Biology subjects

Koenig, F.

Publications and source records attributed to Koenig, F..

4 recordsLinked to original sources

bioRxiv2026

A High-Affinity Nanobody Recognizing mNeonGreen Enables Versatile Biochemical, Cellular, and in vivo Applications.

mNeonGreen (mNG) is among the brightest and most photostable monomeric green fluorescent proteins and is widely used for protein tagging. Here, we present sdAb(mNG), a high-affinity single-domain antibody (sdAb) that enables biochemical capture, imaging, and manipulation of mNG-tagged proteins. A 1.26 [A] crystal structure reveals an extensive interaction surface between mNG and sdAb(mNG), accounting for its high affinity (KD = 0.39 nM) and robust target recognition across diverse experimental conditions. This allows a single sdAb to support applications that typically require multiple specialized tools. We demonstrate the utility of sdAb(mNG) in several example applications including highly specific immunoprecipitation, direct immunofluorescence, and super-resolution imaging. Importantly, sdAb(mNG) retains high-performance target recognition even in intracellular environments. When expressed as an intrabody in living mammalian cells, sdAb(mNG) enables relocalization of mNG-tagged proteins to defined compartments or visualization of synaptic vesicle transport in primary neurons. In zebrafish, fusion of sdAb(mNG) to an F-box degradation domain induces cell-autonomous depletion of an endogenous mNG-tagged transcription factor and produces a clear developmental phenotype. These findings establish sdAb(mNG) as a versatile and robust affinity reagent that converts mNG from a passive fluorescent reporter into a multifunctional handle for imaging, proteomics, and programmable manipulation of endogenous and engineered proteins.

biochemistry↗

bioRxiv2025

Functional genomics of Campylobacter-host interactions in an intestinal tissue model reveals a small lipoprotein essential for flagellar assembly

Campylobacter jejuni is the leading cause of bacterial food-poisoning, with motility being an essential virulence factor. While many aspects of flagella biogenesis have been studied, a complete picture of the components and regulators of these multi-protein machines is still missing. To identify genes crucial for C. jejuni pathogenesis and motility, we applied transposon sequencing in a humanized tissue model. This revealed three largely uncharacterized genes (pflC , pflD , pflE ) as essential for motility. While PflC/D turned out to be components of the flagellar motor disk structures, PflE is a small protein of only 57 aa. PflE strikingly affects motor biogenesis, with complete loss of motor structures upon its deletion. We demonstrate PflE is a lipoprotein and supports outer-membrane localization of the main basal-disk protein FlgP. With motility as a critical Campylobacter virulence factor, our work demonstrates that deletion of a small protein can bring a bacterial pathogen to a halt.

microbiology↗

bioRxiv2022

Vasor: Accurate prediction of variant effects for amino acid substitutions in MDR3

Background / RationaleThe phosphatidylcholine floppase MDR3 is an essential hepatobiliary transport protein. MDR3 dysfunction is associated with various liver diseases, ranging from severe progressive familial intrahepatic cholestasis to transient forms of intrahepatic cholestasis of pregnancy and familial gallstone disease. Single amino acid substitutions are often found as causative of dysfunction, but identifying the substitution effect in in vitro studies is time- and cost-intensive. Main resultsWe developed Vasor (Variant assessor of MDR3), a machine learning-based model to classify novel MDR3 missense variants into the categories benign or pathogenic. Vasor was trained on the, to date, largest dataset specific for MDR3 of benign and pathogenic variants and uses general predictors, namely EVE, EVmutation, PolyPhen-2, I-Mutant2.0, MUpro, MAESTRO, PON-P2, and other variant properties such as half-sphere exposure, PTM site, and secondary structure disruption as input. Vasor consistently outperformed the integrated general predictors and the external prediction tool MutPred2, leading to the current best prediction performance for MDR3 single-site missense variants (on an external test set: F1-score: 0.90, MCC: 0.80). Furthermore, Vasor predictions cover the entire sequence space of MDR3. Vasor is accessible as a webserver at https://cpclab.uni-duesseldorf.de/mdr3_predictor/ for users to rapidly obtain prediction results and a visualization of the substitution site within the MDR3 structure. ConclusionThe MDR3-specific prediction tool Vasor can provide reliable predictions of single site amino acid substitutions, giving users a fast way to assess initially whether a variant is benign or pathogenic.

bioinformatics↗

bioRxiv2019

TMS-EEG signatures of glutamatergic neurotransmission in human cortex

Neuronal activity in the brain is regulated by an excitation-inhibition balance. Glutamate is the main excitatory neurotransmitter. Transcranial magnetic stimulation (TMS) evoked electroencephalographic (EEG) potentials (TEPs) represent a novel way to quantify pharmacological effects on neuronal activity in the human cortex. Here we tested TEPs under the influence of a single oral dose of two anti-glutamatergic drugs, perampanel, an AMPA-receptor antagonist, and dextromethorphan, an NMDA-receptor antagonist, and nimodipine, an L-type voltage-gated calcium channel blocker in 16 healthy adults in a pseudorandomized, double-blinded, placebo-controlled, crossover design. Single-pulse TMS was delivered to the left motor cortex and TEPs were obtained pre-and post-drug intake. Dextromethorphan specifically increased the amplitude of the N45, a negative potential around 45 ms after the TMS pulse, while perampanel reduced the P70 amplitude in the non-stimulated hemisphere. Nimodipine and placebo had no effect on TEPs. These data extend previous pharmaco-TMS-EEG studies by demonstrating that the N45 is regulated by a balance of GABAAergic inhibition and NMDA-receptor-mediated glutamatergic excitation. In contrast, AMPA-receptor-mediated glutamatergic neurotransmission contributes to interhemispherically propagated activity reflected in the P70. These data are important to understand the physiology of TEPs as markers of excitability and propagated activity in the human cortex in health and disease.

neuroscience↗