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 …

[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 …

PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins

H Ghafouri, T Lazar, A Del Conte… - Nucleic acids …, 2024 - academic.oup.com
Abstract The Protein Ensemble Database (PED)(URL: https://proteinensemble. org) is the
primary resource for depositing structural ensembles of intrinsically disordered proteins. This …

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 …

Direct prediction of intrinsically disordered protein conformational properties from sequence

JM Lotthammer, GM Ginell, D Griffith, R Emenecker… - Biophysical …, 2024 - cell.com
Intrinsically 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 stable 3D …

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 …

A coarse‐grained model for disordered and multi‐domain proteins

F Cao, S von Bülow, G Tesei… - Protein …, 2024 - Wiley Online Library
Many proteins contain more than one folded domain, and such modular multi‐domain
proteins help expand the functional repertoire of proteins. Because of their larger size and …

Random, de novo, and conserved proteins: how structure and disorder predictors perform differently

L Middendorf, LA Eicholt - Proteins: Structure, Function, and …, 2024 - Wiley Online Library
Understanding the emergence and structural characteristics of de novo and random proteins
is crucial for unraveling protein evolution and designing novel enzymes. However …

Predicting heteropolymer interactions: Demixing and hypermixing of disordered protein sequences

K Adachi, K Kawaguchi - Physical Review X, 2024 - APS
Cells contain multiple condensates which spontaneously form due to the heterotypic
interactions between their components. Although the proteins and disordered region …

Machine-learning-based methods to generate conformational ensembles of disordered proteins

I Taneja, K Lasker - Biophysical Journal, 2024 - cell.com
Intrinsically disordered proteins are characterized by a conformational ensemble. While
computational approaches such as molecular dynamics simulations have been used to …