Search bioRxiv⌕ Search

Biology subjects

Longhi, S.

Publications and source records attributed to Longhi, S..

12 recordsLinked to original sources
bioRxiv2026

Molecular dynamics insights into biomineralisation mediated by acidic intrinsically disordered proteins: a case study of molluscan Aspein from the pearl oyster Pinctada fucata

Biomineralisation is a ubiquitous phenomenon that still fascinates the scientific community. Mineralised structures are most notably encountered in marine lifeforms the shell or exoskeleton of which are formed by precipitating specific calcium carbonate (CaCO3) polymorphs, known as amorphous (ACC), vaterite, aragonite, and calcite. To control crystalline polymorphism in their shell layers, bivalves have evolved strategies involving ion-binding secretomes composed of shell matrix proteins (SMPs). Secreted in the prismatic layer of the pearl oyster Pinctada fucata, Aspein is an unusually acid-rich protein exclusively aspartic and famously recognised as the most acidic SMP known to date. Through in vitro crystallisation experiments, Aspein was shown to select calcite over aragonite in modern seawater conditions. However, how it exerts its selectivity with respect to its structural properties remains enigmatic. By combining sequence-based predictions with all-atom molecular dynamics simulations, we unveiled that Aspein is an intrinsically disordered organic matrix protein (IDOMP) undergoing ion-specific chain collapse and phase separation. Thanks to its unique Asp density and conformational fuzziness, Aspein first sequesters Ca2+ then attracts CO32- ions before stabilising ACC and calcite-like phases, while precluding the incorporation of Mg2+ to avoid aragonite formation. Indeed, via Asp-Ca2+ bridges, structure-less clusters coalescence into supersaturated protein-CaCO3 assemblies initiates calcite crystallisation. Therefore, Aspein plasticity, condensation susceptibility, and aspartic density critically modulate the pathway that defines CaCO3 polymorphism by inhibiting nucleation and controlling the growth of biogenic minerals. From a broader perspective, our study underpins some of the molecular and physico-chemical principles governing biomineralisation processes mediated by IDOMPs, the overlooked, yet prevalent, role of which was mechanistically unexplored.

biophysics↗
bioRxiv2025

The C-terminal intrinsically disordered region of a fungal LPMO binds copper and displays anti-fungal properties

Lytic Polysaccharide Monooxygenases (LPMOs) are enzymes that play a crucial role in the degradation of complex polysaccharides such as cellulose and chitin. While LPMOs have attracted significant interest for industrial applications to convert biomass into biofuels, emerging evidence suggests alternative functions in fungal plant pathogenesis, microbial diseases and (micro)organism development. The AA14 LPMO family is widely distributed in filamentous fungi but remains enigmatic as its initially-suspected substrate specificity was recently challenged. In this study, we investigated the disordered C-terminal regions (dCTRs), found in more than half of AA14 family members and hypothesized to have functional relevance. Focusing on the Pycnoporus coccineus AA14A LPMO, we used small angle X-ray scattering (SAXS) and circular dichroism to show that its dCTR is highly disordered. It consists of a heavily glycosylated low complexity region followed by a charged C-terminal tail. We uncovered that the PcoAA14A dCTR binds copper ions through histidine residues located in the C-terminal tail. Using electron paramagnetic resonance (EPR), we further demonstrated that dimer formation occurs through an oxidative process involving copper and a redox-sensitive cysteine. Noting similarities between the last residues of the C-terminal tail and antimicrobial peptides, we investigated its potential antimicrobial function. We found that the positively charged region of the C-terminal tail selectively inhibits the growth of basidiomycete fungal spores. These data reveal that the dCTRs appended to AA14 LPMOs are functional regions that must be considered to unveil the role of these atypical LPMOs. Significance StatementLytic polysaccharide monooxygenases (LPMOs) degrade complex polysaccharides and are central to biomass conversion. Their biological relevance is expanding, with emerging roles in fungal development and host interactions. Despite this broad potential, research has largely focused on their catalytic domain. One area that remains poorly understood is the function of their C-terminal region, predicted to be intrinsically disordered (dCTR). The AA14 LPMO family, whose substrate specificity remains enigmatic, is enriched in dCTRs. This study provides the first experimental evidence of the disordered nature of the dCTR of an AA14 LPMO. Using multidisciplinary approaches, we demonstrate that the dCTR binds metals and exhibits antifungal activity. These findings establish dCTRs as functional regions, essential for understanding the biological roles of LPMOs.

biochemistry↗
bioRxiv2025

Unveiling Oligodendrocyte-Lineage Differentiation in the Glioblastoma Infiltrative Zone Through Spatial Transcriptomics

IDH-wildtype glioblastoma (GBM) is the most aggressive primary brain tumor, characterized by limited therapeutic options and inevitable recurrence. This recurrence is driven by the highly infiltrative behavior of GBM cells, which prevents complete resection. Here, we performed spatially resolved transcriptomic profiling of four surgically defined GBM regions to characterize the infiltrative tumor compartment. Across multiple datasets and profiling approaches, the infiltrative zone showed reduced cellular heterogeneity compared with the tumor core. By comparison with an integrated reference of single-cell RNA sequencing data, we revealed that this reduction reflects a preferential differentiation of infiltrative GBM cells toward an oligodendrocyte-like lineage, accompanied by attenuated inflammatory signaling. In contrast, necrotic and proliferative regions display pronounced astrocyte-like and mesenchymal-like programs. Combined immunohistochemistry and fluorescence in situ hybridization confirmed the enrichment of oligodendrocyte-like tumor cells in the infiltrative area. Together, these findings identify the oligodendrocyte-like state as a defining feature and potential therapeutic vulnerability of infiltrative GBM driving brain invasion and relapse.

cancer biology↗
bioRxiv2024

Transient Non-local Interactions Dominate the Dynamics of Measles Virus NTAIL

The RNA genome of measles virus is encapsidated by the nucleoprotein within a helical nucleocapsid that serves as template for both transcription and replication. The intrinsically disordered domain of the nucleoprotein (NTAIL), partly protruding outward from the nucleocapsid, is essential for binding the polymerase complex responsible for viral transcription and replication. As for many IDPs, binding of NTAIL occurs through a short molecular recognition element (MoRE) that folds upon binding, with the majority of NTAIL remaining disordered. Though NTAIL regions far from the MoRE influence the binding affinity, interactions between them and the MoRE have not been investigated in depth. Using an integrated approach, relying on photo-induced electron transfer (PET) experiments between tryptophan and cysteine pairs placed at different positions in the protein under varying salt and pH conditions, combined with simulations and analytical models, we identified transient interactions between two disordered regions distant in sequence, which dominate NTAIL dynamics, and regulate the conformational preferences of both the MoRE and the entire NTAIL domain. Co-evolutionary analysis corroborates our findings and suggests an important functional role for the same intramolecular interactions. We propose mechanisms by which these non-local interactions may regulate binding to the measles phosphoprotein, polymerase recruitment, and ultimately viral transcription and replication. Our findings may be extended to other IDPs, where non-local intra-protein interactions affect the conformational preferences of intermolecular binding sites.

biophysics↗
bioRxiv2024

Redox-dependent formation of a viral amyloid and functional impact

The Hendra and Nipah viruses (HeV and NiV) are zoonotic biosafety level-4 pathogens belonging to the Paramyxoviridae family. We previously showed that their W protein, a key player in the evasion of the host antiviral response, forms highly flexible, curved fibrils in vitro. Here, we show that the cysteine oxidation state acts as a molecular switch controlling the formation of either amorphous aggregates or flexible fibrils, and that residues 2 to 29 are essential for fibrillation. We also uncover that the HeV W protein (WHeV) can also self-assemble in cellula. WHeV forms distinct types of nuclear condensates that exhibit different dependencies on the cysteine redox-state. While deletion of residues 2-29 prevents formation of nuclear filaments, cysteine-to-serine substitution mainly impairs the formation of non-filamentous condensates. Both infection and WHeV ectopic expression trigger oxidative stress presumably favorable to WHeV condensation. Finally, we show that impaired ability to form redox-sensitive, non-filamentous condensates is associated with a reduced W ability to inhibit the NF-{kappa}B pathway, while it conversely enhances W ability to repress the interferon response pathway.

biochemistry↗
bioRxiv2022

Molecular determinants of fibrillation in a viral amyloidogenic domain from combined biochemical and biophysical studies

The Nipah and Hendra viruses (NiV and HeV) are biosafety level 4 human pathogens classified within the Henipavirus genus of the Paramyxoviridae family. In both NiV and HeV, the gene encoding the Phosphoprotein (P protein), an essential polymerase cofactor, also encodes the V and W proteins. These three proteins, which share an intrinsically disordered N-terminal domain (NTD) and have unique C-terminal domains (CTD), are all known to counteract the host innate immune response, with V and W acting by either counteracting or inhibiting Interferon (IFN) signaling. Recently, using a combination of biophysical and structural approaches, the ability of a short region within the shared NTD (PNT3 region) to form amyloid-like structures was reported. Here, we evaluated the relevance of each of three contiguous tyrosine residues located in a previously identified amyloidogenic motif (EYYY) within HeV PNT3 to the fibrillation process. Our results indicate that removal of a single tyrosine in this motif significantly decreases the ability to form fibrils independently of position, mainly affecting the elongation phase. In addition, we show that the C-terminal half of PNT3 has an inhibitory effect on fibril formation that may act as a molecular shield and could thus be a key domain in the regulation of PNT3 fibrillation. Finally, the kinetics of fibril formation for the two PNT3 variants with highest and lowest fibrillation propensity were studied by Taylor Dispersion Analysis (TDA). The results herein presented shed light onto the molecular mechanisms involved in fibril formation. In addition, the PNT3 variants we generated represent valuable tools to further explore the functional impact of V/W fibrillation in transfected and infected cells.

biochemistry↗
bioRxiv2022

MIADE metadata guidelines: Minimum Information About a Disorder Experiment

An unambiguous description of an experimental setup and analysis, and the subsequent biological observation is vital for accurate data interpretation and reproducible results. Consequently, experimental analyses should be described in a concise, unequivocal, and digestible manner. The aim of minimum information guidelines is to define the fundamental complement of data that can support an unambiguous conclusion on experimental observations. In this document, we present the Minimum Information About Disorder Experiments (MIADE) guidelines to define the minimal fundamental parameters required for non-experts to understand the key findings of an experiment studying intrinsically disordered proteins (IDPs) or intrinsically disordered protein regions (IDRs). MIADE guidelines provide recommendations for data producers to describe the results of their experiments at source, for curators to annotate experimental data to community resources and for database developers maintaining community resources to disseminate the data. We give examples of the application of these guidelines in common use cases and describe the implementation of an update to the DisProt IDP database to allow MIADE-compliant annotation. The MIADE guidelines will improve the interpretability of experimental results for data consumers, facilitate direct data submission, simplify data curation, improve data exchange among repositories and standardise the dissemination of the key metadata on an IDP experiment by IDP data sources.

scientific communication and education↗
bioRxiv2020

Predicting substitutions to modulate disorder and stability in coiled-coils

Coiled-coils are described as stable structural motifs, where two or more helices wind around each other. However, coiled-coils are associated with local mobility and intrinsic disorder. Intrinsically disordered regions (IDRs) in proteins are characterized by lack of stable secondary and tertiary structure under physiological conditions in vitro. They are increasingly recognized as important for protein function. However, characterizing their behaviour in solution and determining precisely the extent of disorder of a protein region remains challenging, both experimentally and computationally. In this work, we propose a computational framework to quantify the extent of disorder within a coiled-coil in solution and to help design substitutions modulating such disorder. Our method relies on the analysis of conformational ensembles generated by relatively short all-atom Molecular Dynamics (MD) simulations. We apply it to the phosphoprotein multimerisation domains (PMD) of Measles virus (MeV) and Nipah virus (NiV), both forming tetrameric left-handed coiled-coils. We show that our method can help quantify the extent of disorder of the C-terminus region of MeV and NiV PMDs, without requiring the input MD trajectory to actually sample the unfolded states of these regions. Moreover, this study provided a conceptual framework for the rational design of substitutions aimed at modulating the stability of the coiled-coils. By assessing the impact of four substitutions known to destabilize coiled-coils, we derive a set of rules to control MeV PMD structural stability and cohesiveness. We therefore design two contrasting substitutions, one increasing the stability of the tetramer and the other increasing its flexibility. Consequently, our method can be considered as a platform to reason about how to design substitutions aimed at regulating flexibility and stability.

bioinformatics↗
bioRxiv2020

The m6A reader Ythdf restricts axonal growth in Drosophila through target selection modulation of the Fragile X mental retardation protein

N6-methyladenosine (m6A) regulates a variety of physiological processes through modulation of RNA metabolism. The modification is particularly enriched in the nervous system of several species, and its dysregulation has been associated with neurodevelopmental defects and neural dysfunctions. In Drosophila, loss of m6A alters fly behavior albeit the underlying mechanism and the role of m6A during nervous system development have remained elusive. Here we find that impairment of the m6A pathway leads to axonal overgrowth and misguidance at larval neuromuscular junctions as well as in the adult mushroom bodies. We identify Ythdf as the main m6A reader in the nervous system being required for limiting axonal growth. Mechanistically, we show that Ythdf directly interacts with Fragile X mental retardation protein to inhibit the translation of key transcripts involved in axonal growth regulation. Altogether, this study demonstrates that the m6A pathway controls development of the nervous system by modulating Fmr1 target selection.

molecular biology↗
bioRxiv2018

Phase transition and amyloid formation by a viral protein as an additional molecular mechanism of virus-induced cell toxicity

Henipaviruses are severe human pathogens responsible for severe encephalitis. Their V protein is a key player in the evasion of the host innate immune response. We have previously reported a biophysical characterization of the Henipavirus V proteins and shown that they interact with DDB1, a cellular protein that is a component of the ubiquitin ligase E3 complex. Here, we serendipitously discovered that the Hendra virus V protein undergoes a liquidhydrogel phase transition. By combining experimental and bioinformatics approaches, we have identified the V region responsible for this phenomenon. This region (referred to as PNT3), which falls within the long intrinsically disordered region of V, was further investigated using a combination of biophysical and structural approaches. ThioflavinT and Congo red binding assays, together with negative-staining electron microscopy studies, show that this region forms amyloid-like, {beta}-enriched structures. Such structures are also formed in mammal cells transfected to express PNT3. Those cells also exhibit a reduced viability in the presence of a stress agent. Interestingly, mammal cells expressing a rationally designed, non-amyloidogenic PNT3 variant (PNT33A), appear to be much less sensitive to the stress agent, thus enabling the establishment of a link between fibril formation and cell toxicity. The present findings therefore pinpoint a so far never reported possible mechanism of virus-induced cell toxicity.

biophysics↗
bioRxiv2018

Conformational footprinting of proteins using a combination of top-down electron transfer dissociation and ion mobility

In recent years native mass spectrometry has been increasingly employed to study protein structure. As such a thorough understanding of the effect of the gas-phase on protein structure is becoming increasingly important. We show how a combination of top-down ETD and ion mobility can be used to probe the gas-phase structure of heterogeneous protein ensembles. By applying collisional activation to the non-covalently bound ETD products after IM separation, the peptide fragments can be released while maintaining the conformational information of the protein ion. We studied the unknown gas-phase structures of the measles virus (MeV) phosphoprotein X domain (PXD), which shows a wide range of different conformations in the gas-phase. We then generated structural models by state-of-the-art gas-phase steered molecular dynamics, which we verified using restraints from ion mobility and the fragment patterns observed. Our findings illustrate the applicability of ETD for obtaining conformational specific structural information on heterogeneous protein ensembles.

biophysics↗