Cysteine oxidation in proteins: structure, biophysics, and simulation

D Garrido Ruiz, A Sandoval-Perez, AV Rangarajan… - Biochemistry, 2022 - ACS Publications
Cysteine side chains can exist in distinct oxidation states depending on the pH and redox
potential of the environment, and cysteine oxidation plays important yet complex regulatory …

Predicting equilibrium distributions for molecular systems with deep learning

S Zheng, J He, C Liu, Y Shi, Z Lu, W Feng… - Nature Machine …, 2024 - nature.com
Advances in deep learning have greatly improved structure prediction of molecules.
However, many macroscopic observations that are important for real-world applications are …

Transfer learning in proteins: evaluating novel protein learned representations for bioinformatics tasks

E Fenoy, AA Edera, G Stegmayer - Briefings in Bioinformatics, 2022 - academic.oup.com
A representation method is an algorithm that calculates numerical feature vectors for
samples in a dataset. Such vectors, also known as embeddings, define a relatively low …

ATLAS: protein flexibility description from atomistic molecular dynamics simulations

Y Vander Meersche, G Cretin, A Gheeraert… - Nucleic acids …, 2024 - academic.oup.com
Dynamical behaviour is one of the most crucial protein characteristics. Despite the advances
in the field of protein structure resolution and prediction, analysis and prediction of protein …

[HTML][HTML] Sites of transcription initiation drive mRNA isoform selection

C Alfonso-Gonzalez, I Legnini, S Holec, L Arrigoni… - Cell, 2023 - cell.com
The generation of distinct messenger RNA isoforms through alternative RNA processing
modulates the expression and function of genes, often in a cell-type-specific manner. Here …

Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor

D Zhang, J Ivica, JM Krieger, H Ho, K Yamashita… - Nature, 2023 - nature.com
AMPA glutamate receptors (AMPARs), the primary mediators of excitatory
neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca2+ …

Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants

S Moriyama, Y Anraku, S Taminishi, Y Adachi… - Nature …, 2023 - nature.com
SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS)
antibodies that exist in diverse individuals as public antibody clones. We rationally selected …

Molecular mechanism of high-pressure processing regulates the aggregation of major royal jelly proteins

F Pan, X Li, T Tuersuntuoheti, W Wang, X Zheng… - Food …, 2023 - Elsevier
The aggregation behavior of major royal jelly proteins (MRJPs) significantly impacts their
quality and nutrient bioavailability, yet studies on their aggregate regulation are limited. This …

Discovering selective antiferroptotic inhibitors of the 15LOX/PEBP1 complex noninterfering with biosynthesis of lipid mediators

HH Dar, K Mikulska-Ruminska, YY Tyurina… - Proceedings of the …, 2023 - pnas.org
Programmed ferroptotic death eliminates cells in all major organs and tissues with
imbalanced redox metabolism due to overwhelming iron-catalyzed lipid peroxidation under …