Proteingym: Large-scale benchmarks for protein fitness prediction and design

P Notin, A Kollasch, D Ritter… - Advances in …, 2024 - proceedings.neurips.cc
Predicting the effects of mutations in proteins is critical to many applications, from
understanding genetic disease to designing novel proteins to address our most pressing …

Bridging dietary polysaccharides and gut microbiome: how to achieve precision modulation for gut health promotion

X Sun, Z Pei, H Wang, J Zhao, W Chen, W Lu - Microbiological Research, 2025 - Elsevier
Dietary polysaccharides function not only as indispensable nutrients and energy sources for
the host organism but also as critical substrates for the gut microbiota. Gut microorganisms …

A mutational atlas for Parkin proteostasis

L Clausen, V Voutsinos, M Cagiada… - Nature …, 2024 - nature.com
Proteostasis can be disturbed by mutations affecting folding and stability of the encoded
protein. An example is the ubiquitin ligase Parkin, where gene variants result in autosomal …

Construction of a precise temperature–controlled continuous-flow catalytic reactor based on cellulose and MXene with directional thermal pathway heating and …

CX He, ZZ Lu, XH Yao, T Chen, WG Zhao… - Chemical Engineering …, 2025 - Elsevier
Bioreactors are crucial in industrial production, where enzyme catalysis typically occurs in
water and requires continuous heating, consuming significant energy. This study reports a …

The activity regulation of lipase from Aspergillus fumigatus by ligand through allosteric exploration

F Wang, K Kang, M Zhang, K Fraser, F Zhang… - International Journal of …, 2025 - Elsevier
Lipase activity from Aspergillus fumigatus (AFL) were modulated by an effector (HMD) that
was discovered for an allosteric site on the bioactive macromolecule. Experimental …

Engineering high-activity crosslinked enzyme aggregates via SpyCatcher/SpyTag-mediated self-assembly

X Ma, Y Yang, M Wang, Y Zhang, B Zhao, S Hao… - International Journal of …, 2025 - Elsevier
Abstract Crosslinked Enzyme Aggregates (CLEAs) are favored for their operational stability
and recyclability. However, the traditional CLEAs preparation may distort the enzyme's …

Synthesis of value-added uridine 5'-diphosphate-glucose from sucrose applying an engineered sucrose synthase counteracts the activity-stability trade-off

L Zhao, Z Ma, L Zhang, Y Shen, L Chen, Y Li, S Xu… - Food Chemistry, 2025 - Elsevier
The one-step deconstruction of sucrose into uridine 5′-diphosphate-glucose (UDP-Glc), an
important sugar donor for transglycosylation, employing sucrose synthase (Susy) is …

Functionalized polysaccharides improve sensitivity of tyramide/peroxidase proximity labeling assays through electrostatic interactions

M Heiniger, R Vanella, Z Walsh-Korb… - … Biomaterials Science & …, 2024 - ACS Publications
High-throughput assays that efficiently link genotype and phenotype with high fidelity are
key to successful enzyme engineering campaigns. Among these assays, the …

Dual-domain superoxide dismutase: In silico prediction directed combinatorial mutation for enhanced robustness and catalytic efficiency

J Liu, L Yao, F Zhao, J Zhang, J Gong, J Li… - International Journal of …, 2024 - Elsevier
The robustness and catalytic activity of superoxide dismutase (SOD) are still the main factors
limiting their application in industrial fields. This study aims to further improve the properties …

ProteusAI: An Open-Source and User-Friendly Platform for Machine Learning-Guided Protein Design and Engineering

J Funk, L Machado, SA Bradley, M Napiorkowska… - bioRxiv, 2024 - biorxiv.org
Protein design and engineering are crucial for advancements in biotechnology, medicine,
and sustainability. Machine learning (ML) models are used to design or enhance protein …