of knowledge about the conformational properties of IDRs, partly because the sequences of disordered proteins are poorly conserved and also because only a few of these proteins have been characterized experimentally. The inability to predict structural properties of IDRs across the proteome has limited our understanding of the functional roles of IDRs and how evolution shapes them. As a supplement to previous structural studies of individual IDRs3, we developed an efficient molecular model to generate conformational ensembles of IDRs and thereby to predict their conformational properties from sequences4,5. Here we use this model to simulate nearly all of the IDRs in the human proteome. Examining conformational ensembles of 28,058 IDRs, we show how chain compaction is correlated with cellular function and localization. We provide insights into how sequence features relate to chain compaction and, using a machine-learning model trained on our simulation data, show the conservation of conformational properties across orthologues. Our results recapitulate observations from previous studies of individual protein systems and exemplify how to link—at the proteome scale—conformational ensembles with cellular function and localization, amino acid sequence, evolutionary conservation and disease variants. Our freely available database of conformational properties will encourage further experimental investigation and enable the generation of hypotheses about the biological roles and evolution of IDRs.

Date: 2024
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DOI: 10.1038/s41586-023-07004-5

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