Publications by Matteo Dal Peraro

ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism

Matteo Dal Peraro, Luciano Andres Abriata

Fatty acid β-oxidation is a central catabolic pathway with broad health implications. However, various fatty acids, including 4-hydroxy acids (4-HAs), are largely incompatible with β-oxidation machinery before being modified. Here we reveal that two atypic ...

Springer Science and Business Media LLC2025

Exploring New Nanopore Sensors from the Aerolysin Family

Juan Francisco Bada Juarez, Matteo Dal Peraro, Maria Josefina Marcaida Lopez

Aerolysin‐like proteins are a family of pore‐forming toxins with potential biotechnological applications as nanopore sensors for biomolecular detection and sequencing. Despite their conserved structural fold, the low sequence identity complicates sequence ...

Wiley2025

Uses of aerolysin nanopores

Hilal Lashuel, Matteo Dal Peraro, Chan Cao

The invention relates to use of an aerolysin nanopore for the discrimination of different protein isoforms bearing different post-translational modifications (PTMs) and to methods for detecting adverse medical conditions associated with the presence of pep ...

2025

Aerolysin Nanopore Structures Revealed at High Resolution in a Lipid Environment

Juan Francisco Bada Juarez, Matteo Dal Peraro, Luciano Andres Abriata, Maria Josefina Marcaida Lopez, Jana Susanne Anton

Aerolysin is a beta-pore-forming toxin produced by most Aeromonas bacteria, which has attracted large attention in the field of nanopore sensing due to its narrow and charged pore lumen. Structurally similar proteins, belonging to the aerolysin-like family ...

AMER CHEMICAL SOC2025

Wide-field fluorescence lifetime imaging of single molecules with a gated single-photon camera

Claudio Bruschini, Edoardo Charbon, Aleksandra Radenovic, Matteo Dal Peraro, Nathan Cyprien Arsène Ronceray

Fluorescence lifetime imaging microscopy (FLIM) is a powerful tool to discriminate fluorescent molecules or probe their nanoscale environment. Traditionally, FLIM uses time-correlated single-photon counting (TCSPC), which is precise but intrinsically low-t ...

2025

The Need to Implement Fair Principles in Biomolecular Simulations

Ursula Röthlisberger, Matteo Dal Peraro, Andrea Cavalli

NATURE PORTFOLIO2025

The HP1 box of KAP1 organizes HP1α for silencing of endogenous retroviral elements in embryonic stem cells

Rudolf Hovius, Matteo Dal Peraro, Beat Fierz, Maria Josefina Marcaida Lopez

Repression of endogenous retroviral elements (ERVs) is facilitated by KAP1 (KRAB-associated protein 1)-containing complexes, however the underlying mechanism remains unclear. Here, we show that binding of KAP1 to the major component of the heterochromatin ...

Springer Science and Business Media LLC2025

MolecularWebXR: Multiuser discussions in chemistry and biology through immersive and inclusive augmented and virtual reality

Matteo Dal Peraro, Luciano Andres Abriata, Fabio Jose Cortes Rodriguez, Fernando Augusto Teixeira Pinto Meireles

MolecularWebXR is a new web-based platform for education, science communication and scientific peer discussion in chemistry and biology, based on modern web-based Virtual Reality (VR) and Augmented Reality (AR). With no installs as it is all web-served, Mo ...

2025

Analysis of Integrator-Differentiator Transimpedance Amplifiers: Speed and Gain Tradeoff Introduced by Parasitic Capacitances

Alexandre Schmid, Matteo Dal Peraro, Mehdi Saberi

In this paper, the frequency behavior and stability of current recording systems employing continuous-time integrator-differentiator transimpedance amplifiers (TIAs) are analyzed. The proposed comprehensive analysis provides designers helpful design rules ...

Institute of Electrical and Electronics Engineers (IEEE)2025

Virus adaptation to heparan sulfate comes with capsid stability tradeoff

Matteo Dal Peraro, Valeria Cagno, Aleksandar Antanasijevic

Because of high mutation rates, viruses constantly adapt to new environments. When propagated in cell lines, certain viruses acquire positively charged amino acids on their surface proteins, enabling them to utilize negatively charged heparan sulfate (HS) ...

eLife Sciences Publications, Ltd2024

G–PLIP: Knowledge graph neural network for structure-free protein–ligand bioactivity prediction

Matteo Dal Peraro

Protein–ligand interactions (PLIs) determine the efficacy and safety profiles of small molecule drugs. Existing methods rely on either structural information or resource-intensive computations to predict PLI, casting doubt on whether it is possible to perf ...

2024

A look beyond the QR code of SNARE proteins

Matteo Dal Peraro, Luciano Andres Abriata

Soluble N-ethylmaleimide-sensitive factor Attachment protein REceptor (SNARE) proteins catalyze the fusion process of vesicles with target membranes in eukaryotic cells. To do this, they assemble in a zipper-like fashion into stable complexes between the m ...

2024

OXA β-lactamases from Acinetobacter spp. are membrane bound and secreted into outer membrane vesicles

Matteo Dal Peraro, Fernando Augusto Teixeira Pinto Meireles

β-lactamases from Gram-negative bacteria are generally regarded as soluble, periplasmic enzymes. NDMs have been exceptionally characterized as lipoproteins anchored to the outer membrane. A bioinformatics study on all sequenced beta-lactamases was performe ...

AMER SOC MICROBIOLOGY2024

Mutant aerolysin and uses thereof

Matteo Dal Peraro, Chan Cao

Provided herein are aerolysin polypeptides and/or mutant aerolysin monomers comprising modified amino acid sequences that could have improved substrate analyte, such as (poly)nucleotide and peptide, improved reading properties such as enhanced substrate an ...

2024

PeSTo-Carbs: Geometric Deep Learning for Prediction of Protein-Carbohydrate Binding Interfaces

Matteo Dal Peraro, Lucien Fabrice Krapp

The Protein Structure Transformer (PeSTo), a geometric transformer, has exhibited exceptional performance in predicting protein-protein binding interfaces and distinguishing interfaces with nucleic acids, lipids, small molecules, and ions. In this study, w ...

Amer Chemical Soc2024

A humoral stress response protects Drosophila tissues from antimicrobial peptides

Jean Philippe Boquete, Bruno Lemaitre, Matteo Dal Peraro, Alexia Laurie Carboni, Samuel Rommelaere, Chan Cao, Fernando Augusto Teixeira Pinto Meireles

An efficient immune system must provide protection against a broad range of pathogens without causing excessive collateral tissue damage. While immune effectors have been well characterized, we know less about the resilience mechanisms protecting the host ...

Elsevier BV2024

Missense variants in CMS22 patients reveal that PREPL has both enzymatic and nonenzymatic functions

Matteo Dal Peraro, Maria Josefina Marcaida Lopez, Anastasia Theodoropoulou, Aleksandar Antanasijevic, Edoardo Cavani

Congenital myasthenic syndrome-22 (CMS22, OMIM 616224) is a rare genetic disorder caused by deleterious genetic variation in the prolyl endopeptidase-like (PREPL) gene. Previous reports have described patients with deletions and nonsense variants in PREPL, ...

American Society for Clinical Investigation2024

Differential Effects of Post-translational Modifications on the Membrane Interaction of Huntingtin Protein

Hilal Lashuel, Matteo Dal Peraro, Luciano Andres Abriata, Charlotte Julie Caroline Gehin, Zhidian Zhang

Huntington's disease is a neurodegenerative disorder caused by an expanded polyglutamine stretch near the N-terminus of the huntingtin (HTT) protein, rendering the protein more prone to aggregate. The first 17 residues in HTT (Nt17) interact with lipid mem ...

Amer Chemical Soc2024

Structural characterization of Prolyl endopeptidase-like, a mitochondrial protein involved in congenital myasthenic syndrome-22

Matteo Dal Peraro, Maria Josefina Marcaida Lopez, Anastasia Theodoropoulou, Edoardo Cavani

SPRINGER2023

Using integrative structural biology for the identification of novel aerolysin-like pore forming toxins for nanopore sensing

Juan Francisco Bada Juarez, Matteo Dal Peraro, Maria Josefina Marcaida Lopez, Fernando Augusto Teixeira Pinto Meireles, Jana Susanne Anton

SPRINGER2023