Jochen Kuper
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View article: Anti-tumorigenic properties by trichothiodystrophy mutations in melanocytic cells
Anti-tumorigenic properties by trichothiodystrophy mutations in melanocytic cells Open
Germline mutations in the DNA repair helicase XPD can cause the diseases xeroderma pigmentosum (XP) and trichothiodystrophy (TTD). XP patients bear an increased risk of skin cancer including melanoma. This is not observed for TTD patients …
View article: Chemoproteomic analysis reveals RECQL4 as a mediator of nitroalkene-dependent double-strand break repair inhibition in cancer.
Chemoproteomic analysis reveals RECQL4 as a mediator of nitroalkene-dependent double-strand break repair inhibition in cancer. Open
Nitroalkenes are endogenous products generated by the metabolism of unsaturated fatty acids. They are generated under oxidative stress conditions, mediating important anti-inflammatory signaling activities through covalent modification of …
View article: G-quadruplex-mediated genomic instability drives SNVs in cancer
G-quadruplex-mediated genomic instability drives SNVs in cancer Open
G-quadruplex (G4s) DNA structures have been implicated in inducing genomic instability and contributing to cancer development. However, the relationship between G4s and cancer-related single nucleotide variants (cSNVs) in clinical settings…
View article: Trapped in translocation – Stalling of XPD on a crosslinked DNA substrate
Trapped in translocation – Stalling of XPD on a crosslinked DNA substrate Open
The super family 2 (SF2) helicase XPD is a central component of the general transcription factor II H (TFIIH) which is essential for transcription and nucleotide excision DNA repair (NER) 1 . Within these two processes XPDs helicase functi…
View article: G-quadruplex-mediated genomic instability drives SNVs in cancer
G-quadruplex-mediated genomic instability drives SNVs in cancer Open
This repository contains the supplementary Python and Bash Code used in the manuscript G-quadruplex-mediated genomic instability drives SNVs in cancer by Richl et al. Python Scripts MYC_CDK4.py Cancer_Gene_Density.py Cancer_Type_Standard_D…
View article: Computed structures of core eukaryotic protein complexes
Computed structures of core eukaryotic protein complexes Open
Deep learning for protein interactions The use of deep learning has revolutionized the field of protein modeling. Humphreys et al . combined this approach with proteome-wide, coevolution-guided protein interaction identification to conduct…
View article: Cesium based phasing of macromolecules: a general easy to use approach for solving the phase problem
Cesium based phasing of macromolecules: a general easy to use approach for solving the phase problem Open
Over the last decades the phase problem in macromolecular x-ray crystallography has become more controllable as methods and approaches have diversified and improved. However, solving the phase problem is still one of the biggest obstacles …
View article: The novel <scp><i>KIT</i></scp> exon 11 germline mutation <scp>K558N</scp> is associated with gastrointestinal stromal tumor, mastocytosis, and seminoma development
The novel <span><i>KIT</i></span> exon 11 germline mutation <span>K558N</span> is associated with gastrointestinal stromal tumor, mastocytosis, and seminoma development Open
Familial gastrointestinal stromal tumors (GIST) are dominant genetic disorders that are caused by germline mutations of the type III receptor tyrosine kinase KIT. While sporadic mutations are frequently found in mastocytosis and GISTs, ger…
View article: The Interaction Efficiency of XPD-p44 With Bulky DNA Damages Depends on the Structure of the Damage
The Interaction Efficiency of XPD-p44 With Bulky DNA Damages Depends on the Structure of the Damage Open
The successful elimination of bulky DNA damages via the nucleotide excision repair (NER) system is largely determined by the damage recognition step. This step consists of primary recognition and verification of the damage. The TFIIH helic…
View article: How to limit the speed of a motor: the intricate regulation of the XPB ATPase and translocase in TFIIH
How to limit the speed of a motor: the intricate regulation of the XPB ATPase and translocase in TFIIH Open
The superfamily 2 helicase XPB is an integral part of the general transcription factor TFIIH and assumes essential catalytic functions in transcription initiation and nucleotide excision repair. The ATPase activity of XPB is required in bo…
View article: Structural basis for CDK7 activation by MAT1 and Cyclin H
Structural basis for CDK7 activation by MAT1 and Cyclin H Open
Significance The fundamental processes of cell-cycle regulation and transcription are linked by the heterotrimeric CDK-activating kinase (CAK) complex. We solved the crystal structure of the active CAK complex and provide a molecular ratio…
View article: The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair
The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair Open
Nucleotide excision repair (NER) in eukaryotes is orchestrated by the core form of the general transcription factor TFIIH, containing the helicases XPB, XPD and five ‘structural’ subunits, p62, p44, p34, p52 and p8. Recent cryo-EM structur…
View article: Constitutively active TrkB kinase signalling reduces actin filopodia dynamics and cell migration
Constitutively active TrkB kinase signalling reduces actin filopodia dynamics and cell migration Open
Trk receptors and gene fusions of NTRK are targets in precision oncology. Classical Trk signalling concepts fail to explain ligand-independent signalling of intracellular TrkB or NTRK fusion proteins. Here, we show that abundance of the in…
View article: How to limit the speed of a motor: The intricate regulation of the XPB ATPase and Translocase in TFIIH
How to limit the speed of a motor: The intricate regulation of the XPB ATPase and Translocase in TFIIH Open
The superfamily 2 helicase XPB is an integral part of the general transcription factor TFIIH and assumes essential catalytic functions in transcription initiation and nucleotide excision repair. In both processes the ATPase activity of XPB…
View article: Structural basis for CDK7 activation by MAT1 and Cyclin H
Structural basis for CDK7 activation by MAT1 and Cyclin H Open
CDK7, Cyclin H, and MAT1 form the heterotrimeric CDK-activating kinase (CAK) complex. CAK is a vital factor for the two essential processes of transcription and cell cycle control. When associated with the general transcription factor II H…
View article: Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein
Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein Open
RNA-binding proteins (RBPs) play important roles in bacterial gene expression and physiology but their true number and functional scope remain little understood even in model microbes. To advance global RBP discovery in bacteria, we here e…
View article: Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein
Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein Open
RNA-binding proteins (RBPs) play important roles in bacterial gene expression and physiology but their true number and functional scope remain little understood even in model microbes. To advance global RBP discovery in bacteria, we here e…
View article: The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair
The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair Open
Nucleotide excision repair (NER) protects the genome following exposure to diverse types of DNA damage, including UV light and chemotherapeutics. Mutations in mammalian NER genes lead to diseases such as xeroderma pigmentosum, trichothiody…
View article: Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafish
Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafish Open
In most vertebrates, including zebrafish, the hypothalamic serotonergic cerebrospinal fluid-contacting (CSF-c) cells constitute a prominent population. In contrast to the hindbrain serotonergic neurons, little is known about the developmen…
View article: Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafish
Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafish Open
In most vertebrates, including zebrafish, the hypothalamic serotonergic cerebrospinal fluid-contacting (CSF-c) cells constitute a prominent population. In contrast to the hindbrain serotonergic neurons, little is known about the developmen…
View article: The intricate network between the p34 and p44 subunits is central to the activity of the transcription/DNA repair factor TFIIH
The intricate network between the p34 and p44 subunits is central to the activity of the transcription/DNA repair factor TFIIH Open
The general transcription factor IIH (TFIIH) is a multi-protein complex and its 10 subunits are engaged in an intricate protein-protein interaction network critical for the regulation of its transcription and DNA repair activities that are…
View article: Catabolism of the Cholesterol Side Chain in <i>Mycobacterium tuberculosis</i> Is Controlled by a Redox-Sensitive Thiol Switch
Catabolism of the Cholesterol Side Chain in <i>Mycobacterium tuberculosis</i> Is Controlled by a Redox-Sensitive Thiol Switch Open
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a highly successful human pathogen and has infected approximately one-third of the world's population. Multiple drug resistant (MDR) and extensively drug resist…
View article: Selectivity of Pyridone- and Diphenyl Ether-Based Inhibitors for the <i>Yersinia pestis</i> FabV Enoyl-ACP Reductase
Selectivity of Pyridone- and Diphenyl Ether-Based Inhibitors for the <i>Yersinia pestis</i> FabV Enoyl-ACP Reductase Open
The enoyl-ACP reductase (ENR) catalyzes the last reaction in the elongation cycle of the bacterial type II fatty acid biosynthesis (FAS-II) pathway. While the FabI ENR is a well validated drug target in organisms such as Mycobacterium tube…
View article: FANCM interacts with PCNA to promote replication traverse of DNA interstrand crosslinks
FANCM interacts with PCNA to promote replication traverse of DNA interstrand crosslinks Open
FANCM is a highly conserved DNA remodeling enzyme that promotes the activation of the Fanconi anemia DNA repair pathway and facilitates replication traverse of DNA interstrand crosslinks. However, how FANCM interacts with the replication m…