Aggregation of disordered proteins associated with neurodegeneration

PS Tsoi, MD Quan, JC Ferreon… - International journal of …, 2023 - mdpi.com
Cellular deposition of protein aggregates, one of the hallmarks of neurodegeneration,
disrupts cellular functions and leads to neuronal death. Mutations, posttranslational …

Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins

L Kurgan, G Hu, K Wang, S Ghadermarzi, B Zhao… - Nature …, 2023 - nature.com
Intrinsic disorder is instrumental for a wide range of protein functions, and its analysis, using
computational predictions from primary structures, complements secondary and tertiary …

IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation

G Erdős, M Pajkos, Z Dosztányi - Nucleic acids research, 2021 - academic.oup.com
Intrinsically disordered proteins and protein regions (IDPs/IDRs) exist without a single well-
defined conformation. They carry out important biological functions with multifaceted roles …

MobiDB: 10 years of intrinsically disordered proteins

D Piovesan, A Del Conte, D Clementel… - Nucleic acids …, 2023 - academic.oup.com
The MobiDB database (URL: https://mobidb. org/) is a knowledge base of intrinsically
disordered proteins. MobiDB aggregates disorder annotations derived from the literature …

flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions

G Hu, A Katuwawala, K Wang, Z Wu… - Nature …, 2021 - nature.com
Identification of intrinsic disorder in proteins relies in large part on computational predictors,
which demands that their accuracy should be high. Since intrinsic disorder carries out a …

xTrimoPGLM: unified 100B-scale pre-trained transformer for deciphering the language of protein

B Chen, X Cheng, P Li, Y Geng, J Gong, S Li… - arxiv preprint arxiv …, 2024 - arxiv.org
Protein language models have shown remarkable success in learning biological information
from protein sequences. However, most existing models are limited by either autoencoding …

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

B Mészáros, G Erdős, Z Dosztányi - Nucleic acids research, 2018 - academic.oup.com
The structural states of proteins include ordered globular domains as well as intrinsically
disordered protein regions that exist as highly flexible conformational ensembles in …

Genomic RNA elements drive phase separation of the SARS-CoV-2 nucleocapsid

C Iserman, CA Roden, MA Boerneke, RSG Sealfon… - Molecular cell, 2020 - cell.com
We report that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid
phase separation (LLPS) with viral RNA. N-protein condenses with specific RNA genomic …

eIF4F is a thermo-sensing regulatory node in the translational heat shock response

CD Altamirano, MK Kang, MA Jordan, T Borianne… - Molecular Cell, 2024 - cell.com
Heat-shocked cells prioritize the translation of heat shock (HS) mRNAs, but the underlying
mechanism is unclear. We report that HS in budding yeast induces the disassembly of the …

A de novo evolved gene contributes to rice grain shape difference between indica and japonica

R Chen, N **ao, Y Lu, T Tao, Q Huang, S Wang… - Nature …, 2023 - nature.com
The role of de novo evolved genes from non-coding sequences in regulating morphological
differentiation between species/subspecies remains largely unknown. Here, we show that a …