Biology subjects

Milles, L.

Publications and source records attributed to Milles, L..

4 recordsLinked to original sources

bioRxiv2026

The glucocorticoid dexamethasone influences motility of the sulfate-reducing bacterium Desulfovibrio desulfuricans by targeting the filament cap protein FliD

Glucocorticoids such as dexamethasone (DXE) are first-line treatments for inflammatory bowel disease (IBD). Beyond their effects on the host immune system, accumulating evidence suggests that glucocorticoids can also influence the gut microbiota. Notably, IBD patients exhibit an increased intestinal colonization by sulfate-reducing Desulfovibrio spp. Here, we show that DXE modulates bacterial motility in the gut commensal Desulfovibrio desulfuricans through a metabolism-independent mechanism. To identify bacterial targets, we developed a DXE-derived chemical probe and performed affinity-based protein profiling, which revealed the flagellar cap protein FliD (Ddes_0530) as a principal binding partner. Structural modeling using AlphaFold3 and Boltz2 predicted DXE binding within a conserved groove of the FliD C-terminal domain. Furthermore, the tip of the flagellum of Desulfovibrio, but not that of Escherichia coli, could be fluorescently labeled with TAMRA-DXE, but not with the structurally related steroid probe TAMRA-norethiosterone, indicating that flagellar labeling is specific to DXE rather than the steroid scaffold itself. As a consequence of this interaction, transmission electron microscopy showed that DXE treatment prevented flagellation in a subpopulation and reduced flagellar length in D. desulfuricans strains ATCC 27774 and CCUG 72978, respectively. Quantitative motility tracking revealed a non-monotonic, dose-dependent modulation of swimming velocity, with peak stimulation at 10 {micro}M DXE, accompanied by straighter trajectories and enhanced net displacement. Together, these findings uncover a previously unrecognized mode of action for DXE which directly perturbs flagellar biogenesis and motility of an important gut microbiome member of IBD patients. SignificanceGlucocorticoids are widely prescribed for inflammatory conditions, yet their direct effects on gut bacteria remain largely unexplored. We demonstrate that dexamethasone, a synthetic glucocorticoid, binds to the flagellar cap protein FliD of the gut commensal Desulfovibrio desulfuricans, affecting flagellar assembly and altering motility behavior. Unlike previously characterized steroid-metabolizing bacteria such as Clostridium steroidoreducens, Desulfovibrio does not degrade dexamethasone, indicating that the observed effects result from direct drug-protein interaction. These findings establish a new paradigm for metabolism-independent drug-microbiome interactions and suggest that glucocorticoid effects on gut bacteria extend beyond enzymatic degradation pathways.

microbiology↗

bioRxiv2025

Designed NGF mimetics with reduced nociceptive signatures in neurons

The clinical use of Nerve Growth Factor (NGF) for neuronal regeneration has been hampered by pain sensitization side effects. NGF signals through the receptor tyrosine kinase TrkA and the co-receptor p75NTR; pain sensitization is thought to involve p75NTR. We sought to overcome this limitation by de novo design of a TrkA agonist that does not bind p75NTR. We designed homodimeric TrkA engaging constructs that dimerize TrkA subunits in a variety of geometries, and identified those eliciting the strongest signaling. The resulting designed agonists are able to stimulate transdifferentiated neurons and neuroblastoma cell lines, leading to neurite outgrowth and neuronal differentiation, with considerably reduced transcription of inflammation and pain related genes. These agonists are promising candidates for promoting neuronal regeneration without adverse side effects. HighlightsO_LIDe novo designed TrkA agonists activate MAPK and PI3K-AKT signaling C_LIO_LIRigid fusions allow for highly tunable signaling signatures C_LIO_LITrkA agonists lead to neurite outgrowth in neuroblastoma cells comparable to retinoic acid C_LIO_LIModulation of the TrkA pathway without co-stimulating p75NTR leads to a downregulation of inflammatory and nociceptive signature in neurons. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/648806v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@c48066org.highwire.dtl.DTLVardef@c9c5a7org.highwire.dtl.DTLVardef@cf8ebdorg.highwire.dtl.DTLVardef@a4345a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2020

Design of proteins presenting discontinuous functional sites using deep learning

An outstanding challenge in protein design is the design of binders against therapeutically relevant target proteins via scaffolding the discontinuous binding interfaces present in their often large and complex binding partners. There is currently no method for sampling through the almost unlimited number of possible protein structures for those capable of scaffolding a specified discontinuous functional site; instead, current approaches make the sampling problem tractable by restricting search to structures composed of pre-defined secondary structural elements. Such restriction of search has the disadvantage that considerable trial and error can be required to identify architectures capable of scaffolding an arbitrary discontinuous functional site, and only a tiny fraction of possible architectures can be explored. Here we build on recent advances in de novo protein design by deep network hallucination to develop a solution to this problem which eliminates the need to pre-specify the structure of the scaffolding in any way. We use the trRosetta residual neural network, which maps input sequences to predicted inter-residue distances and orientations, to compute a loss function which simultaneously rewards recapitulation of a desired structural motif and the ideality of the surrounding scaffold, and generate diverse structures harboring the desired binding interface by optimizing this loss function by gradient descent. We illustrate the power and versatility of the method by scaffolding binding sites from proteins involved in key signaling pathways with a wide range of secondary structure compositions and geometries. The method should be broadly useful for designing small stable proteins containing complex functional sites.

biochemistry↗

bioRxiv2019

Is mechanical receptor ligand dissociation driven by unfolding or unbinding?

Mechanical force can play a pivotal role in biological systems. Single Molecule Force Spectroscopy, is a powerful tool to probe the mechanics of proteins and their binding partners. Yet, it remains unclear how complex dissociation of a protein-protein interaction under mechanical forces occurs. Are receptor and ligand unbinding, or are they unfolding? We utilize an approach wherein receptor and ligand are expressed as a single molecule fused by a long flexible linker. Force is applied to the complex via an ultrastable handle. Consequently, the events during and following complex dissociation can be monitored. We investigate two high-affinity systems: The cohesin-dockerin type I interaction in which we find that a binding partner unfolds upon complex dissociation, and a colicin-immunity protein complex in which both proteins unfold completely upon unbinding. Mechanical receptor ligand dissociation thus can encompass unfolding of one or both binding partners.

biophysics↗