Abstract Cell-penetrating peptides (CPPs) remain a leading nonviral strategy for the intracellular delivery of polynucleotides and folded proteins, but native α-peptide CPPs are constrained by proteolysis, dose-dependent cytotoxicity, and endosomal entrapment. Peptidomimetic redesign addresses these limitations by repl...
Protein misfolding diseases arise from topological phase transitions in the E8 fiber bundle where non-trivial holonomy around closed loops in configuration space creates wall crossings that trap proteins in pathological configurations. The 240 root vectors define "stability chambers" in fold space, and disease states o...
Andrew Stewart Caldin· Zenodo (CERN European Organi...· 0 citations
Mixed bacterial infections, including Gram-positive and Gram-negative pathogens, remain a major global health concern. Achieving efficient treatment of synergistic polymicrobial infections stills a tremendous clinical challenge due to antibiotic permeability barriers and resistance. Here, we construct a defect-engineer...
Path collective variables reduce a high-dimensional transition to a progress coordinate, s, and an orthogonal distance, z. Computing the free energy along s often requires restraining z, so that sampling embraces a tube centered on the reference path. However, a conventional fixed half-harmonic wall demands an a priori...
Radu A. Talmazan, Cheng Giuseppe Chen, Chenyu Tang et al.· The Journal of Chemical Phys...· 0 citations
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Delay is an inherent feature of genetic regulatory networks. It represents the time required for the assembly of functional regulator proteins. The protein production process is complex, as it includes transcription, translocation, translation, folding, and oligomerization. Because these steps are noisy, the resulting...
Sean Campbell, Courtney C. White, Amanda M. Alexander et al.· SIAM Journal on Life Science...· 0 citations
Sequence differences between deposited macromolecular models and their UniProt references are recorded in the mmCIF category _struct_ref_seq_dif, and intentional substitutions are expected to populate _entity_poly.pdbx_mutation, the field that structured queries read. When a substitution is not declared, the difference...
Michael T. Varman· Zenodo (CERN European Organi...· 0 citations
Cyclic oligonucleotide-based antiphage signaling systems (CBASS) protect bacteria from bacteriophage infection by producing cyclic nucleotide second messengers that activate downstream effector proteins. Cyclic guanosine monophosphate-adenosine monophosphate (cGAMP)-activated phospholipase in Vibrio (CapV) is a prevale...
Samson Marvellous Oladeji, Shay Adio, C. Vennard et al.· ACS Chemical Biology· 0 citations
Ultrasonography (USG) is central to the diagnosis of pediatric appendicitis, but operator dependency and limited access can delay triage. This study aimed to develop an explainable machine learning model that estimates the USG-assisted clinical diagnosis of appendicitis from pre-imaging clinical and laboratory data alo...
Hilal Yumrutaş, Selahaddin Batuhan Akben, Yavuz Selim İşler· Bratislavské lekárske list...· 0 citations
It is reported that PML-1 itself harbors a previously structurally uncharacterized nucleic acid-binding domain, termed PXL, which is unique to isoform 1 and specifically binds G-rich oligonucleotides implicated in G-quadruplex formation and displays a strong in vitro preference for polyUG RNA.
Daniel Fairchild, Irina V. Semenova, Dane H. Geddes-Buehre et al.· Nucleic Acids Research· 0 citations
This work defines a previously unrecognized class of oncogenic fusions that preserve protein structure but replace the 5' untranslated region (5' UTR), thereby rewiring translational regulation in cancer patients.
M. Cerqua, Estelle Bigot, Cédric Chaveroux et al.· Cell Reports· 0 citations
This review underscores the potential of BamA as a next-generation antibacterial target and outlines future directions for the development of effective therapeutics against multidrug-resistant Gram-negative bacteria.
A. Al-Karmalawy, A. A. Al Khatib, S. Hawas· RSC Advances· 0 citations
In six cancer proteomics cohorts, 334 small-protein candidates were identified, including 36 differentially expressed small proteins (DESPs) exhibiting strong cancer-type specificity, suggesting specialized functional roles in tumor biology and underscore the potential of SPROTify as a robust, protein-centric engine fo...
Chien-Han Yuan, Pei-Wen Wu, Ing-Luen Shyu et al.· New Biotechnology· 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.
