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Matteo Dal Peraro

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Related publications (139)

Page 5 of 7

An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis

Matteo Dal Peraro, Deniz Aydin

The biosynthesis of coenzyme Q presents a paradigm for how cells surmount hydrophobic barriers in lipid biology. In eukaryotes, CoQ precursors-among nature's most hydrophobic molecules-must somehow be presented to a series of enzymes peripherally associate ...

CELL PRESS2019

A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo

We present our assessment of tertiary structure predictions for hard targets in Critical Assessment of Structure Prediction round 13 (CASP13). The analysis includes (a) assignment and discussion of best models through scores-aided visual inspection of mode ...

WILEY2019

Evolution of Acid-Sensing Olfactory Circuits in Drosophilids

Matteo Dal Peraro

Animals adapt their behaviors to specific ecological niches, but the genetic and cellular basis of nervous system evolution is poorly understood. We have compared the olfactory circuits of the specialist Drosophila sechellia-which feeds exclusively on Mori ...

Elsevier2017

Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies

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

Predicting the structure of large molecular assemblies remains a challenging task in structural biology when using integrative modeling approaches. One of the main issues stems from the treatment of heterogeneous experimental data used to predict the archi ...

Nature Research2017

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

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

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

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

Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism

Matteo Dal Peraro

Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkages that form the backbone of the RNA strand in RNA x DNA hybrids. This enzyme is implicated in replication initiation and DNA topology ...

2008

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

Eva Maria Schier, Danaé Axelle Terrien-Ferey, 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

Alzheimer's disease mutations in APP but not γ-secretase modulators affect epsilon-cleavage-dependent AICD production

Matteo Dal Peraro, Freddy Radtke, Patrick Fraering, Mitko Dimitrov, Thomas Lemmin, Rajwinder Lehal, Jemila Houacine

Pathological amino-acid substitutions in the amyloid precursor protein (APP) and chemical gamma-secretase modulators affect the processing of APP by the gamma-secretase complex and the production of the amyloid-beta peptide A beta 42, the accumulation of w ...

Nature Publishing Group2013

A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria

Matteo Dal Peraro, John McKinney, Florence Pojer, Giulia Fonti, Paul Murima, Tarun Chopra

Fatty acid metabolism is an important feature of the pathogenicity of Mycobacterium tuberculosis during infection. Consumption of fatty acids requires regulation of carbon flux bifurcation between the oxidative TCA cycle and the glyoxylate shunt. In Escher ...

Nature Publishing Group2016

Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms

Matteo Dal Peraro, Oliver Hantschel, Florence Pojer, Sandrine Madeleine Suzanne Georgeon, Maria Josefina Marcaida Lopez, Allan Joaquim Lamontanara, Grégory La Sala, Tim Kükenshöner, Daniel Pereira Duarte

Bruton's tyrosine kinase (Btk) is critical for B-cell maturation and activation. Btk loss-of-function mutations cause human X-linked agammaglobulinemia (XLA). In contrast, Btk signaling sustains growth of several B-cell neoplasms which may be treated with ...

Nature Publishing Group2020

KAP1 is an antiparallel dimer with a functional asymmetry

Didier Trono, Matteo Dal Peraro, Beat Fierz, Davide Demurtas, Louise Catherine Bryan, Maria Josefina Marcaida Lopez, Giulia Fonti, Pierre-Yves Joseph Laurent Helleboid, Alexandra Styliani Kalantzi

KAP1 (KRAB domain-associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular i ...

Life Science Alliance, LLC2019

Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus

Matteo Dal Peraro

The M2 protein of influenza A virus performs the crucial function of transporting protons to the interior of virions enclosed in the endosome. Adamantane drugs, amantadine (AMN) and rimantidine (RMN), block the proton conduction in some strains, and have b ...

2011

In situ structural analysis of the Yersinia enterocolitica injectisome

Matteo Dal Peraro, Henning Paul-Julius Stahlberg, Marco Stenta, Matteo Thomas Degiacomi

Injectisomes are multi-protein transmembrane machines allowing pathogenic bacteria to inject effector proteins into eukaryotic host cells, a process called type III secretion. Here we present the first three-dimensional structure of Yersinia enterocolitica ...

Elife Sciences Publications Ltd2013

Overcoming the hydrophobic barrier of the membrane: The role of COQ9 in promoting coenzyme Q biosynthesis

Matteo Dal Peraro, Deniz Aydin

AMER CHEMICAL SOC2019

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

Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins

Matteo Dal Peraro, Michele Cascella

We present a new method to incorporate electrostatic interactions in coarse-grained representations of proteins. The model is based on a topologically reconstructed multipolar expansion of the all-atom centers of charge, specifically of the backbone dipole ...

2008

TAL Effectors Specificity Stems from Negative Discrimination

Matteo Dal Peraro, Marco Stenta

Transcription Activator-Like (TAL) effectors are DNA-binding proteins secreted by phytopathogenic bacteria that interfere with native cellular functions by binding to plant DNA promoters. The key element of their architecture is a domain of tandem-repeats ...

Public Library of Science2013

GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis

Stewart Cole, Matteo Dal Peraro, Luciano Andres Abriata, Claudia Sala, Gaëlle Séraphine Kolly, Mahé Cécile Raccaud, Raju Mukherjee

Mycobacterium tuberculosis possesses a thick and highly hydrophobic cell wall principally composed of a mycolyl-arabinogalactan-peptidoglycan complex, which is critical for survival and virulence. DprE1 is a well-characterized component of decaprenyl-phosp ...

American Society for Microbiology2015

Molecular Simulations Give Insights into the NDM-1/Membrane Interaction that Causes Rise of a Super-Bacterium

Matteo Dal Peraro, Alessio Prunotto

CELL PRESS2019