Biology subjects

Nicoli, A.

Publications and source records attributed to Nicoli, A..

5 recordsLinked to original sources

bioRxiv2026

Membrane controlled Mechanoregulation in PIEZO1 Interactions

PIEZO channels are mechanosensitive membrane proteins whose activation is governed by the surrounding lipid environment. However, the direct mechanistic contribution of native membrane composition to the molecular interactions remains unclear. In this study, a systematic comparison is made between PIEZO1 reconstituted in detergent micelles and in cell membrane-derived nanodiscs, which preserve the native lipid composition. Initial characterization employing a combination of atomic force microscopy and coarse-grained molecular dynamics simulations unveils distinct physical signatures of PIEZO1 in these two environments. Single-molecule force spectroscopy measurements demonstrate that interaction between the extracellular domain of PIEZO1 and a specific antibody exhibits unique mechanical responses strongly influenced by the surrounding membrane. In nanodiscs, PIEZO1 exhibits reversible, elastic-like behavior with preserved structural integrity and consistent adhesion forces even when modulated by Yoda1 (agonist) and Dooku1 (antagonist). Conversely, micelles induce a plastic response with altered mechanosensitivity and functional stability. Based on these findings, we propose a possible membrane-mediated force transmission pathway and quantify a simplified interaction energy landscape. Collectively, our findings offer the initial direct evidence of how the native lipid environment mechanistically governs PIEZO1 interactions, establishing native membranes as critical determinants for mechanotransduction.

biophysics↗

bioRxiv2026

The plant immune receptor LORE binds agonistic and antagonistic 3-hydroxy fatty acid ligands via a dynamic loop in its G-type lectin domain

The Arabidopsis thaliana S-domain receptor kinase LORE senses bacterial medium-chain 3-hydroxy fatty acids (mc-3-OH-FAs) as microbe-associated molecular patterns to activate pattern-triggered immunity. How LORE recognises these fatty acid ligands at the molecular level remains unknown. Here, we combined protein structure prediction, protein-ligand interaction modelling and molecular dynamics (MD) simulations with ligand-binding assays using chimeric and mutant receptor ectodomains, and functional analysis of receptor activation to characterise the mc-3-OH-FA binding mechanism. Domain-swap experiments between LORE and its non-binding paralog AtSD1-23 identify the lectin 2 (L2) domain as the ligand-binding domain. Mutational analysis and reverse engineering confirm a hydrophobic pocket in the L2 core as the primary ligand-binding site. Multiple walker Supervised MD (mwSuMD) simulations reveal that the acyl tail enters the pocket first, whilst polar interactions between the headgroup and a flexible L2 loop guide and stabilise the bound state. In support of this model, 3-OH-C10:0 analogues with bulky headgroup modifications dock into the pocket but act as antagonists, presumably by preventing the loop from adopting the conformation required for signalling. Together, these data suggest that the flexible L2 loop has multiple functions: it acts as a dynamic gate regulating pocket access, provides essential anchoring points once the ligand is bound, and contributes to receptor activation. These findings provide a mechanistic framework for immunogenic mc-3-OH-FA sensing by LORE.

plant biology↗

bioRxiv2025

Myelin maintenance and addition regulate synaptic plasticity in the adult mouse cortex

Myelination of the developing central nervous system (CNS) increases action potential conduction velocity but can also act as a plasticity brake, limiting neurite reorganisation and synaptic plasticity. As myelination is a life-long process, the myelin laid down in development or adulthood could also affect synapse number or plasticity across the lifespan. We report that conditionally deleting the transcription factor, myelin regulatory factor (Myrf), to disrupt the myelin maintenance program in oligodendrocytes (OLs) from P57 (Plp-CreERT2 :: Myrf fl/fl mice), led to significant myelin loss and impaired action potential conduction and gross motor performance. By sparsely labelling layer V pyramidal neurons in the primary motor cortex, we could visualise the apical and basal dendrites and their excitatory post-synaptic dendritic spines and determined that spine density was normal in P57+60 Plp-CreERT2 :: Myrf fl/fl mice. However, a higher proportion of the dendritic spines were large, stable mushroom spines and generated larger amplitude miniature excitatory post-synaptic currents. These data indicate that the myelin maintenance program is critical for preserving neuron adaptability, homeostasis and glutamate sensitivity. When we instead prevented the addition of new OLs and myelin from P57, action potential conduction velocity and gross motor performance appeared normal. Spine density was also normal in Pdgfr-CreERTM :: Myrf fl/fl mice, however, spine morphology was changed along the basal dendrites of layer V M1 pyramidal neurons. At P117, the basal dendrites were frozen in a state that resembled P57 dendrites, as they retained a higher proportion of thin, plastic spines. These data suggest that adult myelination supports the life-long accumulation of stable spines within the basal but not apical dendritic compartment and have important implications for understanding dendritic plasticity rules in the motor circuit. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/695322v1_ufig1.gif" ALT="Figure 1"> View larger version (77K): org.highwire.dtl.DTLVardef@1a7928org.highwire.dtl.DTLVardef@83e7borg.highwire.dtl.DTLVardef@13e1e14org.highwire.dtl.DTLVardef@128e2df_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAdult myelin maintenance regulates synaptic plasticity and neuron homeostasis C_LIO_LIExisting myelin regulates layer V pyramidal neuron glutamate sensitivity C_LIO_LIOligodendrocytes born in young adulthood undergo age-related loss C_LIO_LINew myelin stabilises synapses in the basal but not apical dendritic compartment C_LI eTOC blurbMyelin regulates axon branching, metabolism and action potential conduction speed. We report that myelin also preserves neuron adaptability, homeostasis and glutamate sensitivity in the adult motor cortex. Furthermore, new myelin allows the accumulation of stable synapse on basal but not apical layer V pyramidal neuron dendrites over time.

neuroscience↗

bioRxiv2025

Synthetic Mucins as Glycan-Defined Prebiotics

The human microbiome contains at least as many bacterial cells as human cells. The mucosal layer that lines all epithelial cells organizes, cultivates, and regulates these bacterial inhabitants. Some commensal bacteria offer benefits, like improving gut barrier function, suppressing pathobiont growth, and modulating host immunity. These health benefits have fueled the popularity of probiotics, but their retention is often hindered by their low colonization efficiency and mucosal adhesion. Mucins, the primary structural components of the mucosal layer, are essential for the organization and regulation of microbial populations, promoting growth and offering sites for adhesion through their multivalent presentation of O-glycosylation. The molecular mechanisms of mucin- probiotic interactions remain understudied due, in part, to the inability to incisively manipulate native mucin sequences or the glycans they bear. In this investigation, we developed synthetic mucins with defined glycan presentations to interrogate glycan-dependent interactions between mucus and probiotic Lactobacillus species. Though synthetic mucins can dampen the effects of pathogens, toxins, and viruses, their impact on probiotic bacteria as prebiotics or binding sites is unclear. We synthesized mucin surrogates that bind to three investigated Lactobacillus species. The nutrient conditions under which bacteria were cultured influenced glycan binding preferences, suggesting mucin-probiotic interactions change with nutrient availability. The addition of synthetic mucins to native mucin increased Lactobacillus fermentum adherence. Additionally, an increase in Lactobacillus glycosidase activity indicated that native and synthetic mucins both function as prebiotics, as probiotic bacteria can cleave the displayed O-glycans. Thus, synthetic mucins can cultivate target probiotic bacteria and increase adhesion as binding sites, highlighting their value as tools for elucidating native mucin functions and as promising agents for promoting human health.

biochemistry↗

bioRxiv2022

Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

With approximately 400 encoding genes in humans, odorant receptors (ORs) are the largest subfamily of class A G protein-coupled receptors (GPCRs). Despite its high relevance and representation, the odorant-GPCRome is structurally poorly characterized: no experimental structures are available, and the low sequence identity of ORs to experimentally solved GPCRs is a significant challenge for their modeling. Moreover, the receptive range of most ORs is unknown. The odorant receptor OR5K1 was recently and comprehensively characterized in terms of cognate agonists. Here we report two additional agonists and functional data of the most potent compound on two mutants, L1043.32 and L2556.51. Experimental data was used to guide the investigation of the binding modes of OR5K1 ligands into the orthosteric binding site using structural information from AI-driven modeling, as recently released in the AlphaFold Protein Structure Database, and from homology modeling. Induced-fit docking simulations were used to sample the binding site conformational space for ensemble docking. Mutagenesis data guided side chain residue sampling and model selection. We obtained models that could better rationalize the different activity of active (agonist) versus inactive molecules with respect to starting models, and also capture differences in activity related to minor structural differences. Therefore, we provide a model refinement protocol that can be applied to model the orthosteric binding site of ORs as well as that of GPCRs with low sequence identity to available templates.

molecular biology↗