Publications by Matteo Dal Peraro

Related publications (139)

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics

Matteo Dal Peraro, Luciano Andres Abriata, Enrico Spiga

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known e ...

Cell Press2016

MoleculARweb: A Web Site for Chemistry and Structural Biology Education through Interactive Augmented Reality out of the Box in Commodity Devices

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

Augmented/virtual realities (ARs/VRs) promise to revolutionize STEM education. However, most easy-to-use tools are limited to static visualizations, which limits the approachable content, whereas more interactive and dynamic alternatives require costly har ...

AMER CHEMICAL SOC2021

State-of-the-art web services for de novo protein structure prediction

Matteo Dal Peraro

Residue coevolution estimations coupled to machine learning methods are revolutionizing the ability of protein structure prediction approaches to model proteins that lack clear homologous templates in the Protein Data Bank (PDB). This has been patent in th ...

OXFORD UNIV PRESS2021

Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2

Matteo Dal Peraro, Thomas Lemmin

P4-ATPases (flippases) translocate specific phospholipids such as phosphatidylserine from the exoplasmic leaflet of the cell membrane to the cytosolic leaflet, upholding an essential membrane asymmetry. The mechanism of flipping this giant substrate has re ...

National Academy of Sciences2014

How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme

Matteo Dal Peraro, Luciano Andres Abriata

The need for interfacing structural biology and biophysics to molecular evolution is being increasingly recognized. One part of the big problem is to understand how physics and chemistry shape the sequence space available to functional proteins, while sati ...

Public Library Science2015

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

Matteo Dal Peraro, Luciano Andres Abriata

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

Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase

Matteo Dal Peraro, Marco Stenta, Matteo Thomas Degiacomi, Thomas Lemmin, Christophe Bovigny

The stereospecific oxidative decomposition of urate into allantoin is the core of purine catabolism in many organisms. The spontaneous decomposition of upstream intermediates and the nonenzymatic racemization of allantoin lead to an accumulation of (R)-all ...

Amer Chemical Soc2014

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

Common mechanistic features among metallo-β-lactamases: a computational study of Aeromonas hydrophila CphA enzyme

Matteo Dal Peraro, Andrea Cavalli

Metallo-β-lactamases (MβLs) constitute an increasingly serious clinical threat by giving rise to β-lactam antibiotic resistance. They accommodate in their catalytic pocket one or two zinc ions, which are responsible for the hydrolysis of β-lactams. Recent ...

2009

Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis?

Matteo Dal Peraro

Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase superfamily and hydrolyzes the phosphodiester linkage on the RNA strand of a DNA/RNA hybrid duplex. Due to its activity in HIV reverse transcription, it represents a promising target for anti- ...

2010

Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces

Tamar Kohn, Matteo Dal Peraro, Alessio Prunotto, Simon Meister

Enteroviruses are common agents of infectious disease that are spread by the fecal-oral route. They are readily inactivated by mild heat, which causes the viral capsid to disintegrate or undergo conformational change. While beneficial for the thermal treat ...

American Society for Microbiology2020

Perturbations of the Straight Transmembrane alpha-Helical Structure of the Amyloid Precursor Protein Affect Its Processing by gamma-Secretase

Matteo Dal Peraro, Patrick Fraering, Mitko Dimitrov, Thomas Lemmin

Background: Amyloid- neurotoxicity depends on the specificity of the proteolytic cleavage of the amyloid precursor protein (APP) transmembrane domain. Results: The APP transmembrane -helix is straight in a biological membrane bilayer. Conclusion: The flexi ...

American Society for Biochemistry and Molecular Biology2014

Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase

Matteo Dal Peraro, Alessio Prunotto

Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, ...

2021

Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins

Matteo Dal Peraro, Luciano Andres Abriata

Parainfluenza virus 5 (PIV5) is an enveloped, single-stranded, negative-sense RNA virus of the Paramyxoviridae family. PIV5 fusion and entry are mediated by the coordinated action of the receptor-binding protein, hemagglutinin-neuraminidase (HN), and the f ...

National Academy of Sciences2016

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

Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin

Matteo Dal Peraro, Françoise Gisou van der Goot Grunberg, Matteo Thomas Degiacomi, Mircea Ioan Iacovache, Sylvia Ho

Throughout evolution, one of the most ancient forms of aggression between cells or organisms has been the production of proteins or peptides affecting the permeability of the target cell membrane. This class of virulence factors includes the largest family ...

2011

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior

Matteo Dal Peraro, Bart Deplancke, Vincent Roland Julien Gardeux, Julie Marie Russeil, Alessio Prunotto, Maria Litovchenko, Michael Vincent Frochaux, Antonio Carlos Alves Meireles Filho, Brian Dennis Hollis, Roel Paulus Josephus Bevers, Virginie Sandra Braman

Natural genetic variation affects circadian rhythms across the evolutionary tree, but the underlying molecular mechanisms are poorly understood. We investigated population-level, molecular circadian clock variation by generating >700 tissue-specific transc ...

2021

In-depth analysis of hyaline fibromatosis syndrome frameshift mutations at the same site reveal the necessity of personalized therapy

Matteo Dal Peraro, Françoise Gisou van der Goot Grunberg, Thomas Lemmin, Shixu Yan

Hyaline fibromatosis syndrome is an autosomal recessive disease caused by mutations in ANTXR2, a gene involved in extracellular matrix homeostasis. Sixty percent of patients carry frameshift mutations at a mutational hotspot in exon 13. We show in patient ...

Wiley-Blackwell2013

Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus

Matteo Dal Peraro

The M2 protein of the influenza A virus is activated by low endosomal pH and performs the essential function of proton transfer into the viral interior. The resulting decrease in pH within the virion is essential for the uncoating and further replication o ...

2009

A look beyond the QR code of SNARE proteins

Matteo Dal Peraro, Luciano Andres Abriata

Soluble N-ethylmaleimide-sensitive factor Attachment protein REceptor (SNARE) proteins catalyze the fusion process of vesicles with target membranes in eukaryotic cells. To do this, they assemble in a zipper-like fashion into stable complexes between the m ...

2024