The molecular basis for cellular function of intrinsically disordered protein regions

AS Holehouse, BB Kragelund - Nature Reviews Molecular Cell Biology, 2024 - nature.com
Intrinsically disordered protein regions exist in a collection of dynamic interconverting
conformations that lack a stable 3D structure. These regions are structurally heterogeneous …

Overview of AlphaFold2 and breakthroughs in overcoming its limitations.

L Wang, Z Wen, SW Liu, L Zhang, C Finley… - Computers in Biology …, 2024 - Elsevier
Abstract Predicting three-dimensional (3D) protein structures has been challenging for
decades. The emergence of AlphaFold2 (AF2), a deep learning-based machine learning …

Conformational ensembles of the human intrinsically disordered proteome

G Tesei, AI Trolle, N Jonsson, J Betz, FE Knudsen… - Nature, 2024 - nature.com
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 …

Design of intrinsically disordered protein variants with diverse structural properties

F Pesce, A Bremer, G Tesei, JB Hopkins, CR Grace… - Science …, 2024 - science.org
Intrinsically disordered proteins (IDPs) perform a broad range of functions in biology,
suggesting that the ability to design IDPs could help expand the repertoire of proteins with …

AIUPred: combining energy estimation with deep learning for the enhanced prediction of protein disorder

G Erdős, Z Dosztányi - Nucleic Acids Research, 2024 - academic.oup.com
Intrinsically disordered proteins and protein regions (IDPs/IDRs) carry out important
biological functions without relying on a single well-defined conformation. As these proteins …

Identification of plant transcriptional activation domains

N Morffy, L Van den Broeck, C Miller, RJ Emenecker… - Nature, 2024 - nature.com
Gene expression in Arabidopsis is regulated by more than 1,900 transcription factors (TFs),
which have been identified genome-wide by the presence of well-conserved DNA-binding …

SOURSOP: A Python package for the analysis of simulations of intrinsically disordered proteins

JM Lalmansingh, AT Keeley, KM Ruff… - Journal of chemical …, 2023 - ACS Publications
Conformational heterogeneity is a defining hallmark of intrinsically disordered proteins and
protein regions (IDRs). The functions of IDRs and the emergent cellular phenotypes they …

[HTML][HTML] Biomolecular NMR spectroscopy in the era of artificial intelligence

VK Shukla, GT Heller, DF Hansen - Structure, 2023 - cell.com
Biomolecular nuclear magnetic resonance (NMR) spectroscopy and artificial intelligence
(AI) have a burgeoning synergy. Deep learning-based structural predictors have forever …

Differential Effects of Sequence-Local versus Nonlocal Charge Patterns on Phase Separation and Conformational Dimensions of Polyampholytes as Model …

T Pal, J Wessén, S Das, HS Chan - The journal of physical …, 2024 - ACS Publications
Conformational properties of intrinsically disordered proteins (IDPs) are governed by a
sequence-ensemble relationship. To differentiate the impact of sequence-local versus …

Programmability and biomedical utility of intrinsically-disordered protein polymers

MC Giraldo-Castano, KA Littlejohn… - Advanced Drug Delivery …, 2024 - Elsevier
Intrinsically disordered proteins (IDPs) exhibit molecular-level conformational dynamics that
are functionally harnessed across a wide range of fascinating biological phenomena. The …