Rapid and sensitive protein complex alignment with Foldseek-Multimer

Nature Methods, Год журнала: 2025, Номер unknown

Опубликована: Фев. 5, 2025

Abstract Advances in computational structure prediction will vastly augment the hundreds of thousands currently available protein complex structures. Translating these into discoveries requires aligning them, which is computationally prohibitive. Foldseek-Multimer computes alignments from compatible chain-to-chain alignments, identified by efficiently clustering their superposition vectors. 3–4 orders magnitudes faster than gold standard, while producing comparable alignments; this allows it to compare billions pairs 11 h. open-source software at GitHub via https://github.com/steineggerlab/foldseek/ , https://search.foldseek.com/search/ and BFMD database.

Язык: Английский

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Structure-based prediction of protein-nucleic acid binding using graph neural networks

Biophysical Reviews, Год журнала: 2024, Номер 16(3), С. 297 - 314

Опубликована: Июнь 1, 2024

Abstract Protein-nucleic acid (PNA) binding plays critical roles in the transcription, translation, regulation, and three-dimensional organization of genome. Structural models proteins bound to nucleic acids (NA) provide insights into chemical, electrostatic, geometric properties protein structure that give rise NA but are scarce relative unbound proteins. We developed a deep learning approach for predicting PNA given we call PNAbind. Our method utilizes graph neural networks encode spatial distribution physicochemical structures predictive binding. Using global encodings, our predict overall function protein, using local they location individual residues. can discriminate between specificity DNA or RNA binding, show predictions made on computationally derived be used gain mechanistic understanding chemical structural features determine recognition. Binding site were validated against benchmark datasets, achieving AUROC scores range 0.92–0.95. applied HIV-1 restriction factor APOBEC3G showed model consistent with help explain experimental data.

Язык: Английский

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STK19 positions TFIIH for cell-free transcription-coupled DNA repair

Cell, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 1, 2024

In transcription-coupled nucleotide excision repair (TC-NER), stalled RNA polymerase II (RNA Pol II) binds CSB and CRL4

Язык: Английский

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Bias in, bias out – AlphaFold-Multimer and the structural complexity of protein interfaces

Current Opinion in Structural Biology, Год журнала: 2025, Номер 91, С. 103002 - 103002

Опубликована: Фев. 12, 2025

Язык: Английский

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Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 14, 2024

Advances in computational structure prediction will vastly augment the hundreds of thousands currently-available protein complex structures. Translating these into discoveries requires aligning them, which is computationally prohibitive. Foldseek-Multimer computes alignments from compatible chain-to-chain alignments, identified by efficiently clustering their superposition vectors. 3-4 orders magnitudes faster than gold standard, while producing comparable alignments; allowing it to compare billions complex-pairs 11 hours. open-source software: github.com/steineggerlab/foldseek , webserver: search.foldseek.com and BFMD database.

Язык: Английский

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EndoMAPV1, a Structural Protein Complex Landscape of Human Endosomes

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 9, 2025

ABSTRACT Early/sorting endosomes are dynamic organelles that play key roles in proteome control by triaging plasma membrane proteins for either recycling or degradation the lysosome 1,2,3 . These events coordinated numerous transiently-associated regulatory complexes and integral components contribute to organelle identity during endosome maturation 4 While a subset of several hundred protein cargoes known associate with have been studied at biochemical and/or structural level, interaction partners higher order molecular assemblies many endosomal remain unknown. Here, we combine cross-linking native gel mass spectrometry 5-8 purified early AlphaFold 9,10 computational analysis create systematic human interactome. We present dozens models pairs supported experimental cross-links from their subcellular context, suggesting mechanisms previously reported processes. Using induced neurons, validate two candidate whose interactions crosslinks predictions: TMEM230 as subunit ATP8/11 lipid flippases 11 TMEM9/9B subunits CLCN3/4/5 chloride-proton antiporters 12 This resource its accompanying network viewer provide an framework understanding organellar interactomes large-scale validation predictions.

Язык: Английский

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Rēs ipSAE loquunt: What′s wrong with AlphaFold′s ipTM score and how to fix it

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 14, 2025

AlphaFold's ipTM metric is used to predict the accuracy of structural predictions protein-protein interactions (PPIs) and probability that two proteins interact. Many AF2/AF3 users have experienced phenomenon if they trim full-length sequence constructs (e.g. from UniProt) interacting domains (or domain+peptide), their scores go up, even though structure prediction interaction unchanged. The reason this happens due mathematical formulation in AF2/AF3, which whole chains. If both chains a PPI complex contain large amounts disorder or accessory do not form primary domain-domain domain/peptide interaction, score can be lowered significantly. then does accurately represent nor whether actually We solved problem by: 1) including only residue pairs good predicted aligned error ( PAE ) scores; 2) by adjusting d 0 parameter (a function length query sequences) TM equation include number residues with interchain s residue; 3) using value itself distributions over calculate pairwise residue-residue pTM values into calculation. first are crucial calculating high for domain-peptide presence many hundreds disordered regions and/or domains. third allows us require common output json files AF2 AF3 (including server output) without having change AlphaFold code affecting accuracy. show benchmark new score, called ipSAE (interaction Score Aligned Errors), able separate true false complexes more efficiently than AlphaFold2's score. resulting program freely available at https://github.com/dunbracklab/IPSAE .

Язык: Английский

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Competition for the nascent leading strand shapes the requirements for PCNA loading in the replisome

The EMBO Journal, Год журнала: 2025, Номер unknown

Опубликована: Фев. 28, 2025

Abstract During DNA replication, the polymerases Pol δ and ε utilise ring-shaped sliding clamp PCNA to enhance their processivity. loading onto is accomplished by loaders RFC Ctf18-RFC, which function primarily on lagging leading strand, respectively. activity essential for lagging-strand replication δ, but it unclear why Ctf18-RFC required leading-strand cannot fulfil this function. Here, we show that load once has been incorporated into budding yeast replisome commenced synthesis, state maintained during progression. By contrast, find uniquely equipped strand requires a direct interaction between Ctf18 CMG (Cdc45-MCM-GINS) helicase. Our work uncovers mechanistic basis replisomes require dedicated loader.

Язык: Английский

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Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome

Chemical Reviews, Год журнала: 2025, Номер unknown

Опубликована: Апрель 3, 2025

The cell surface proteome, or surfaceome, is the hub for cells to interact and communicate with outside world. Many disease-associated changes are hard-wired within yet approved drugs target less than 50 proteins. In past decade, proteomics community has made significant strides in developing new technologies tailored studying surfaceome all its complexity. this review, we first dive into unique characteristics functions of emphasizing necessity specialized labeling, enrichment, proteomic approaches. An overview surfaceomics methods provided, detailing techniques measure protein expression how leads novel discovery. Next, highlight advances proximity labeling (PLP), showcasing various enzymatic photoaffinity can map protein-protein interactions membrane complexes on surface. We then review role extracellular post-translational modifications, focusing glycosylation, proteolytic remodeling, secretome. Finally, discuss identifying tumor-specific peptide MHC they have shaped therapeutic development. This emerging field neo-protein epitopes constantly evolving, where targets identified at proteome level encompass defined PTMs, complexes, dysregulated cellular tissue locations. Given functional importance biology therapy, view as a critical piece quest neo-epitope

Язык: Английский

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STK19 positions TFIIH for cell-free transcription-coupled DNA repair

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 23, 2024

In transcription-coupled repair, stalled RNA polymerase II (Pol II) is recognized by CSB and CRL4 CSA , which co-operate with UVSSSA ELOF1 to recruit TFIIH for nucleotide excision repair (TC-NER). To explore the mechanism of TC-NER, we recapitulated this reaction in vitro . When a plasmid containing site-specific lesion transcribed frog egg extract, error-free observed that depends on CSB, UVSSA, ELOF1. Repair also STK19, factor previously implicated transcription recovery after UV exposure. A 1.9 Å cryo-electron microscopy structure shows STK19 joins TC-NER complex binding RPB1 subunit Pol II. Furthermore, AlphaFold predicts interacts XPD TFIIH, disrupting interface impairs cell-free repair. Molecular modeling suggests positions ahead verification. summary, our analysis couples stalling downstream events.

Язык: Английский

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