Direct Prediction of Intrinsically Disordered Protein Conformational Properties From Sequence

Abstract

ABSTRACTIntrinsically disordered regions (IDRs) are ubiquitous across all domains of life and play a range of functional roles. While folded domains are generally well-described by a single 3D structure, IDRs exist in a collection of interconverting states known as an ensemble. This structural heterogeneity means IDRs are largely absent from the PDB, contributing to a lack of computational approaches to predict ensemble conformational properties from sequence. Here we combine rational sequence design, large-scale molecular simulations, and deep learning to develop ALBATROSS, a deep learning model for predicting IDR ensemble dimensions from sequence. ALBATROSS enables the instantaneous prediction of ensemble average properties at proteome-wide scale. ALBATROSS is lightweight, easy-to-use, and accessible as both a locally installable software package and a point-and-click style interface in the cloud. We first demonstrate the applicability of our predictors by examining the generalizability of sequence-ensemble relationships in IDRs. Then, we leverage the high-throughput nature of ALBATROSS to characterize emergent biophysical behavior of IDRs within and between proteomes.Update from previous versionThis preprint reports an updated version of the ALBATROSS network weights trained on simulations of over 42,000 sequences.In addition, we provide new colab notebooks that enable proteome-wide IDR prediction and annotation in minutes.All conclusions and observations made in versions 1 and 2 of this manuscript remain true and robust.