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Matteo Dal Peraro

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Publications associées (149)

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

Daniel Constam, Matteo Dal Peraro, 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

Structural mechanism of mitochondrial membrane remodelling by human OPA1

Matteo Dal Peraro, Luciano Andres Abriata

Distinct morphologies of the mitochondrial network support divergent metabolic and regulatory processes that determine cell function and fate1-3. The mechanochemical GTPase optic atrophy 1 (OPA1) influences the architecture of cristae and catalyses the fus ...

Nature Portfolio2023

Deep Learning-Assisted Single-Molecule Detection of Protein Post-translational Modifications with a Biological Nanopore

Hilal Lashuel, Anass Chiki, Juan Francisco Bada Juarez, Matteo Dal Peraro, Lucien Fabrice Krapp, Chan Cao, Simon Finn Mayer, Pedro José Santana Ribeiro Magalhães

Protein post-translational modifications (PTMs) play a crucial role in countless biological processes, profoundly modulating protein properties on both spatial and temporal scales. Protein PTMs have also emerged as reliable biomarkers for several diseases. ...

Amer Chemical Soc2023

Visualization, Interactive Handling and Simulation of Molecules in Commodity Augmented Reality in Web Browsers Using moleculARweb's Virtual Modeling Kits

Matteo Dal Peraro, Luciano Andres Abriata, Lucien Fabrice Krapp, Fabio Jose Cortes Rodriguez

moleculARweb (https://molecularweb.epfl.ch) began as a website for education and outreach in chemistry and structural biology through augmented reality (AR) content that runs in the web browsers of regular devices like smartphones, tablets, and computers. ...

SWISS CHEMICAL SOC2022

Systems and methods for digital information decoding and data storage in hybrid macromolecules

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

Systems and methods for data storage and readout using hybrid nucleic acid- polymeric molecules are herein disclosed. A molecular data storage medium is presented comprising a header and a footer, each comprising or consisting of at least one unit of a fir ...

2022

Bacterial nanopores open the future of data storage

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

In the era of "big data" finding solutions for data storage alternative to those based on silicon or magnetic tapes is an urgent need for our society. The development of polymers that can store information at the molecular level has opened up new opportuni ...

IEEE2022

The role of PTM crosstalks in Httex1 structure, aggregation and membrane interaction

Hilal Lashuel, Anass Chiki, Matteo Dal Peraro, Luciano Andres Abriata, Lucien Fabrice Krapp, Driss Boudeffa, Rajasekhar Kolla, Charlotte Julie Caroline Gehin, Zhidian Zhang

CELL PRESS2022

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 ...

2022

Ultrasensitive Label-Free Detection of Protein–Membrane Interaction Exemplified by Toxin-Liposome Insertion

Mircea Ioan Iacovache, Matteo Dal Peraro, Sylvie Roke, Halil Ibrahim Okur, Chan Cao, Tereza Schönfeldová

Measuring the high-affinity binding of proteins to liposome membranes remains a challenge. Here, we show an ultrasensitive and direct detection of protein binding to liposome membranes using high throughput second harmonic scattering (SHS). Perfringolysin ...

2022

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

Mutant aerolysin and uses thereof

Matteo Dal Peraro, Chan Cao

Aerolysin polypeptides and/or mutant aerolysin monomers include modified amino acid sequences that could have improved substrate analyte, such as (poly)nucleotide and peptide, improved reading properties such as enhanced substrate analyte capture and impro ...

2022

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

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

Democratizing interactive, immersive experiences for science education with WebXR

Matteo Dal Peraro, Luciano Andres Abriata, Fabio Jose Cortes Rodriguez

SPRINGERNATURE2021

Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains

Françoise Gisou van der Goot Grunberg, Laurence Gouzi Abrami, Patrick Alain Sandoz, Florence Pojer, Matteo Dal Peraro, Sylvia Ho, Martina Audagnotto, Giulia Fonti, Maria Josefina Marcaida Lopez, Muhammad Umair Anwar, Francisco De Magalhães Sarmento R De Mesquita

Acyl protein thioesterase APT2 interacts with membranes via its charged beta-tongue, becomes palmitoylated by ZDHHC3/7 and deforms the bilayer to extract substrate acyl chains. APT2 deacylation leads to its membrane release and degradation. ...

NATURE RESEARCH2021

Investigating Crosstalk Among PTMs Provides Novel Insight Into the Structural Basis Underlying the Differential Effects of Nt17 PTMs on Mutant Httex1 Aggregation

Hilal Lashuel, Anass Chiki, Matteo Dal Peraro, Luciano Andres Abriata, Lucien Fabrice Krapp, Driss Boudeffa, Rajasekhar Kolla, Zhidian Zhang, Iman Rostami

Post-translational modifications (PTMs) within the first 17 amino acids (Nt17) of the Huntingtin protein (Htt) have been shown to inhibit the aggregation and attenuate the toxicity of mutant Htt proteins in vitro and in various models of Huntington’s disea ...

2021

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

Matteo Dal Peraro, Alessio Prunotto, Guillermo Bahr

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

CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles

Matteo Dal Peraro, Sylvain Träger, Martina Audagnotto, Giorgio Elikem Tamo, Deniz Aydin, Giulia Fonti

Motivation: Proteins are intrinsically dynamic entities. Flexibility sampling methods, such as molecular dynamics or those arising from integrative modeling strategies, are now commonplace and enable the study of molecular conformational landscapes in many ...

OXFORD UNIV PRESS2021

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

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

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

BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy

Matteo Dal Peraro, Mykola Dergai, Ying Hu

BET1 is required, together with its SNARE complex partners GOSR2, SEC22b, and Syntaxin-5 for fusion of endoplasmic reticulum-derived vesicles with the ER-Golgi intermediate compartment (ERGIC) and the cis-Golgi. Here, we report three individuals, from two ...

WILEY2021

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