Biology subjects

Rigoli, M.

Publications and source records attributed to Rigoli, M..

9 recordsLinked to original sources

bioRxiv2026

Branching Suppresses Self-Aggregation while Preserving Membrane Association in SET-M33: An Atomistic Molecular Dynamics Study

Branched antimicrobial peptides offer a promising strategy for improving the stability and activity of membrane-active peptides, but how branching alters self-association and membrane binding remains unclear. We used all-atom molecular dynamics simulations to compare tetra-branched SET-M33 with its linear branch sequence Q33 (KKIRVRLSA) in water and at an anionic bacterial-membrane model, to do this, systems containing equivalent numbers of Q33 sequence units were simulated. Q33 formed dimers and higher-order oligomers, particularly at the membrane interface and under hydration-tuned enhanced sampling. In contrast, SET-M33 remained more dispersed, as the branched scaffold and its high cationic charge limited peptide-peptide association while allowing multivalent membrane binding. Both architectures associated rapidly with the bilayer but remained predominantly surface-bound, without persistent pore formation or complete insertion. Q33 showed stronger membrane-induced helical stabilization, whereas SET-M33 retained a more heterogeneous conformational ensemble. Overall, branching primarily altered lateral peptide organization while preserving close membrane association, suppressing uncontrolled self-aggregation and providing an atomistic rationale for the distinct behavior of SET-M33 relative to Q33.

biophysics↗

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↗

bioRxiv2025

Unfold to refold: Tracking the initial steps of PrPC unfolding in the context of PrPSc propagation

It might have been believed that elucidation of the atomistic structure of PrPSc would lead to an immediate understanding of the mechanism of prion propagation. However, PrPSc, now known to be a "simple" amyloid, can just template a previously unfolded polypeptide chain. Therefore, PrPSc can easily template the disordered [~]90-120 domain of an incoming PrPC molecule, but not its [~]121-231 folded domain (FD). The FD needs to accommodate into the [~]121-230 PrPSc surface, an inert "procrustean bed". Thus, a mechanism for concerted unfolding/refolding of the FD must exist, with FD unfolding as a key element. To explore how this might happen, we performed thermal unfolding of recombinant bank vole PrPC(90-231), that is a universal PrPSc propagator PrPSc, tracking changes at the residue level with solution NMR to pinpoint early unfolding propensity. Our data suggest that a key early event is the destabilization of the short {beta}1-{beta}2 assembly, and that the segment contiguous to the disordered tail, [~]121-140, encompassing {beta}1 and its adjacent coils, is the most likely region to unfold first. Spectroscopic data obtained at higher temperatures suggest that portions of alpha helix 2 are likely the last elements of the FD to unfold and refold into the PrPSc conformation. Molecular Dynamics simulations assisted the interpretation of these changes and suggest separation of 1 from the rest of the FD ensemble. Our data provide a conceivable timeline of the early events in PrPSc-assisted conversion of PrPC and should serve as a starting framework to develop a future atomistic model of PrPSc propagation.

biochemistry↗

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

In search of a dynamical vocabulary: a pipeline to construct a basis of shared traits in large-scale motions of proteins

The paradigmatic sequence-structure-dynamics-function relation in proteins is nowadays well established in the scientific community; in particular, large effort has been spent to probe the first connection, indeed providing convincing evidence of its strength and rationalising it in a quantitative and general framework. In contrast, however, the role of dynamics as a link between structure and function has eluded a similarly clear-cut verification and description. In this work, we propose a pipeline aimed at building a basis for the quantitative characterisation of the large-scale dynamics of a set of proteins, starting from the sole knowledge of their native structures. The method hinges on a dynamics-based clusterization, which allows a straightforward comparison with structural and functional protein classifications. The resulting basis set, obtained through the application to a group of related proteins, is shown to reproduce the salient large-scale dynamical features of the dataset. Most interestingly, the basis set is shown to encode the fluctuation patterns of homologous proteins not belonging to the initial dataset, thus highlighting the general applicability of the pipeline used to build it.

biophysics↗

bioRxiv2022

Structural Basis of Mutation-Dependent p53 Tetramerization Deficiency

The formation of a tetrameric assembly is essential for the ability of the tumor suppressor protein p53 to act as a transcription factor. Such a quaternary conformation is driven by a specific tetramerization domain, separated from the central DNA binding domain by a flexible linker. Despite the distance, functional crosstalk between the two domains has been reported. This phenomenon can explain the pathogenicity of some inherited or somatically acquired mutations in the tetramerization domain, including the widespread R337H missense mutation occurring in the population of south Brazil. In this work, we have combined computational predictions through extended all-atom molecular dynamics simulations with functional assays in a genetically defined yeast-based model system to reveal structural features of p53 tetramerization domains and their transactivation capacity and specificity. Besides the germline and cancer-associated R337H and R337C, other rationally designed missense mutations targeting a significant salt bridge interaction that stabilizes the p53 tetramerization domain were studied (R337D, D352R, and the double mutation R337D plus D352R). Simulations revealed a destabilizing effect of pathogenic mutations within the p53 tetramerization domain and highlighted the importance of electrostatic interactions between residues 337 and 352. The transactivation assay performed in yeast by tuning the expression of wild-type and mutant p53 proteins revealed that p53 tetramerization mutations could decrease transactivation potential and alter transactivation specificity, in particular, by better tolerating the negative features in weak DNA binding sites. These results establish the effect of naturally occurring variations at positions 337 and 352 on p53 conformational stability and function.

cancer biology↗

bioRxiv2021

How Communication Pathways Bridge Local and Global Conformations in an IgG4 Antibody: a Molecular Dynamics Study

The affinity of an antibody for its antigen is primarily determined by the specific sequence and structural arrangement of the complementarity-determining regions (CDRs). Recently, however, evidence has accumulated that points toward a nontrivial relation between the CDR and distal sites on the antibody structure: variations in the binding strengths have been observed upon mutating amino acids separated from the paratope by several nanometers, thus suggesting the existence of a communication network within antibodies whose extension and relevance might be deeper than insofar expected. In this work, we test this hypothesis by means of molecular dynamics (MD) simulations of the IgG4 monoclonal antibody pembrolizumab, an approved drug that targets the programmed cell death protein 1 (PD-1). The molecule is simulated in both the apo and holo states, totalling 4s of MD trajectory. The analysis of these simulations shows that the bound antibody explores a restricted range of conformations with respect to the apo one, and that the global conformation of the molecule correlates with that of the CDR; a pivotal role in this relationship is played by the relatively short hinge, which mechanically couples Fab and Fc domains. These results support the hypothesis that pembrolizumab behaves as a complex machinery, with a multi-scale hierarchy of global and local conformational changes that communicate with one another. The analysis pipeline developed in this work is general, and it can help shed further light on the mechanistic aspects of antibody function. SynopsisAntigen binding restricts the conformational variability of the therapeutic antibody pembrolizumab in an interplay between the paratope and hinge region, mediated by a full-scale interaction network. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/449604v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@d64d7corg.highwire.dtl.DTLVardef@17919c2org.highwire.dtl.DTLVardef@18a21bforg.highwire.dtl.DTLVardef@1adb5a7_HPS_FORMAT_FIGEXP M_FIG C_FIG

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↗