DALI shines a light on remote homologs: One hundred discoveries

Protein Science, Journal Year: 2022, Volume and Issue: 32(1)

Published: Nov. 24, 2022

Structural comparison reveals remote homology that often fails to be detected by sequence comparison. The DALI web server (http://ekhidna2.biocenter.helsinki.fi/dali) is a platform for structural analysis provides database searches and interactive visualization, including alignments annotated with secondary structure, protein families logos, 3D structure superimposition supported color-coded conservation. Here, we are using mine the AlphaFold Database version 1, which increased coverage of 20%. We found 100 homologous relationships hitherto unreported in current reference domains, Pfam 35.0. In particular, linked 35 domains unknown function (DUFs) previously characterized families, generating functional hypothesis can explored downstream biology studies. Other findings include gene fusions, tandem duplications, adjustments domain boundaries. evidence browsed interactively through live examples on DALI's website.

Language: Английский

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AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Sept. 27, 2023

Abstract Adapted plant pathogens from various microbial kingdoms produce hundreds of unrelated small secreted proteins (SSPs) with elusive roles. Here, we used AlphaFold-Multimer (AFM) to screen 1879 SSPs seven tomato for interacting six defence-related hydrolases tomato. This 11,274 protein pairs identified 15 non-annotated that are predicted obstruct the active site chitinases and proteases an intrinsic fold. Four were experimentally verified be inhibitors pathogenesis-related subtilase P69B, including extracellular protein-36 (Ecp36) secreted-into-xylem-15 (Six15) fungal Cladosporium fulvum Fusarium oxysporum , respectively. Together a P69B inhibitor bacterial pathogen Xanthomonas perforans Kazal-like oomycete Phytophthora infestans emerges as effector hub targeted by different kingdoms, consistent diversification orthologs paralogs. study demonstrates power artificial intelligence predict cross-kingdom interactions at plant-pathogen interface.

Language: Английский

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RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments

Bioinformatics, Journal Year: 2024, Volume and Issue: 40(6)

Published: June 1, 2024

Abstract Motivation Tools for pairwise alignments between 3D structures of proteins are fundamental importance structural biology and bioinformatics, enabling visual exploration evolutionary functional relationships. However, the absence a user-friendly, browser-based tool creating visualizing them at both 1D sequence levels makes this process unnecessarily cumbersome. Results We introduce novel structure alignment (rcsb.org/alignment) that seamlessly integrates into RCSB Protein Data Bank (RCSB PDB) research-focused RCSB.org web portal. Our its underlying application programming interface (alignment.rcsb.org) empowers users to align several protein chains with reference by providing access established algorithms (FATCAT, CE, TM-align, or Smith–Waterman 3D). The user-friendly simplifies parameter setup input selection. Within seconds, our enables visualization results in (1D) (3D) perspectives through PDB Sequence Annotations viewer Mol* viewer, respectively. Users can effortlessly compare deposited archive alongside more than million incorporated Computed Structure Models coming from ModelArchive AlphaFold DB. Moreover, be used custom data link/URL uploading atomic coordinate files directly. Importantly, bookmarked shared collaborators. By bridging gap proteins, facilitates deeper understanding complex relationships among comprehensive analyses. Availability implementation is part portal available rcsb.org/alignment. Programmatic via alignment.rcsb.org. Frontend code has been published github.com/rcsb/rcsb-pecos-app. Visualization powered open-source (github.com/molstar/molstar github.com/molstar/rcsb-molstar) plus Viewer (github.com/rcsb/rcsb-saguaro-3d).

Language: Английский

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Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

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A screening method for polyester films-degrading microorganisms and enzymes

Journal of Hazardous Materials, Journal Year: 2025, Volume and Issue: 487, P. 137177 - 137177

Published: Jan. 10, 2025

Enzymatic degradation of plastic pollution offers a promising environmentally friendly waste management strategy, however, suitable biocatalysts must be screened and developed. Traditional screening methods using soluble or solubilised polymers do not necessarily identify enzymes that are effective against solid crystalline polymers. This study presents simple, time-saving cost-effective method for identifying microorganisms capable degrading polymeric films. The was tested on polycaprolactone (PCL), polyethylene terephthalate (PET), polylactate (PLA) polyhydroxybutyrate/polyhydroxyvalerate (PHB/PHV) It involves two steps: first, PCL diol (PCLD)-degrading agar plates, second, testing these polyester Using this method, over 100 PCLD-degrading 27 E. coli clones carrying genomic metagenomic DNA fragments have been isolated. In addition, recombinant cutinases from Streptomyces scabiei Thermobifida fusca tested. Approximately 66 % the forming halos PCLD plates hydrolysed 6 - biaxially oriented PET film. five PLA- four PHB/PHV-degrading esterases identified. proposed is detecting both wild-type microorganisms, as well in vitro transcription-translation reactions. Screening thermostable thermophilic enzymes, including those resistant to organic solvents environmental inhibitors, also easily implemented.

Language: Английский

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A historical perspective on the multifunctional outer membrane channel protein TolC in Escherichia coli

npj Antimicrobials and Resistance, Journal Year: 2025, Volume and Issue: 3(1)

Published: Jan. 25, 2025

Since its discovery nearly 60 years ago, TolC has been associated with various cellular functions in Escherichia coli, including the efflux of environmental stressors and virulence factors. It also acts as a receptor for specific bacteriophages colicin E1 toxin. This review highlights key discoveries over past six decades emphasizes remaining gaps understanding how contributes to physiological E. coli.

Language: Английский

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Template and target-site recognition by human LINE-1 in retrotransposition

Nature, Journal Year: 2023, Volume and Issue: 626(7997), P. 186 - 193

Published: Dec. 14, 2023

Abstract The long interspersed element-1 (LINE-1, hereafter L1) retrotransposon has generated nearly one-third of the human genome and serves as an active source genetic diversity disease 1 . L1 spreads through a mechanism termed target-primed reverse transcription, in which encoded enzyme (ORF2p) nicks target DNA to prime transcription its own or non-self RNAs 2 Here we purified full-length ORF2p biochemically reconstituted robust with template RNA target-site DNA. We report cryo-electron microscopy structures complete bound structured initiating cDNA synthesis. polyadenosine tract is recognized sequence-specific manner by five distinct domains. Among them, RNA-binding domain bends backbone allow engagement hairpin stem C-terminal segment. Moreover, structure biochemical reconstitutions demonstrate unexpected requirement: relies on upstream single-stranded position adjacent duplex endonuclease site for nicking longer strand, single nick generating staggered break. Our research provides insights into ongoing transposition informs engineering proteins gene therapy.

Language: Английский

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An intramolecular macrocyclase in plant ribosomal peptide biosynthesis

Nature Chemical Biology, Journal Year: 2024, Volume and Issue: 20(4), P. 530 - 540

Published: Feb. 14, 2024

Language: Английский

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Binding and sensing diverse small molecules using shape-complementary pseudocycles

Science, Journal Year: 2024, Volume and Issue: 385(6706), P. 276 - 282

Published: July 18, 2024

We describe an approach for designing high-affinity small molecule–binding proteins poised downstream sensing. use deep learning–generated pseudocycles with repeating structural units surrounding central binding pockets widely varying shapes that depend on the geometry and number of repeat units. dock molecules interest into most shape complementary these pseudocycles, design interaction surfaces high affinity, experimentally screen to identify designs highest affinity. obtain binders four diverse molecules, including polar flexible methotrexate thyroxine. Taking advantage modular structure pockets, we construct chemically induced dimerization systems low-noise nanopore sensors by splitting domains reassemble upon ligand addition.

Language: Английский

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Characterization, Structural Analysis, and Thermal Stability Mutation of a New Zearalenone-Degrading Enzyme Mined from Bacillus subtilis

Journal of Agricultural and Food Chemistry, Journal Year: 2024, Volume and Issue: 72(6), P. 3025 - 3035

Published: Feb. 1, 2024

Zearalenone (ZEN) is a widespread mycotoxin that causes serious damage to animal husbandry and poses threat human health. A screen of ZEN-degrading soil bacteria yielded Bacillus subtilis YT-4, which 80% ZEN degradation after 6 h 95% 36 h. The gene sequence encoding the degradative enzyme ZENY was mined from genome YT-4 expressed in yeast. an α/β-hydrolase with optimal activity at 37 °C pH 8. By breaking lactone ring ZEN, it produces ZENY-C18H24O5 molecular weight 320.16 g/mol. Sequence comparison docking analyses identified catalytic triad 99S-245H-123E primary ZEN-binding mode within hydrophobic pocket enzyme. To improve thermal stability for industrial applications, we introduced mutation N-terminus, specifically replacing fifth residue N V, achieved 25% improvement 45 °C. These findings aim achieve biodegradation provide insight into structure function hydrolases.

Language: Английский

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