Home

Person

Matteo Dal Peraro

About
Privacy
Disclaimer

Graph Chatbot

Related publications (149)

Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling

Matteo Thomas Degiacomi, Matteo Dal Peraro

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

Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase

Matteo Dal Peraro, Marco Stenta, Andrea Cavalli

Type II topoisomerase (topoII) is a metalloenzyme targeted by clinical antibiotics and anticancer agents. Here, we integrate existing structural data with molecular simulation and propose a model for the yet uncharacterized structure of the reactant state ...

Amer Chemical Soc2013

Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism

Henning Paul-Julius Stahlberg, Matteo Thomas Degiacomi, Françoise Gisou van der Goot Grunberg, Mircea Ioan Iacovache, Matteo Dal Peraro

Aerolysin is the founding member of a superfamily of (beta-pore-forming toxins whose pore structure is unknown. We have combined X-ray crystallography, cryo-EM, molecular dynamics and computational modeling to determine the structures of aerolysin mutants ...

Nature Publishing Group2013

Intrinsic Transmembrane Flexibility of the Amyloid Precursor Protein Explored by Molecular Simulations

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

Cell Press2013

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

Matteo Thomas Degiacomi, Matteo Dal Peraro

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

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

Thomas Lemmin, Françoise Gisou van der Goot Grunberg, Suzanne Salvi, Matteo Dal Peraro, 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

Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations

Thomas Lemmin, Matteo Dal Peraro

The PhoQP two-component system is a signaling complex essential for bacterial virulence and cationic antimicrobial peptide resistance. PhoQ is the histidine kinase chemoreceptor of this tandem machine and assembles in a homodimer conformation spanning the ...

Public Library Science2013

Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes

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

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

Matteo Thomas Degiacomi, Michele Cascella, Matteo Dal Peraro, 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

The Molecular Assembly of the Aerolysin Pore Reveals a Unique Swirling Membrane-Insertion Mechanism

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

Cell Press2013

Dynamics of catalytic metals during DNA cleavage in type II topoisomerase

Matteo Dal Peraro, Marco Stenta, Giulia Palermo, Andrea Cavalli

Amer Chemical Soc2013

All-atom simulations of crowding effects on ubiquitin dynamics

Matteo Dal Peraro, Enrico Spiga, Luciano Andres Abriata

It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to pro ...

Iop Publishing Ltd2013

TAL Effectors Specificity Stems from Negative Discrimination

Matteo Dal Peraro, Basile Isidore Martin Wicky, 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

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

Matteo Dal Peraro, Paolo Carloni

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

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

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

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

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

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

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

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

Michele Cascella, Matteo Dal Peraro, Francesca Collu, 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

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

Page 7 of 8