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Matteo Dal Peraro

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Publications associées (139)

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Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control

Matteo Dal Peraro, Luciano Andres Abriata

Cupredoxins perform copper-mediated long-range electron transfer (ET) in biological systems. Their copper-binding sites have evolved to force copper ions into ET-competent systems with decreased reorganization energy, increased reduction potential, and a d ...

Springer2014

On the active site of mononuclear B1 metallo beta-lactamases: a computational study

Matteo Dal Peraro

Metallo-beta-lactamases (M beta Ls) are Zn(II)-based bacterial enzymes that hydrolyze beta-lactam antibiotics, hampering their beneficial effects. In the most relevant subclass (B1), X-ray crystallography studies on the enzyme from point to either two zinc ...

2012

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

Catalytic Metal Ions and Enzymatic Processing of DNA and RNA

Matteo Dal Peraro, Giulia Palermo, Andrea Cavalli

Two-metal-ion-dependent nucleases cleave the phosphodiester bonds of nucleic acids via the two-metal-ion (2M) mechanism. Several high-resolution X-ray structures portraying the two-metal-aided catalytic site, together with mutagenesis and kinetics studies, ...

American Chemical Society2015

Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling

Matteo Dal Peraro, Michele Cascella

We review the state-of-the-art in computational molecular simulations for biological systems. We limit our discussion to three fields: all-atom simulations, coarse-grained models, and novel multiscale approaches. While molecular dynamics simulations are br ...

2009

Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-eta

Matteo Dal Peraro

Trans-lesion synthesis polymerases, like DNA Polymerase-eta (Pol-eta), are essential for cell survival. Pol-eta bypasses ultraviolet-induced DNA damages via a two-metal-ion mechanism that assures DNA strand elongation, with formation of the leaving group p ...

Oxford University Press (OUP)2016

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

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

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

Matteo Dal Peraro, Bart Deplancke, Felix Naef, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger, Sunil Kumar Raghav, Irina Krier, Guillaume Rey, Alexandra Styliani Kalantzi, Jonathan Aryeh Sobel

Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles ...

Public Library of Science2017

Lipid Builder: A Framework To Build Realistic Models for Biological Membranes

Matteo Dal Peraro, Thomas Lemmin, Giorgio Elikem Tamo, Christophe Bovigny, Nicolas Grégoire Maïno

The physical and chemical characterization of biological membranes is of fundamental importance for understanding the functional role of lipid bilayers in shaping cells and organelles, steering vesicle trafficking and promoting membrane-protein signaling. ...

Amer Chemical Soc2015

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

Matteo Dal Peraro

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

Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation

Matteo Dal Peraro

The protein farnesyltransferase (FTase) is a Zn2+-metalloenzyme that catalyzes the farnesylation reaction, i.e., the transfer of the 15-carbon atom farnesyl group from farnesyl diphosphate (FPP) to a specific cysteine of protein substrates. Oncogenic Ras p ...

2009

The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain

Matteo Dal Peraro, Maria Josefina Marcaida Lopez, Giorgio Elikem Tamo

The polyQ expansion in huntingtin protein (HTT) is the prime cause of Huntington's disease (HD). The recent cryoelectron microscopy (cryo-EM) structure of HTT-HAP40 complex provided the structural information on its HEAT-repeat domains. Here, we present an ...

CELL PRESS2020

A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements

Matteo Dal Peraro, Michele Cascella, Davide Alemani

We introduce a nonradial potential term for coarse-grained (CG) molecular simulations of proteins. This term mimics the backbone dipole−dipole interactions and accounts for the needed directionality to form stable folded secondary structure elements. We sh ...

2010

Aerolysin Nanopore Structures Revealed at High Resolution in a Lipid Environment

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

Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins

Matteo Dal Peraro, Michele Cascella, Matteo Thomas Degiacomi, Enrico Spiga, Davide Alemani

We present a new generation of coarse-grained (CG) potentials that account for a simplified electrostatic description of soluble proteins. The treatment of permanent electrostatic dipoles of the backbone and polar side-chains allows to simulate proteins, p ...

Amer Chemical Soc2013

Functional Dissection of Intersubunit Interactions in the EspR Virulence Regulator of Mycobacterium tuberculosis

Stewart Cole, Giovanni Dietler, Matteo Dal Peraro, Florence Pojer, Marco Stenta, Aleksandre Japaridze, Benjamin Blasco

The nucleoid-associated protein EspR, a chromosome organizer, has pleiotropic effects on expression of genes associated with cell wall function and pathogenesis in Mycobacterium tuberculosis. In particular, EspR binds to several sites upstream of the espAC ...

American Society for Microbiology2014

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

Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling

Matteo Dal Peraro, Matteo Thomas Degiacomi

Proteins often assemble in multimeric complexes to perform a specific biologic function. However, trapping these high-order conformations is difficult experimentally. Therefore, predicting how proteins assemble using in silico techniques can be of great he ...

Cell Press2013

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

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

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

New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly

Matteo Dal Peraro, Matteo Thomas Degiacomi, Enrico Spiga

Data reporting on structure and dynamics of cellular constituents are growing with increasing pace enabling, as never before, the understanding of fine mechanistic aspects of biological systems and providing the possibility to affect them in controlled way ...

Elsevier Academic Press Inc2014