TY - JOUR

T1 - Conformational ensembles of the human intrinsically disordered proteome

AU - Tesei, Giulio

AU - Trolle, Anna Ida

AU - Jonsson, Nicolas

AU - Betz, Johannes

AU - Knudsen, Frederik E.

AU - Pesce, Francesco

AU - Johansson, Kristoffer E.

AU - Lindorff-Larsen, Kresten

N1 - Publisher Copyright: © 2024, The Author(s), under exclusive licence to Springer Nature Limited.

PY - 2024

Y1 - 2024

N2 - 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 relationships 1. Developments in protein science have made it possible to predict the three-dimensional structures of folded proteins at the proteome scale 2. 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 IDRs 3, we developed an efficient molecular model to generate conformational ensembles of IDRs and thereby to predict their conformational properties from sequences 4,5. 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.

AB - 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 relationships 1. Developments in protein science have made it possible to predict the three-dimensional structures of folded proteins at the proteome scale 2. 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 IDRs 3, we developed an efficient molecular model to generate conformational ensembles of IDRs and thereby to predict their conformational properties from sequences 4,5. 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.

U2 - 10.1038/s41586-023-07004-5

DO - 10.1038/s41586-023-07004-5

M3 - Journal article

C2 - 38297118

AN - SCOPUS:85183679295

VL - 626

SP - 897

EP - 904

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

ER -