Katja Luck
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View article: Toxoplasma effector TgROP1 establishes membrane contact sites with the endoplasmic reticulum during infection
Toxoplasma effector TgROP1 establishes membrane contact sites with the endoplasmic reticulum during infection Open
Membrane contact sites (MCS) are essential for organelle communication in eukaryotic cells. Pathogens also establish MCS with host organelles, but the mechanisms underlying these interactions and their role in infection remain poorly under…
View article: Bidirectional control of a metabolic transition by the GID ubiquitin ligase
Bidirectional control of a metabolic transition by the GID ubiquitin ligase Open
Summary The GID/CTLH ubiquitin ligase is a multisubunit E3 conserved across eukaryotes. GID/CTLH has been implicated in a variety of processes, including metabolic regulation, cell proliferation, embryonic development and cell differentiat…
View article: Variant characterization in the intrinsically disordered human proteome
Variant characterization in the intrinsically disordered human proteome Open
Variant effect prediction remains a key challenge to resolve in precision medicine. Sophisticated computational models that exploit sequence conservation and structure are increasingly successful in the characterization of missense variant…
View article: Unveiling IRF4-steered regulation of context-dependent effector programs in CD4+ T cells under Th17- and Treg-skewing conditions
Unveiling IRF4-steered regulation of context-dependent effector programs in CD4+ T cells under Th17- and Treg-skewing conditions Open
The transcription factor interferon regulatory factor 4 (IRF4) is crucial for the fate determination of pro-inflammatory T helper (Th) 17 and the functionally opposing group of immunomodulatory regulatory T (Treg) cells. However, the molec…
View article: Bias in, bias out – AlphaFold-Multimer and the structural complexity of protein interfaces
Bias in, bias out – AlphaFold-Multimer and the structural complexity of protein interfaces Open
A structural understanding of protein-protein interactions is a key component of many facets of applied molecular biology research. AlphaFold-Multimer (AF-MM) provided a breakthrough in the ability to predict protein-protein interface stru…
View article: Histone variant macroH2A1 regulates synchronous firing of replication origins in the inactive X chromosome
Histone variant macroH2A1 regulates synchronous firing of replication origins in the inactive X chromosome Open
MacroH2A has been linked to transcriptional silencing, cell identity, and is a hallmark of the inactive X chromosome (Xi). However, it remains unclear whether macroH2A plays a role in DNA replication. Using knockdown/knockout cells for eac…
View article: Generation of a high confidence set of domain–domain interface types to guide protein complex structure predictions by AlphaFold
Generation of a high confidence set of domain–domain interface types to guide protein complex structure predictions by AlphaFold Open
Motivation While the release of AlphaFold (AF) represented a breakthrough for the prediction of protein complex structures, its sensitivity, especially when using full length protein sequences, still remains limited. Modeling success rates…
View article: An extended Tudor domain within Vreteno interconnects <scp>Gtsf1L</scp> and Ago3 for <scp>piRNA</scp> biogenesis in <i>Bombyx mori</i>
An extended Tudor domain within Vreteno interconnects <span>Gtsf1L</span> and Ago3 for <span>piRNA</span> biogenesis in <i>Bombyx mori</i> Open
Piwi‐interacting RNAs (piRNAs) direct PIWI proteins to transposons to silence them, thereby preserving genome integrity and fertility. The piRNA population can be expanded in the ping‐pong amplification loop. Within this process, piRNA‐ass…
View article: Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation Open
Structural resolution of protein interactions enables mechanistic and functional studies as well as interpretation of disease variants. However, structural data is still missing for most protein interactions because we lack computational a…
View article: FUBP1 is a general splicing factor facilitating 3′ splice site recognition and splicing of long introns
FUBP1 is a general splicing factor facilitating 3′ splice site recognition and splicing of long introns Open
Splicing of pre-mRNAs critically contributes to gene regulation and proteome expansion in eukaryotes, but our understanding of the recognition and pairing of splice sites during spliceosome assembly lacks detail. Here, we identify the mult…
View article: Dynamic X-chromosomal reactivation enhances female brain resilience
Dynamic X-chromosomal reactivation enhances female brain resilience Open
Summary While random X-chromosome inactivation in female cells of placental mammalians silences one allele of the majority of X-chromosomal genes, a considerable fraction is only incompletely and variably inactivated resulting in a tissue-…
View article: RNA-dependent interactome allows network-based assignment of RNA-binding protein function
RNA-dependent interactome allows network-based assignment of RNA-binding protein function Open
RNA-binding proteins (RBPs) form highly diverse and dynamic ribonucleoprotein complexes, whose functions determine the molecular fate of the bound RNA. In the model organism Sacchromyces cerevisiae, the number of proteins identified as RBP…
View article: An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis in<i>Bombyx mori</i>
An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis in<i>Bombyx mori</i> Open
Piwi-interacting RNAs (piRNAs) direct PIWI proteins to transposons to silence them, thereby preserving genome integrity and fertility. The piRNA population can be expanded in the ping-pong amplification loop. Within this process, piRNA-ass…
View article: PARP1 proximity proteomics reveals interaction partners at stressed replication forks
PARP1 proximity proteomics reveals interaction partners at stressed replication forks Open
PARP1 mediates poly-ADP-ribosylation of proteins on chromatin in response to different types of DNA lesions. PARP inhibitors are used for the treatment of BRCA1/2-deficient breast, ovarian, and prostate cancer. Loss of DNA replication fork…
View article: Proteome effects of genome-wide single gene perturbations
Proteome effects of genome-wide single gene perturbations Open
Protein abundance is controlled at the transcriptional, translational and post-translational levels, and its regulatory principles are starting to emerge. Investigating these principles requires large-scale proteomics data and cannot just …
View article: Next-generation large-scale binary protein interaction network for <i>Drosophila</i>
Next-generation large-scale binary protein interaction network for <i>Drosophila</i> Open
Generating reference maps of the interactome networks underlying most cellular functions can greatly illuminate genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processe…
View article: OpenPIP: An Open-source Platform for Hosting, Visualizing and Analyzing Protein Interaction Data
OpenPIP: An Open-source Platform for Hosting, Visualizing and Analyzing Protein Interaction Data Open
Knowing which proteins interact with each other is essential information for understanding how most biological processes at the cellular and organismal level operate and how their perturbation can cause disease. Continuous technical and me…
View article: Binary interactome models of inner- versus outer-complexome organisation
Binary interactome models of inner- versus outer-complexome organisation Open
Summary Hundreds of different protein complexes that perform important functions across all cellular processes, collectively comprising the “complexome” of an organism, have been identified 1 . However, less is known about the fraction of …
View article: A reference map of the human protein interactome
A reference map of the human protein interactome Open
Global insights into cellular organization and function require comprehensive understanding of interactome networks. Similar to how a reference genome sequence revolutionized human genetics, a reference map of the human interactome network…
View article: Towards an “assayome” for binary interactome mapping
Towards an “assayome” for binary interactome mapping Open
Complementary assays are required to comprehensively map complex biological entities such as genomes, proteomes and interactome networks. However, how various assays can be optimally combined to approach completeness while maintaining high…
View article: Network-based prediction of protein interactions
Network-based prediction of protein interactions Open
As biological function emerges through interactions between a cell’s molecular constituents, understanding cellular mechanisms requires us to catalogue all physical interactions between proteins [1–4]. Despite spectacular advances in high-…