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| http://dx.doi.org/10.1038/s41422-020-0366-x | DOI Listing |
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Molecular dynamics and machine learning stratify motion-dependent activity profiles of S-layer destabilizing nanobodies.
PNAS Nexus
December 2024
Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO 80401, USA.
Nanobody (Nb)-induced disassembly of surface array protein (Sap) S-layers, a two-dimensional paracrystalline protein lattice from , has been presented as a therapeutic intervention for lethal anthrax infections. However, only a subset of existing Nbs with affinity to Sap exhibit depolymerization activity, suggesting that affinity and epitope recognition are not enough to explain inhibitory activity. In this study, we performed all-atom molecular dynamics simulations of each Nb bound to the Sap binding site and trained a collection of machine learning classifiers to predict whether each Nb induces depolymerization.
View Article and Find Full Text PDFFrom a better knowledge of periodontal disease to Porphyromonas gingivalis target for rheumatoid arthritis disease activity.
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Inserm, SAINBIOSE U1059, Rheumatology Departement, Mines Saint-Étienne, Université Jean-Monnet Saint-Étienne, CHU de Saint-Etienne, 42023 Saint-Étienne, France. Electronic address:
Periodontal disease (PD) and rheumatoid arthritis (RA) are both inflammatory diseases affecting the tooth and joint, with local inflammation associated with bone loss. Bacterial infections by oral bacteria are involved in periodontal inflammation, and the best known to be associated with PD is Porphyromonas gingivalis (Pg). A large body of recent data suggests a strong involvement of this specific bacteria, Pg, in PD outcomes, but also in RA.
View Article and Find Full Text PDFMining the secreted and membrane transcriptome of Hyalomma dromedarii ticks for identification of potential protective antigens.
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Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Cairo, Egypt.
Article Synopsis
- - The study focuses on Hyalomma dromedarii ticks, which are significant for transmitting pathogens to large animals in Egypt, especially as camels and cattle are imported from neighboring countries.
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Machine learning accelerates the discovery of epitope-based dual-bioactive peptides against skin infections.
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December 2024
Department of Critical Care Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, PR China. Electronic address:
Objectives: Skin injuries and infections are an inevitable part of daily human life, particularly with chronic wounds, becoming an increasing socioeconomic burden. In treating skin infections and promoting wound healing, bioactive peptides may hold significant potential, particularly those possessing antimicrobial and anti-inflammatory properties. However, obtaining these peptides solely through traditional wet laboratory experiments is costly and time-consuming, and peptides identified by current computer-assisted predictive models largely lack validation of their effects via wet laboratory experiments.
View Article and Find Full Text PDFRapid affinity optimization of an anti-TREM2 clinical lead antibody by cross-lineage immune repertoire mining.
Nat Commun
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Department of Antibody Engineering, Genentech, South San Francisco, CA, 94080, USA.
We describe a process for rapid antibody affinity optimization by repertoire mining to identify clones across B cell clonal lineages based on convergent immune responses where antigen-specific clones with the same heavy (V) and light chain germline segment pairs, or parallel lineages, bind a single epitope on the antigen. We use this convergence framework to mine unique and distinct V lineages from rat anti-triggering receptor on myeloid cells 2 (TREM2) antibody repertoire datasets with high diversity in the third complementarity-determining loop region (CDR H3) to further affinity-optimize a high-affinity agonistic anti-TREM2 antibody while retaining critical functional properties. Structural analyses confirm a nearly identical binding mode of anti-TREM2 variants with subtle but significant structural differences in the binding interface.
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