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Matteo Dal Peraro

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Related publications (139)

Page 4 of 7

Arranged Sevenfold: Structural Insights into the C-Terminal Oligomerization Domain of Human C4b-Binding Protein

Matteo Dal Peraro, Matteo Thomas Degiacomi

The complement system as a major part of innate immunity is the first line of defense against invading microorganisms. Orchestrated by more than 60 proteins, its major task is to discriminate between host cells and pathogens and to initiate immune response ...

Academic Press Ltd- Elsevier Science Ltd2013

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

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

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 University Press2021

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

Parth Bibekar, 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

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

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

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

NAR Breakthrough Article Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination

Matteo Dal Peraro, Alexandra Styliani Kalantzi

In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex by a yet-unclear mechanism. Here, the crystal structure of Hop2-Mnd1 reveals that it form ...

Oxford University Press2015

Bacterial nanopores open the future of data storage

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

Palmitoylated calnexin is a key component of the ribosome-translocon complex

Françoise Gisou van der Goot Grunberg, Matteo Dal Peraro, Laurence Gouzi Abrami, Thomas Lemmin, Béatrice Kunz, Sanja Blaskovic

A third of the human genome encodes N-glycosylated proteins. These are co-translationally translocated into the lumen/membrane of the endoplasmic reticulum (ER) where they fold and assemble before they are transported to their final destination. Here, we s ...

2012

Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer

Matteo Dal Peraro, Alessandro Barducci, Thomas Lemmin, Martina Audagnotto

The proteolytic cleavage of the transmembrane (TM) domain of the amyloid precursor protein (APP) releases amyloid-beta (A beta) peptides, which accumulation in the brain tissue is an early indicator of Alzheimer's disease. We used multiscale molecular dyna ...

Amer Chemical Soc2016

Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes

Matteo Dal Peraro, Diane Virginie Marie Lançon, Thomas Lemmin, Christophe Bovigny

Present in bacterial and mitochondrial membranes, cardiolipins have a unique dimeric structure, which carries up to two charges (i.e., one per phosphate group) and, under physiological conditions, can be unprotonated or singly protonated. Exhaustive models ...

Amer Chemical Soc2013

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

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

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

A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP

Matteo Dal Peraro, Luciano Andres Abriata

CueP confers bacterial copper resistance in the periplasm, particularly under anaerobic conditions, through an unknown mechanism. The only available structure and limited solution data suggest that CueP forms noncovalent timers in solution, whereas sequenc ...

Elsevier Science Inc2014

Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP)

Matteo Dal Peraro, Marco Stenta, Lisa Christina Metzger

The needle length of the Yersinia spp. injectisome is determined by Yop secretion protein P (YscP), an early substrate of the injectisome itself. There is a linear correlation between the length of YscP and the length of the needle, suggesting that YscP ac ...

National Academy of Sciences2010

ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells

Aleksandra Radenovic, Matteo Dal Peraro, Melanie Blokesch, Roman Bulushev, Lorenz Jan Steinbock, Patrick Martin Seitz, Hasan Pezeshgi Modarres

The DNA uptake of naturally competent bacteria has been attributed to the action of DNA uptake machineries resembling type IV pilus complexes. However, the protein(s) for pulling the DNA across the outer membrane of Gram-negative bacteria remain speculativ ...

Public Library Science2014

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

Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations

Matteo Dal Peraro, Giulia Palermo

FRONTIERS MEDIA SA2020

Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function

Matteo Dal Peraro, Maria Josefina Marcaida Lopez

Deficiency of the serine hydrolase prolyl endopeptidase-like (PREPL) causes a recessive metabolic disorder characterized by neonatal hypotonia, feeding difficulties, and growth hormone deficiency. The pathophysiology of PREPL deficiency and the physiologic ...

CELL PRESS2021

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

Matteo Dal Peraro, Luciano Andres Abriata, Christophe Bovigny

Background: Protein variability can now be studied by measuring high-resolution tolerance-to-substitution maps and fitness landscapes in saturated mutational libraries. But these rich and expensive datasets are typically interpreted coarsely, restricting d ...

2016

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

Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores

Aleksandra Radenovic, Matteo Dal Peraro, Chan Cao

Nanopore sensing is a powerful single-molecule approach for the detection of biomolecules. Recent studies have demonstrated that aerolysin is a promising candidate to improve the accuracy of DNA sequencing and to develop novel single-molecule proteomic str ...

Nature Research2019

One Constraint at a Time: Using Viability Principles in Integrative Modeling of Macromolecular Assemblies

Dario Floreano, Matteo Dal Peraro, Matteo Thomas Degiacomi, Andrea Maesani, Giorgio Elikem Tamo

Cell Press2017