The intricate balance between microRNA‐induced mRNA decay and translational repression

P Naeli, T Winter, AP Hackett, L Alboushi… - The FEBS …, 2023 - Wiley Online Library
Post‐transcriptional regulation of messenger RNAs (mRNAs)(ie, mechanisms that control
translation, stability and localization) is a critical focal point in spatiotemporal regulation of …

Structural and molecular mechanisms for the control of eukaryotic 5′–3′ mRNA decay

JS Mugridge, J Coller, JD Gross - Nature structural & molecular biology, 2018 - nature.com
3′ RNA decay pathways are critical for quality control and regulation of gene expression.
Structural and biochemical studies have provided insights into the key nucleases that carry …

DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model

Y Fang, Y Jiang, L Wei, Q Ma, Z Ren, Q Yuan… - …, 2023 - academic.oup.com
Motivation Identifying the functional sites of a protein, such as the binding sites of proteins,
peptides, or other biological components, is crucial for understanding related biological …

Predicting protein–peptide interactions: benchmarking deep learning techniques and a comparison with focused docking

S Shanker, MF Sanner - Journal of Chemical Information and …, 2023 - ACS Publications
The accurate prediction of protein structures achieved by deep learning (DL) methods is a
significant milestone and has deeply impacted structural biology. Shortly after its release …

New insights into decap** enzymes and selective mRNA decay

E Grudzien‐Nogalska… - Wiley Interdisciplinary …, 2017 - Wiley Online Library
Removal of the 5′ end cap is a critical determinant controlling mRNA stability and efficient
gene expression. Removal of the cap is exquisitely controlled by multiple direct and indirect …

Eukaryotic mRNA decap** activation

E Vidya, TF Duchaine - Frontiers in Genetics, 2022 - frontiersin.org
The 5′-terminal cap is a fundamental determinant of eukaryotic gene expression which
facilitates cap-dependent translation and protects mRNAs from exonucleolytic degradation …

Messenger RNA 5′ NAD+ cap** is a dynamic regulatory epitranscriptome mark that is required for proper response to abscisic acid in Arabidopsis

X Yu, MR Willmann, LE Vandivier, S Trefely… - Developmental Cell, 2021 - cell.com
Although eukaryotic messenger RNAs (mRNAs) normally possess a 5′ end N 7-methyl
guanosine (m 7 G) cap, a non-canonical 5′ nicotinamide adenine dinucleotide (NAD+) cap …

The importance of non-accessible crosslinks and solvent accessible surface distance in modeling proteins with restraints from crosslinking mass spectrometry

JMA Bullock, J Schwab, K Thalassinos… - Molecular & Cellular …, 2016 - ASBMB
Crosslinking mass spectrometry (XL-MS) is becoming an increasingly popular technique for
modeling protein monomers and complexes. The distance restraints garnered from these …

Eukaryotic mRNA decap** factors: molecular mechanisms and activity

F He, A Jacobson - The FEBS journal, 2023 - Wiley Online Library
Decap** is the enzymatic removal of 5′ cap structures from mRNAs in eukaryotic cells.
Cap structures normally enhance mRNA translation and stability, and their excision commits …

Dcp2 C-terminal cis-binding elements control selective targeting of the decap** enzyme by forming distinct decap** complexes

F He, C Wu, A Jacobson - Elife, 2022 - elifesciences.org
A single Dcp1–Dcp2 decap** enzyme targets diverse classes of yeast mRNAs for
decap**-dependent 5′ to 3′ decay, but the molecular mechanisms controlling mRNA …