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Matteo Dal Peraro

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Related publications (139)

Page 3 of 7

Transmembrane Prolines Mediate Signal Sensing and Decoding in Bacillus subtilis DesK Histidine Kinase

Matteo Dal Peraro, Luciano Andres Abriata

Environmental awareness is an essential attribute of all organisms. The homeoviscous adaptation system of Bacillus subtilis provides a powerful experimental model for the investigation of stimulus detection and signaling mechanisms at the molecular level. ...

2019

Olfactory receptor pseudo-pseudogenes

Matteo Dal Peraro

Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes(1). Although certain pseudogene-derived RNAs have regulatory roles(2), and some pseudogene fragments are tr ...

Nature Publishing Group2016

Aerolysin nanopores decode digital information stored in tailored macromolecular analytes

Aleksandra Radenovic, Matteo Dal Peraro, Chan Cao, Lucien Fabrice Krapp

Digital data storage is a growing need for our society and finding alternative solutions than those based on silicon or magnetic tapes is a challenge in the era of “big data.” The recent development of polymers that can store information at the molecular l ...

2020

Bicc1 ribonucleoprotein complexes specifying organ laterality are licensed by ANKS6-induced structural remodeling of associated ANKS3

Matteo Dal Peraro, Daniel Constam, Benjamin Marcel Daniel Rothé, Simon Fortier, Zhidian Zhang

Organ laterality of vertebrates is specified by accelerated asymmetric decay of Dand5 mRNA mediated by Bicaudal-C1 (Bicc1) on the left side, but whether binding of this or any other mRNA to Bicc1 can be regulated is unknown. Here, we found that a CRISPR-en ...

PUBLIC LIBRARY SCIENCE2023

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

Matteo Dal Peraro, Luciano Andres Abriata

Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dime ...

Nature Publishing Group2015

A humoral stress response protects Drosophila tissues from antimicrobial peptides

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

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

S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity

Didier Trono, Matteo Dal Peraro, Françoise Gisou van der Goot Grunberg, Priscilla Turelli, Luciano Andres Abriata, Laurence Gouzi Abrami, Giovanni D'Angelo, Charlène Mireille Raymonde Raclot, Béatrice Kunz, Francisco De Magalhães Sarmento Ribeiro De Mesquita, Oksana Andrei Sergeeva

SARS-CoV-2 virions are surrounded by a lipid bilayer that contains membrane proteins such as spike, responsible for target-cell binding and virus fusion. We found that during SARS-CoV-2 infection, spike becomes lipid modified, through the sequential action ...

Cell Press - Elsevier2021

Molecular Bases of the Membrane Association Mechanism Potentiating Antibiotic Resistance by New Delhi Metallo-beta-lactamase 1

Matteo Dal Peraro, Alessio Prunotto

Resistance to last-resort carbapenem antibiotics is an increasing threat to human health, as it critically limits therapeutic options. Metallo-beta-lactamases (MBLs) are the largest family of carbapenemases, enzymes that inactivate these drugs. Among MBLs, ...

AMER CHEMICAL SOC2020

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

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

Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization

Matteo Dal Peraro, Luciano Andres Abriata

Continuous assessment of transferable forcefields for molecular simulations is essential to identify their weaknesses and direct improvement efforts. The latest efforts focused on better describing disordered proteins while retaining proper description of ...

2021

Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction?

Matteo Dal Peraro, Luciano Andres Abriata

Protein dynamics is undoubtedly a pervasive ingredient in all biological functions. However, structural biology has been strongly driven by a static-centered view of protein architecture. We argue that the recent advances of cryo-electron microscopy (EM) h ...

AMER CHEMICAL SOC2020

Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations

Matteo Dal Peraro, Thomas Lemmin

The PhoQP two-component system is a signaling complex essential for bacterial virulence and cationic antimicrobial peptide resistance. PhoQ is the histidine kinase chemoreceptor of this tandem machine and assembles in a homodimer conformation spanning the ...

Public Library Science2013

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

Specific Protein-Membrane Interactions Promote Packaging of Metallo-beta-Lactamases into Outer Membrane Vesicles

Matteo Dal Peraro, Alessio Prunotto

Outer membrane vesicles (OMVs) act as carriers of bacterial products such as plasmids and resistance determinants, including metallo-beta-lactamases. The lipidated, membrane-anchored metallo-beta-lactamase NDM-1 can be detected in Gram-negative OMVs. The s ...

AMER SOC MICROBIOLOGY2021

Article Structure and functionality of a multimeric human COQ7:COQ9 complex

Matteo Dal Peraro, Luciano Andres Abriata

Coenzyme Q (CoQ) is a redox-active lipid essential for core metabolic pathways and antioxidant defense. CoQ is synthesized upon the mitochondrial inner membrane by an ill-defined "complex Q" metabolon. Here, we present structure-function analyses of a lipi ...

CELL PRESS2022

Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism

Matteo Dal Peraro, Françoise Gisou van der Goot Grunberg, Henning Paul-Julius Stahlberg, Matteo Thomas Degiacomi, Mircea Ioan Iacovache

Aerolysin is the founding member of a superfamily of (beta-pore-forming toxins whose pore structure is unknown. We have combined X-ray crystallography, cryo-EM, molecular dynamics and computational modeling to determine the structures of aerolysin mutants ...

Nature Publishing Group2013

Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics

Matteo Dal Peraro, Luciano Andres Abriata, Francesco Piazza, Enrico Spiga

We present herein a thorough description of the effects of high glucose concentrations on the diffusion, hydration and internal dynamics of ubiquitin, as predicted from extensive molecular dynamics simulations on several systems described at fully atomisti ...

Amer Chemical Soc2014

Online tools to easily build virtual molecular models for display in augmented and virtual reality on the web

Matteo Dal Peraro, Fabio Jose Cortes Rodriguez

Several groups developed in the last years augmented and virtual reality (AR/VR) software to visualize 3D molecules, most rather static, limited in content, and requiring software installs, some even requiring expensive hardware. We launched in 2020 molecu ...

ELSEVIER SCIENCE INC2022

Biological nanopores for single-molecule sensing

Matteo Dal Peraro, Chan Cao, Simon Finn Mayer

Evolution has found countless ways to transport material across cells and cellular compartments separated by membranes. Protein assemblies are the cornerstone for the formation of channels and pores that enable this regulated passage of molecules in and ou ...

Cell Press2022

Peptide-Based Vaccinology: Experimental and Computational Approaches to Target Hypervariable Viruses through the Fine Characterization of Protective Epitopes Recognized by Monoclonal Antibodies and the Identification of T-Cell-Activating Peptides

Matteo Dal Peraro

Defining immunogenic domains of viral proteins capable of eliciting a protective immune response is crucial in the development of novel epitope-based prophylactic strategies. This is particularly important for the selective targeting of conserved regions s ...

Hindawi Publishing Corporation2013