Abstract Intrinsically disordered proteins (IDPs) drive a large fraction of cellular signaling, transcription, and assembly through interfaces that often lack a defined geometry, making the prediction of their binding energies challenging for methods developed primarily for folded complexes. Here, we introduce FlexENN,...
Maryum Irshad, Kassandra Ori-McKenney, Ruxandra I. Dima· Journal of Chemical Informat...· 0 citations
Understanding of PCD variants in the Indian population is enhanced and the value of combining clinical evaluations with genomic and structural analyses is highlighted, as PPI and GO analyses reveal disrupted ciliary pathways linked to PCD.
Janani Balaji, Anitha M. Barney, Madhan Kumar et al.· Lung India· 0 citations
G-quadruplexes (G4s) in functional RNAs regulate telomere maintenance, mRNA processing, and disease pathways, but their detection in long transcripts is limited by biophysical methods. Herein, we engineered RHAU-RNase HI, fusing the G4-binding RHAU domain (aa 53-192) with RNase HI (Bacillus halodurans), to probe RNA G4...
K. H. Ngo, T. T. Nguyen, D. T. Dang· Archives of Biochemistry and...· 0 citations
Together, these results establish recurrent catalytic-state change and physicochemical remodeling of the ancestral HEPN cleft, whether such remodeling corresponds to altered binding, regulation, or another molecular function remains a hypothesis requiring experimental testing.
M. Zimmer· Journal of Molecular Biology· 0 citations
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This study presents a pioneering model for predicting the frequency of protein K-PTM types, and examines the relationship between protein similarity and differences in K-PTM-type frequency to investigate why the model can successfully predict this target.
Lei Chen, Xin-Xiang Zhu, Xiao-Hui Wang et al.· International Journal of Bio...· 0 citations
Toxicogenomic studies increasingly promote microRNA (miRNA) expression changes as chemical-toxicity biomarkers and infer their meaning from computationally predicted messenger RNA (mRNA) targets, rarely testing those predictions against matched mRNA data. We present the Coherence Response Index (CRI), an open, expressi...
An ensemble-based model in which pre-existing conformational organization shapes how the protein responds to the matched mutations is supported and stability-engineering mutations should be evaluated in the context of the parent ensemble is argued.
Shiqinrui Xu, Yi Yuan, Shuo-Cheng Wang et al.· Physical Chemistry, Chemical...· 0 citations
Findings identify autophagy-regulated amino acid homeostasis as a critical mechanism that sustains Foxo1 protein abundance and supports glucagon-responsive hepatic metabolic adaptation during fasting.
Zheng Shen, Wan-Bao Yang, Quan Pan et al.· Diabetes, obesity and metabo...· 0 citations
The results provide the first integrated characterization of nsLTPs in Cereus, supporting a gate-modulation hypothesis in which structural variation concentrated at tunnel entrances may contribute to functional diversification while preserving the conserved nsLTP fold (four-helix scaffold).
M. I. O. Cardoso, J. A. Teodoro, T. Costa-Silva et al.· Journal of Molecular Evoluti...· 0 citations
The mechanisms of protein folding, misfolding, aggregation, and prion-like propagation in major neurodegenerative proteinopathies, including amyloid-beta and tau in Alzheimer's disease, alpha-synuclein in synucleinopathies, TDP-43 and FUS in ALS/FTLD, polyglutamine-expanded proteins, prion proteins, and rare hereditary...
A. Choudhury, Sneh Prabha, Mohammad Umar Saeed et al.· Expert opinion on therapeuti...· 0 citations
AIMS
Aeromonas hydrophila is a zoonotic pathogen, and its prevalence of drug resistance underscores the urgency of elucidating alternative bactericidal strategies. This study employed the oxytetracycline-resistant strain OTC-A01 to investigate the bactericidal mechanism of ε-polylysine (ε-PL).
METHODS AND RESULTS
Wit...
Huan Lin, Dan-Feng Zhang, Qiu-Qiang Zhu et al.· Journal of Applied Microbiol...· 0 citations
BACKGROUND
Moulting is a crucial process in the growth and development of insects and is also a key focus in the development of insecticides. Cyromazine, a moulting disruptor, is widely used to control dipteran pests, yet its mechanism of action and the genetic basis of resistance remain unclear. This study aimed to sy...
Fan Zhang, Yu-Qiu Xie, Yan-Chao Zhang et al.· Pest Management Science· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
