Biology subjects

Fornili, A.

Publications and source records attributed to Fornili, A..

7 recordsLinked to original sources

bioRxiv2026

Architecture of the type II secretion system

The virulence of emerging Gram-negative pathogens frequently arises from toxins delivered by the type II secretion system1. Cryo-EM single particle analysis and cryo-electron tomography and have defined the outer membrane secretin pore in detail, but the organisation of proteins within the periplasm and inner membrane that form the pilus assembly platform is not well resolved2,3. Here we combine AlphaFold4 models with single particle cryo-EM to define the organisation of the pilus assembly platform. We show that CLM heterotrimers form a continuous link from the cytoplasmic ATPase, across the inner membrane and periplasm, to the base of the secretin channel. AlphaFold models of the inner membrane spanning rotor and cytoplasmic ATPase fit readily within the cryo-EM density. The resolved secretion system exhibits an offset between the inner membrane assembly platform and the outer membrane secretin pore, together with profound asymmetry and an unexpectedly open periplasmic architecture. This architecture provides a route by which large, folded proteins access the secretion channel from the periplasm and suggests that substrate engagement may trigger the final steps in secretion system assembly leading to secretion.

microbiology↗

bioRxiv2026

Learning fragment-based segmentation of binding sites from molecular dynamics: a proof-of-concept on cardiac myosin.

The geometric and chemical features of protein binding sites tend to change as a consequence of conformational dynamics. In the ligand-unbound (apo) state, a binding site might be only transiently organised in a way that can accommodate a given ligand, with the relevant regions of the protein coming together in a suitable arrangement only in a subset of conformations. Ligand binding itself can also induce further changes in the binding site. Because most ligands can be decomposed into smaller fragments, we hypothesised that mapping onto the binding site surface the propensity of binding specific fragments could be used to monitor changes in the overall ability of the site to bind a ligand. This task can be formulated as semantic segmentation, which can now be performed successfully using deep learning methods. Here we introduce the Fragment-Based protein Ensemble semantic Segmentation Tool for Myosin (FragBEST-Myo), a deep learning method based on a 3D U-Net architecture, trained to partition the omecamtiv mecarbil (OM) binding site of cardiac myosin into fragment-specific regions using only local shape and physico-chemical features. The model was trained on labelled Molecular Dynamics (MD) trajectories of OM-bound myosin in both post-rigor (PR) and pre-power-stroke (PPS) states, achieving an accuracy of ~95% and a mean Intersection over Union (mIoU) > 0.75 on unseen trajectories from both states. When applied to apo trajectories, FragBEST-Myo-derived descriptors produced rankings consistent with similarity to holo conformations. Moreover, selecting apo frames based on FragBEST-Myo ranking increased the chance of recovering holo-like OM docking poses relative to randomly chosen control frames, supporting its use as a screening tool for ensemble docking. Beyond frame selection, fragment maps provide a compact representation to assess docking poses and to guide fragment-based design. Our proof-of-concept provides a basis for developing future general models applicable to a broader range of proteins and ligands, with the fragment-based formulation offering a natural route to generalisation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/703009v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1551255org.highwire.dtl.DTLVardef@26bf73org.highwire.dtl.DTLVardef@1e3181forg.highwire.dtl.DTLVardef@44baf7_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

TrIPP: a Trajectory Iterative pKa Predictor

The protonation propensity of ionisable residues in proteins can change in response to changes in the local residue environment. The link between protein dynamics and pKa is particularly important in pH regulation of protein structure and function. Here, we introduce TrIPP (Trajectory Iterative pKa Predictor), a Python tool to monitor and analyse changes in the pKa of ionisable residues during Molecular Dynamics simulations of proteins. We show how TrIPP can be used to identify residues with physiologically relevant variations in their predicted pKa values during the simulations, and link them to changes in the local and global environment. TrIPP is available at https://github.com/fornililab/TrIPP.

bioinformatics↗

bioRxiv2023

The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans

Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans (GAGs) on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual dynamic trimer arrangement with a positively charged external surface and a negatively charged solvent exposed internal cavity. Through Molecular Dynamics (MD) simulations, we show how the GAG chondroitin-4-sulphate associates with the Lcl-CTD surface via unique binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate binding mechanism.

microbiology↗

bioRxiv2023

Elucidating the activation mechanism of the proton-sensing GPR68 receptor

GPR68 is a proton-sensing G-protein Coupled Receptor (GPCR) involved in a variety of physiological processes and disorders including neoplastic pathologies. While GPR68 and few other GPCRs have been shown to be activated by a decrease in the extracellular pH, the molecular mechanism of their activation remains largely unknown. In this work, we used a combined computational and in vitro approach to provide new insight into the activation mechanism of the receptor. Molecular Dynamics simulations of GPR68 were used to model the changes in residue interactions and motions triggered by pH. Global and local rearrangements consistent with partial activation were observed upon protonation of the inactive state. Selected extracellular histidine and transmembrane acidic residues were found to have significantly upshifted pKa values during the simulations, consistently with their previously hypothesised role in activation through changes in protonation state. Moreover, a novel pairing between histidine and acidic residues in the extracellular region was highlighted by both sequence analyses and simulation data and tested through site-directed mutagenesis. At last, we identified a previously unknown hydrophobic lock in the extracellular region that might stabilise the inactive conformation and regulate the transition to the active state.g

molecular biology↗

bioRxiv2021

N4BP1 is dimerization-dependent linear ubiquitin reader regulating TNFR1 signalling through linear ubiquitin binding and Caspase-8-mediated processing

Signalling through TNFR1 modulates proinflammatory gene transcription and programmed cell death, and its impairment causes autoimmune diseases and cancer. NEDD4-binding protein 1 (N4BP1) was recently identified as a critical suppressor of proinflammatory cytokine production1, whose mode of action remained unknown. Here, we show that N4BP1 is a novel linear ubiquitin reader that negatively regulates NF{kappa}B signalling by its unique dimerizationdependent ubiquitin-binding module that we named LUBIN. Dimeric N4BP1 strategically positions two non-selective ubiquitin-binding domains to ensure exclusive recognition of linear ubiquitin. Under proinflammatory conditions, N4BP1 is recruited to the nascent TNFR1 signalling complex, where it regulates duration of proinflammatory signalling in LUBIN-dependent manner. N4BP1 deficiency accelerates TNF-induced cell death by increasing complex II assembly. Under proapoptotic conditions, Caspase-8 mediates proteolytic processing of N4BP1 and the resulting cleavage fragment of N4BP1, which retains the ability to bind linear ubiquitin, is rapidly degraded by the 26S proteasome, accelerating apoptosis. In summary, our findings demonstrate that N4BP1 dimerization creates a unique linear ubiquitin reader that ensures timely and coordinated regulation of TNFR1-mediated inflammation and cell death.

biochemistry↗

bioRxiv2019

Structure and functional analysis of the Legionella chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradation

Chitinases are important enzymes that contribute to the generation of carbon and nitrogen from chitin, a long chain polymer of N-acetylglucosamine that is abundant in insects, fungi, invertebrates and fish. Although mammals do not produce chitin, chitinases have been identified in bacteria that are key virulence factors in severe respiratory, gastrointestinal and urinary diseases. However, it is unclear how these enzymes are able to carry out this dual function. Legionella pneumophila is the causative agent of Legionnaires disease, an often-fatal pneumonia and its chitinase ChiA is essential for the survival of L. pneumophila in the lung. Here we report the first atomic resolution insight into the pathogenic mechanism of a bacterial chitinase. We derive an experimental model of intact ChiA and show how its N-terminal region targets ChiA to the bacterial surface after its secretion. We provide the first evidence that L. pneumophila can bind mucins on its surface but this is not dependent on chiA. This demonstrates that additional peripheral mucin binding proteins are also expressed in L. pneumophila. Finally, we show that the ChiA C-terminal chitinase domain has novel metal-dependent peptidase activity against mammalian mucins. These findings suggest that ChiA facilitates bacterial penetration of the alveolar mucosa and ChiA may be a promising target for vaccine development.

microbiology↗