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Matteo Dal Peraro

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Publications associées (149)

Editorial overview: The future after the cryo-EM resolution revolution

Matteo Dal Peraro

CURRENT BIOLOGY LTD2019

An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in beta-lactam resistance

Matteo Dal Peraro, Luciano Andres Abriata

The treatment of hospital- and community-associated infections by methicillin-resistant Staphylococcus aureus (MRSA) is a perpetual challenge. This Gram-positive bacterium is resistant specifically to beta-lactam antibiotics, and generally to many other an ...

Springer Nature2019

Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes

Matteo Dal Peraro, Luciano Andres Abriata, Alexander Mayorov

A recent analysis of evolutionary rates in >500 globular soluble enzymes revealed pervasive conservation gradients toward catalytic residues. By looking at amino acid preference profiles rather than evolutionary rates in the same data set, we quantified th ...

OXFORD UNIV PRESS2019

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

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

Modelling structures in cryo-EM maps

Matteo Dal Peraro, Sylvain Träger

Recent advances in structure determination of sub-cellular structures using cryo-electron microscopy and tomography have enabled us to understand their architecture in a more detailed manner and gain insight into their function. The choice of approach to u ...

CURRENT BIOLOGY LTD2019

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

Matteo Dal Peraro, Deniz Aydin

AMER CHEMICAL SOC2019

A Combined Computational and Experimental Study to Investigate the Role of COQ9 in Promoting COQ Biosynthesis

Matteo Dal Peraro, Deniz Aydin

2018

Assessment of data-assisted prediction by inclusion of crosslinking/mass-spectrometry and small angle X-ray scattering data in the 12(th) Critical Assessment of protein Structure Prediction experiment

Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo, Giulia Fonti

2018

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods

Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo

2018

Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family

Matteo Dal Peraro, Deniz Aydin

2018

Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics

Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo

2018

Mapping the sensing spots of aerolysin for single oligonucleotides analysis

Matteo Dal Peraro, Nuria Cirauqui Diaz, Chan Cao

Nature Publishing Group2018

Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway

Matteo Dal Peraro, Luciano Andres Abriata

2018

Recruitment of the amyloid precursor protein by gamma-secretase at the synaptic plasma membrane

Matteo Dal Peraro, Martina Audagnotto, Alexander Kengo Lorkowski

2018

Exploiting the role of membrane anchoring on the peculiar biological behaviour of multi-drug resistant enzyme New Delhi metallo-beta-lactamase 1

Matteo Dal Peraro, Alessio Prunotto, Guillermo Bahr

AMER CHEMICAL SOC2018

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

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

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

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

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

Cell Press2017

Evolution of Acid-Sensing Olfactory Circuits in Drosophilids

Matteo Dal Peraro, Benoîte Bargeton

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

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

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