From interaction networks to interfaces, scanning intrinsically disordered regions using AlphaFold2

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Янв. 18, 2024

The revolution brought about by AlphaFold2 opens promising perspectives to unravel the complexity of protein-protein interaction networks. analysis networks obtained from proteomics experiments does not systematically provide delimitations regions. This is particular concern in case interactions mediated intrinsically disordered regions, which site generally small. Using a dataset protein-peptide complexes involving regions that are non-redundant with structures used training, we show when using full sequences proteins, AlphaFold2-Multimer only achieves 40% success rate identifying correct and structure interface. By delineating region into fragments decreasing size combining different strategies for integrating evolutionary information, manage raise this up 90%. We obtain similar rates much larger protein taken ELM database. Beyond identification site, our study also explores specificity issues. advantages limitations confidence score discriminate between alternative binding partners, task can be particularly challenging small motifs.

Язык: Английский

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Inhibitors of bacterial immune systems: discovery, mechanisms and applications

Nature Reviews Genetics, Год журнала: 2024, Номер 25(4), С. 237 - 254

Опубликована: Янв. 30, 2024

Язык: Английский

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Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions

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

Опубликована: Апрель 12, 2024

Protein-protein interactions (PPIs) are ubiquitous in biology, yet a comprehensive structural characterization of the PPIs underlying biochemical processes is lacking. Although AlphaFold-Multimer (AF-M) has potential to fill this knowledge gap, standard AF-M confidence metrics do not reliably separate relevant from an abundance false positive predictions. To address limitation, we used machine learning on well curated datasets train Structure Prediction and Omics informed Classifier called SPOC that shows excellent performance separating true PPIs, including proteome-wide screens. We applied all-by-all matrix nearly 300 human genome maintenance proteins, generating ~40,000 predictions can be viewed at predictomes.org, where users also score their own with SPOC. High discovered using our approach suggest novel hypotheses maintenance. Our results provide framework for interpreting large scale screens help lay foundation interactome.

Язык: Английский

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Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions

Molecular Cell, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Protein-protein interactions (PPIs) are ubiquitous in biology, yet a comprehensive structural characterization of the PPIs underlying cellular processes is lacking. AlphaFold-Multimer (AF-M) has potential to fill this knowledge gap, but standard AF-M confidence metrics do not reliably separate relevant from an abundance false positive predictions. To address limitation, we used machine learning on curated datasets train structure prediction and omics-informed classifier (SPOC) that effectively separates true predictions PPIs, including proteome-wide screens. We applied SPOC all-by-all matrix nearly 300 human genome maintenance proteins, generating ∼40,000 can be viewed at predictomes.org, where users also score their own with SPOC. High-confidence discovered using our approach enable hypothesis generation maintenance. Our results provide framework for interpreting large-scale screens help lay foundation interactome.

Язык: Английский

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Updated protein domain annotation of the PARP protein family sheds new light on biological function

Nucleic Acids Research, Год журнала: 2023, Номер 51(15), С. 8217 - 8236

Опубликована: Июнь 3, 2023

AlphaFold2 and related computational tools have greatly aided studies of structural biology through their ability to accurately predict protein structures. In the present work, we explored AF2 models 17 canonical members human PARP family supplemented this analysis with new experiments an overview recent published data. proteins are typically involved in modification nucleic acids mono or poly(ADP-ribosyl)ation, but function can be modulated by presence various auxiliary domains. Our provides a comprehensive view structured domains long intrinsically disordered regions within PARPs, offering revised basis for understanding these proteins. Among other functional insights, study model PARP1 domain dynamics DNA-free DNA-bound states enhances connection between ADP-ribosylation RNA ubiquitin-like modifications predicting putative RNA-binding E2-related RWD certain PARPs. line bioinformatic analysis, demonstrate first time PARP14's capability activity vitro. While our insights align existing experimental data probably accurate, they need further validation experiments.

Язык: Английский

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Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization

International Journal of Biological Macromolecules, Год журнала: 2023, Номер 247, С. 125733 - 125733

Опубликована: Июль 7, 2023

Routinely screened antibody fragments usually require further in vitro maturation to achieve the desired biophysical properties. Blind strategies can produce improved ligands by introducing random mutations into original sequences and selecting resulting clones under more stringent conditions. Rational approaches exploit an alternative perspective that aims first at identifying specific residues potentially involved control of mechanisms, such as affinity or stability, then evaluate what could improve those characteristics. The understanding antigen-antibody interactions is instrumental develop this process reliability which, consequently, strongly depends on quality completeness structural information. Recently, methods based deep learning critically speed accuracy model building are promising tools for accelerating docking step. Here, we review features available bioinformatic instruments analyze reports illustrating result obtained with their application optimize fragments, nanobodies particular. Finally, emerging trends open questions summarized.

Язык: Английский

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Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer

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

Опубликована: Фев. 21, 2024

Abstract Accurately mapping protein-protein interactions (PPIs) is critical for elucidating cellular functions and has significant implications health disease. Conventional experimental approaches, while foundational, often fall short in capturing direct, dynamic interactions, especially those with transient or small interfaces. Our study leverages AlphaFold-Multimer (AFM) to re-evaluate high-confidence PPI datasets from Drosophila human. analysis uncovers a limitation of the AFM-derived interface pTM (ipTM) metric, which, reflective structural integrity, can miss physiologically relevant at interfaces within flexible regions. To bridge this gap, we introduce Local Interaction Score (LIS), derived AFM’s Predicted Aligned Error (PAE), focusing on areas low PAE values, indicative high confidence interaction predictions. The LIS method demonstrates enhanced sensitivity detecting PPIs, particularly among that involve By applying large-scale datasets, enhance detection direct interactions. Moreover, present FlyPredictome, an online platform integrates our AFM-based predictions additional information such as gene expression correlations subcellular localization This not only improves upon utility prediction but also highlights potential computational methods complement approaches identification networks.

Язык: Английский

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Mapping protein–protein interactions by mass spectrometry

Mass Spectrometry Reviews, Год журнала: 2024, Номер unknown

Опубликована: Май 14, 2024

Abstract Protein–protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization function of proteome, their perturbation is associated with various diseases, such as cancer, neurodegeneration, infectious diseases. Recent advances mass spectrometry (MS)‐based protein interactomics have significantly expanded our understanding PPIs cells, techniques that continue to improve terms sensitivity, specificity providing new opportunities study diverse systems. These differ depending on type interaction being studied, each approach having its set advantages, disadvantages, applicability. This review highlights recent enrichment methodologies interactomes before MS analysis compares unique features specifications. It emphasizes prospects further improvement potential applications advancing knowledge contexts.

Язык: Английский

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AlphaFold two years on: Validation and impact

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(34)

Опубликована: Авг. 12, 2024

Two years on from the initial release of AlphaFold, we have seen its widespread adoption as a structure prediction tool. Here, discuss some latest work based with particular focus use within structural biology community. This encompasses cases like speeding up determination itself, enabling new computational studies, and building tools workflows. We also look at ongoing validation predictions continue to be compared against large numbers experimental structures further delineate model’s capabilities limitations.

Язык: Английский

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Co-translational binding of importins to nascent proteins

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

Опубликована: Июнь 9, 2023

Various cellular quality control mechanisms support proteostasis. While, ribosome-associated chaperones prevent the misfolding of nascent chains during translation, importins were shown to aggregation specific cargoes in a post-translational mechanism prior import into nucleoplasm. Here, we hypothesize that may already bind cargo co-translational manner. We systematically measure chain association all Saccharomyces cerevisiae by selective ribosome profiling. identify subset wide range nascent, often uncharacterized cargoes. This includes ribosomal proteins, chromatin remodelers and RNA binding proteins are prone cytosol. show act consecutively with other chaperones. Thus, nuclear system is directly intertwined folding chaperoning.

Язык: Английский

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