DALI shines a light on remote homologs: One hundred discoveries

Protein Science, Год журнала: 2022, Номер 32(1)

Опубликована: Ноя. 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.

Язык: Английский

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

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 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.

Язык: Английский

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

Bioinformatics, Год журнала: 2024, Номер 40(6)

Опубликована: Июнь 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).

Язык: Английский

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

Cell, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Язык: Английский

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A screening method for polyester films-degrading microorganisms and enzymes

Journal of Hazardous Materials, Год журнала: 2025, Номер 487, С. 137177 - 137177

Опубликована: Янв. 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.

Язык: Английский

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Solute carriers: The gatekeepers of metabolism

Cell, Год журнала: 2025, Номер 188(4), С. 869 - 884

Опубликована: Фев. 1, 2025

Язык: Английский

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

Nature, Год журнала: 2023, Номер 626(7997), С. 186 - 193

Опубликована: Дек. 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.

Язык: Английский

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Substrate Promiscuity, Crystal Structure, and Application of a Plant UDP-Glycosyltransferase UGT74AN3

ACS Catalysis, Год журнала: 2023, Номер 14(1), С. 475 - 488

Опубликована: Дек. 21, 2023

Glycosyltransferases are effective enzymes for glycosylating natural products (NPs), and some of them have the unusual property being exceedingly promiscuous catalytically toward a range substrates. UGT74AN3 is plant glycosyltransferase identified from Catharanthus roseus in our previous work. In this study, we found that exhibits high substrate promiscuity 78 acceptors 6 sugar donors also N-/S-glycosylation activity simple aromatic compounds. The crystal structures complex with various NPs were solved. Sugar donor recognition was altered by structure-based mutagenesis, T145V mutant shifted its preference UDP-Glc to UDP-Xyl. Structural analysis reveals spacious U-shaped hydrophobic binding pocket accounts UGT74AN3. residues E85 F193 might serve as gatekeepers control binding. addition, rare mode discovered structure UGT74AN3, process flipping charted molecular dynamics simulations. Moreover, cost-effective one-pot system coupling AtSuSy, sucrose synthase, established situ generating recycling UDP glycosylate NPs. Our study structural basis underlying provides an efficient economical enzymatic synthesis strategy producing valuable glycosides drug discovery.

Язык: Английский

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An intramolecular macrocyclase in plant ribosomal peptide biosynthesis

Nature Chemical Biology, Год журнала: 2024, Номер 20(4), С. 530 - 540

Опубликована: Фев. 14, 2024

Язык: Английский

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Binding and sensing diverse small molecules using shape-complementary pseudocycles

Science, Год журнала: 2024, Номер 385(6706), С. 276 - 282

Опубликована: Июль 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.

Язык: Английский

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