Intrinsic disorder and other malleable arsenals of evolved protein multifunctionality

A Aftab, S Sil, S Nath, A Basu, S Basu - Journal of Molecular Evolution, 2024 - Springer
Microscopic evolution at the functional biomolecular level is an ongoing process.
Leveraging functional and high-throughput assays, along with computational data mining …

Benchmarking methods for PROTAC ternary complex structure prediction

E Rovers, M Schapira - Journal of Chemical Information and …, 2024 - ACS Publications
Proteolysis targeting chimeras (PROTACs) are bifunctional compounds that recruit an E3
ligase to a target protein to induce ubiquitination and degradation of the target. Rational …

[HTML][HTML] Recent Advances in Mass Spectrometry-based Protein Interactome Studies

S Wu, S Zhang, CM Liu, AR Fernie, S Yan - Molecular & Cellular Proteomics, 2024 - Elsevier
The foundation of all biological processes is the network of diverse and dynamic protein
interactions with other molecules in cells known as the interactome. Understanding the …

Structural basis for the conformational protection of nitrogenase from O2

SM Narehood, BD Cook, S Srisantitham, VH Eng… - Nature, 2025 - nature.com
The low reduction potentials required for the reduction of dinitrogen (N2) render metal-
based nitrogen-fixation catalysts vulnerable to irreversible damage by dioxygen (O2) …

Elucidation of the noncovalent interactions driving enzyme activity guides branching enzyme engineering for α-glucan modification

Z Zong, X Zhang, P Chen, Z Fu, Y Zeng… - Nature …, 2024 - nature.com
Branching enzymes (BEs) confer to α-glucans, the primary energy-storage reservoir in
nature, a variety of features, like slow digestion. The full catalytic cycle of BEs can be divided …

Discovery of highly bioactive peptides through hierarchical structural information and molecular dynamics simulations

S Li, L Peng, L Chen, L Que, W Kang… - Journal of Chemical …, 2024 - ACS Publications
Peptide drugs play an essential role in modern therapeutics, but the computational design of
these molecules is hindered by several challenges. Traditional methods like molecular …

Nuclear adenine activates hnRNPA2B1 to enhance antibacterial innate immunity

S Zhang, Z Cui, D Zhang, D Zhang, K **, Z Li, B Li… - Cell Metabolism, 2025 - cell.com
Bacterial infection reprograms cellular metabolism and epigenetic status, but how the
metabolic-epigenetic crosstalk empowers host antibacterial defense remains unclear. Here …

[HTML][HTML] Evaluation of Structure Prediction and Molecular Docking Tools for Therapeutic Peptides in Clinical Use and Trials Targeting Coronary Artery Disease

N Alotaiq, D Dermawan - International Journal of Molecular Sciences, 2025 - mdpi.com
This study evaluates the performance of various structure prediction tools and molecular
docking platforms for therapeutic peptides targeting coronary artery disease (CAD) …

In silico antiviral effect assessment of some venom gland peptides from Odontobuthus doriae scorpion against SARS-CoV-2

MN Soorki - Toxicon, 2025 - Elsevier
SARS-CoV-2 is from the enveloped virus family responsible for the COVID-19 pandemic. No
efficient drugs are currently available to treat infection explicitly caused by this virus …

G-quadruplex-forming small RNA inhibits coronavirus and influenza A virus replication

R Sekine, K Takeda, T Suenaga, S Tsuno… - Communications …, 2025 - nature.com
Future pandemic threats may be caused by novel coronaviruses and influenza A viruses.
Here we show that when directly added to a cell culture, 12mer guanine RNA (G12) and its …