Biology subjects

Menin, L.

Publications and source records attributed to Menin, L..

7 recordsLinked to original sources

bioRxiv2026

De novo design of light-controlled conformational protein switches

Light-responsive proteins offer the ability to control biology at an unmatched resolution. Yet, optogenetics is limited to a relatively small number of natural and engineered photoreceptors. The design of light-responsive proteins with native-like complexity is challenging as they must incorporate a light-responsive chromophore, couple chemical changes in the chromophore to structural changes in the protein, and ultimately propagate these changes to downstream effectors. Here, we present the computational design of new light-responsive proteins entirely from the bottom-up. We design de novo proteins that accurately bind a retinal chromophore and further design a protein conformational switching motion linked to retinal isomerisation. This switch unlocks a new protein-peptide interaction, creating light-activated heterodimers with an over 30-fold increase in binding upon illumination. Moreover, we show that the designed heterodimers are customisable, with tuneable wavelengths, sensitivities, and specificities. Further, we use the designed heterodimers to control biological function, regulating intracellular protein-protein interactions and cell-signalling receptors. Finally, we use real-time light-activated NMR to demonstrate that they undergo a defined light-activated conformational change. Overall, we computationally design a new class of light-responsive proteins that may open a new optogenetics toolbox with applications in biology.

biochemistry↗

bioRxiv2026

Computational design of microbial and animal rhodopsin soluble analogues

The computational design of soluble analogues of membrane proteins has unlocked exciting opportunities for the integration of unique membrane protein functions into soluble proteins. Here, we use AF2seq to generate accurate soluble analogues of both animal and microbial rhodopsins, based on the membrane GPCR topology, and the microbial rhodopsin transmembrane fold. We characterize the analogues and demonstrate that they are well-folded and highly thermostable. Furthermore, they exhibit the expected red shift characteristic of retinal binding. Top-down mass spectrometry confirms the placement of retinal covalent attachment, while X-ray crystallography validates the structural fidelity of the microbial rhodopsin analogue. Notably, the microbial rhodopsin analogue retains the primary reaction of the retinal photocycle, closely matching that of the native membrane protein. Overall, this work advances the possibility to transfer unique membrane protein functions, such as retinal photoswitching, into the soluble proteome.

Synthetic Biology↗

bioRxiv2026

Redox-regulated cysteine acylation governs β-lactam sensing by the Vibrio histidine kinase VbrK

The ability of pathogens to develop resistance mechanisms makes the continuous search for novel therapeutic targets indispensable. Resistance-activating systems are promising targets for restoring the efficacy of existing antibiotics. VbrK/VbrR is a two-component system from Vibrio parahaemolyticus reported as the first sensing system in gram-negatives that directly detects {beta}-lactam antibiotics. {beta}-Lactam-induced activation of this system results in the expression of the serine {beta}-lactamase CARB. In this study, we provide insights into the mechanism of {beta}-lactam binding to the periplasmic sensor domain of the histidine kinase VbrK. Our results demonstrate that the interaction depends on the redox state of cysteines C86 and C107, highlighting the role of disulfide bond dynamics in modulating ligand recognition. We further show that formation of a non-covalent complex leads to acylation of the sensor domain by {beta}-lactams, a modification that is slowly reversed through de-acylation, yielding the hydrolyzed {beta}-lactam ring and allowing for recovery from induction once the antibiotic has been depleted from the environment. Together, these findings reveal a previously unrecognized redox- and covalent chemistry-dependent mode of {beta}-lactam interaction with histidine kinases, providing a molecular framework to understand how VbrK detects and responds to {beta}-lactam antibiotics, and opening new avenues to prevent manifestation of resistance. Short broader audience statementBacterial pathogens can sense the presence of antibiotics and trigger resistance responses, making infections increasingly difficult to treat. In this study, we uncover a previously unknown mechanism by which {beta}-lactam antibiotics interact with a sensor protein that activates resistance in Vibrio parahaemolyticus. These findings pave the way for designing new compounds that can block this interaction and thus restore the effectiveness of {beta}-lactam antibiotics against gastrointestinal infections caused by resistant bacteria.

microbiology↗

bioRxiv2023

A planar-polarized MYO6-DOCK7-RAC1 axis promotes tissue fluidification in mammary epithelia

Tissue fluidification and collective motility are pivotal in regulating embryonic morphogenesis, wound healing and tumor metastasis. These processes frequently require that each cell constituent of a tissue coordinates its migration activity and directed motion through the oriented extension of lamellipodia cell protrusions, promoted by RAC1 activity. While the upstream RAC1 regulators in individual migratory cells or leader cells during invasion or wound healing are well characterized, how RAC1 is controlled in follower cells remains unknown. Here, we identify a novel MYO6-DOCK7 axis that is critical for spatially restriction of RAC1 activity in a planar polarized fashion in model tissue monolayers. The MYO6-DOCK7 axis specifically controls the extension of cryptic lamellipodia required to drive tissue fluidification and cooperative mode motion in otherwise solid and static carcinoma cell collectives. HighlightsO_LICollective motion of jammed epithelia requires myosin VI activity C_LIO_LIThe MYO6-DOCK7 axis is critical to restrict the activity of RAC1 in a planar polarized fashion C_LIO_LIMYO6-DOCK7-RAC1 activation ensures long-range coordination of movements by promoting orientation and persistence of cryptic lamellipodia C_LIO_LIMyosin VI overexpression is exploited by infiltrating breast cancer cells C_LI

cell biology↗

bioRxiv2022

On demand nanoliter sampling probe for collection of brain fluid

Continuous fluidic sampling systems allow collection of brain biomarkers in vivo. Here, we propose a new sampling paradigm, Droplet on Demand (DoD), implemented in a microfabricated neural probe. It allows sampling droplets loaded with molecules from the brain extracellular fluid punctually, without the long transient equilibration periods typical of continuous methods. It uses an accurate fluidic sequence and correct operation is verified by the embedded electrodes. As a proof of concept, we demonstrated the application of this novel approach in vitro and in vivo, to collect glucose in the brain of mice, with a temporal resolution of 1-2 minutes and without transient regime. Absolute quantification of the glucose level in the samples was performed by direct infusion nanoelectrospray ionization Fourier transform mass spectrometry (nanoESI-FTMS). By adjusting the diffusion time and the perfusion volume of DoD, the fraction of molecules recovered in the samples can be tuned to mirror the tissue concentration at accurate points in time. This makes quantification of biomarkers in the brain possible within acute experiments of only 20 to 120 minutes. DoD provides a complementary tool to continuous microdialysis and push-pull sampling probes. The advances allowed by DoD will benefit quantitative molecular studies in the brain, namely for molecules involved in volume transmission or for protein aggregates that form in neurodegenerative diseases over long periods. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/487549v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1edeb56org.highwire.dtl.DTLVardef@f573aforg.highwire.dtl.DTLVardef@7dfd38org.highwire.dtl.DTLVardef@17b7b46_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2020

Nature-inspired Circular-economy Recycling (NaCRe) for Proteins: Proof of Concept

The billion tons of synthetic polymer-based materials (i.e. plastics) produced every year are one of the greatest challenges that humanity has to face. Nature produces even more natural polymers, yet they are sustainable. For example, proteins are sequence-defined natural polymers, that are constantly recycled when living systems feed. Indeed, digestion is the protein depolymerization into amino acids (i.e. the monomers) followed by their re-assembly into new proteins of arbitrarily different sequence and function. This process breaks a common recycling paradigm where a material is recycled into itself. Organisms feed of random protein mixtures that are recycled into new proteins whose identity depends on the cells needs at the time of protein synthesis. Currently, advanced materials are increasingly made of proteins, but the abovementioned ideal recyclability of such materials has yet to be recognized and established. In this study mixtures of several (up to >30) peptides and/or proteins were depolymerized into their amino acid constituents, and these amino acids were used to synthesize new fluorescent, and bio-active proteins extra-cellularly by using an amino acid-free cell-free transcription-translation system. Proteins with high relevance in materials engineering ({beta}-lactoglobulin films, used for water filtration, or silk fibroin solutions) were successfully recycled into biotechnologically relevant proteins (green, and red fluorescent proteins, catechol 2,3-dioxygenase). The potential long-term impact of this approach to recycling lies in its compatibility with circular-economy models where raw materials remain in use as long as possible, thus reducing the burden on the planet.

biochemistry↗

bioRxiv2018

Consumption of carotenoids not increased by bacterial infection in brown trout embryos (Salmo trutta)

Carotenoids are organic pigment molecules that play important roles in signalling, control of oxidative stress, and immunity. Fish allocate carotenoids to their eggs, which gives them the typical yellow to red colouration and supports their resistance against microbial infections. However, it is still unclear whether carotenoids act mainly as a shield against infection or are used up during the embryos immune defence. We investigated this question with experimental families produced from wild-caught brown trout (Salmo trutta). Singly raised embryos were either exposed to the bacterial pathogen Pseudomonas fluorescens or sham-treated at one of two stages during their development. A previous study on these experimental families reported positive effects of egg carotenoids on embryo growth and resistance against the infection. Here, we quantified carotenoid consumption in these infected and sham-infected maternal sib groups. We found that carotenoid contents mostly decreased during embryogenesis. However, these decreases were neither linked to the virulence induced by the pathogen nor dependent on the time point of infection. We conclude that egg carotenoids are not significantly used up by the embryos immune defence.

ecology↗