Biology subjects

Faccioli, P.

Publications and source records attributed to Faccioli, P..

6 recordsLinked to original sources

bioRxiv2026

Loss of the Central Region Reshapes the Dynamic Landscape of the Cellular Prion Protein and Its Plasma Membrane Interaction

Prion diseases are fatal neurodegenerative disorders driven by the conversion of the cellular prion protein (PrP) into a misfolded, pathogenic conformer. Beyond serving as a substrate for prion propagation, PrP is also thought to mediate neurotoxic signaling. Within this framework, the central region of PrP has emerged as a critical regulatory element. Notably, deletion of residues 105-125 ({Delta}CR) leads to spontaneous neurodegeneration in vivo and induces abnormal ionic currents in cultured cells and primary neurons, indicating that this region is essential for controlling the toxicity of the N-terminal domain. Current models propose that the N-terminus functions as a toxic effector whose activity is modulated by the C-terminal domain. This intramolecular interplay is likely central to the physiological role of PrP, and its disruption may contribute to neurodegeneration. Here, we investigated how deletion of the central region affects the structure and dynamics of full-length PrP. We generated membrane-bound models of full-length, diglycosylated wild-type (WT) PrP and the neurotoxic {Delta}CR mutant, and compared their conformational dynamics using molecular dynamics simulations. The two proteins exhibited markedly distinct behaviours. WT PrP adopted a more compact conformational ensemble of the N-terminal domain, consistent with stabilizing interactions between the flexible N-terminus and the globular C-terminal domain. In contrast, the {Delta}CR variant displayed more extended conformations and a substantial redistribution of intramolecular contacts, including the loss of specific interactions between the disordered N-terminal tail and the globular domain. This altered structural organization was accompanied by an increased propensity of the N-terminal domain to approach the membrane surface in the mutant. Our results provide a molecular model in which the central region engages intramolecular interaction networks that ultimately help regulate N-terminal residence at the plasma membrane, offering mechanistic insight into how CR deletion shifts the conformational ensemble toward membrane-associated states that may be associated with neurotoxic activity.

biochemistry↗

bioRxiv2026

MOAflow: how re-design a pipeline with Nextflow streamlines data analysis

BackgroundAdvances in high-throughput DNA sequencing technologies have dramatically reduced the time and cost required to generate genomic data. As sequencing is no longer a limiting factor, increasing attention must be paid to optimizing the analyses of the large-scale datasets produced. Efficient processing of such data is essential to reduce computational time and operational costs. In this context, workflow management systems (WMSs) have become key instruments for orchestrating complex bioinformatic pipelines. Among these systems, Nextflow has emerged as one of the most widely adopted solutions in bioinformatics. MethodsTo improve scalability and computational efficiency, we employed Nextflow to re-design an already existing pipeline dedicated to the analysis of MNase-defined cistrome-Occupancy (MOA-seq) data. The re-engineering process focused on modularizing the workflow and integrating containerization technologies to ensure reproducibility and easier deployment across heterogeneous computing environments. ResultsThe resulting workflow, named MOAflow, represents a modernized and fully containerized pipeline for MOA-seq data analysis. With only Docker and Nextflow required, the pipeline guarantees high portability and reproducibility. The data of the original article was used to benchmark the new pipeline. Its outputs closely match those of the original study with minor variations. ConclusionsMOAflow demonstrates how the adoption of robust WMS can substantially enhance the performance and usability of pre-existing bioinformatic pipelines. By leveraging containerization and Nextflow, it ensures consistent results across platforms while minimizing setup complexity. This work highlights the value of modern WMS-driven approaches in meeting the computational demands.

bioinformatics↗

bioRxiv2024

Mapping Cryptic Phosphorylation Sites in the Human Proteome

Advances in computational and experimental methods have revealed the existence of transient, non-native protein folding intermediates that could play roles in disparate biological processes, from regulation of protein expression to disease-relevant misfolding mechanisms. Here, we tested the possibility that specific post-translational modifications may involve residues exposed during the folding process by assessing the solvent accessibility of 87,138 post-translationally modified amino acids in the human proteome. Unexpectedly, we found that one-third of phosphorylated proteins present at least one phosphosite completely buried within the proteins inner core. Computational and experimental analyses suggest that these cryptic phosphosites may become exposed during the folding process, where their modification could destabilize native structures and trigger protein degradation. Phylogenetic investigation also reveals that cryptic phosphosites are more conserved than surface-exposed phosphorylated residues. Finally, cross-referencing with cancer mutation databases suggests that phosphomimetic mutations in cryptic phosphosites can increase tumor fitness by inactivating specific onco-suppressors. These findings define a novel role for co-translational phosphorylation in shaping protein folding and expression, laying the groundwork for exploring the implications of cryptic phosphosites in health and disease.

biochemistry↗

bioRxiv2022

Long range allostery mediates the regulation of plasminogen activator inhibitor 1 by vitronectin

The serpin plasminogen activator inhibitor 1 (PAI-1) spontaneously undergoes a massive structural change from a metastable, active conformation, with a solvent accessible reactive center loop (RCL), to a stable, inactive or latent conformation in which the RCL has inserted into the central {beta} sheet. Physiologically, conversion to the latent state is regulated by the binding of vitronectin which retards the rate of this latency transition approximately 2-fold. We investigated the effects of vitronectin on the PAI-1 latency transition using all-atom path sampling simulations in explicit solvent. In simulated latency transitions of free PAI-1, the RCL is quite mobile as is the gate, the region that impedes RCL access to the central {beta} sheet. This mobility allows the formation of a transient salt bridge that facilitates the transition, and this finding rationalizes existing mutagenesis results. Vitronectin binding reduces RCL and gate mobility by allosterically rigidifying structural elements over 40 [A] away from the binding site thus blocking the transition to the latent conformation. The effects of vitronectin are propagated by a network of dynamically correlated residues including a number of conserved sites that have previously been identified as important for PAI-1 stability. Simulations also revealed a transient pocket populated only in the vitronectin bound state which corresponds to a cryptic drug binding site identified by crystallography. Overall, these results shed new light on regulation of the PAI-1 latency transition by vitronectin and illustrate the potential of path sampling simulations for understanding functional conformational changes in proteins and for facilitating drug discovery.

biophysics↗

bioRxiv2020

PHARMACOLOGICAL PROTEIN INACTIVATION BY TARGETING FOLDING INTERMEDIATES

Recent computational advancements in the simulation of biochemical processes allow investigating the mechanisms involved in protein regulation with realistic physics-based models, at an atomistic level of resolution. Using these techniques to study the negative regulation of the androgen receptor (AR), we discovered a key functional role played by non-native metastable states appearing along the folding pathway of this protein. This unexpected observation inspired us to design a completely novel drug discovery approach, named Pharmacological Protein Inactivation by Folding Intermediate Targeting (PPI-FIT), based on the rationale of negatively regulating protein expression by targeting folding intermediates. Here, PPI-FIT was tested for the first time on the cellular prion protein (PrP), a cell surface glycoprotein playing a key role in fatal and transmissible neurodegenerative pathologies known as prion diseases. We predicted the all-atom structure of an intermediate appearing along the folding pathway of PrP, and identified four different small molecule ligands for this conformer, all capable of selectively lowering the expression of the protein by promoting its degradation. Our data support the notion that the level of target proteins could be modulated by acting on their folding pathways, implying a previously unappreciated role for folding intermediates in the biological regulation of protein expression.

biochemistry↗

bioRxiv2018

Full Atomistic Model Of Prion Structure And Conversion

Prions are unusual protein assemblies that propagate their conformationally-encoded information in absence of nucleic acids. The first prion identified, the scrapie isoform (PrPSc) of the cellular prion protein (PrPC), is the only one known to cause epidemic and epizootic episodes(1). Most aggregates of other misfolding-prone proteins are amyloids, often arranged in a Parallel-In-Register-{beta}-Sheet (PIRIBS)(2) or {beta}-solenoid conformations(3). Similar folding models have also been proposed for PrPSc, although none of these have been confirmed experimentally. Recent cryo-electron microscopy (cryo-EM) and X-ray fiber-diffraction studies provided evidence that PrPSc is structured as a 4-rung {beta}-solenoid (4R{beta}S)(4, 5). Here, we combined different experimental data and computational techniques to build the first physically-plausible, atomic resolution model of mouse PrPSc, based on the 4R{beta}S architecture. The stability of this new PrPSc model, as assessed by Molecular Dynamics (MD) simulations, was found to be comparable to that of the prion forming domain of Het-s, a naturally-occurring {beta}-solenoid. Importantly, the 4R{beta}S arrangement allowed the first simulation of the sequence of events underlying PrPC conversion into PrPSc. Our results provide the most updated, experimentally-driven and physically-coherent model of PrPSc, together with an unprecedented reconstruction of the mechanism underlying the self-catalytic propagation of prions.\n\nSignificanceSince the original hypothesis by Stanley Prusiner, prions have represented enigmatic agents diverging from the classical concept of genetic inheritance. However, the structure of PrPSc, the infectious isoform of the cellular prion protein (PrPC), has so far remained elusive, mostly due to technical challenges posed by its aggregation propensity. Here, we present a new high resolution model of PrPSc derived from the integration of a wide array of recent experimental constraints. By coupling the information of such model with a newly developed computational method, we reconstructed for the first time the conformational transition of PrPC to PrPSc. This study offers a unique workbench for designing therapeutics against prion diseases, and a physically-plausible mechanism explaining how protein conformation could self-propagate.

biochemistry↗