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Matteo Dal Peraro

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Publications associées (149)

The importance of dynamics in integrative modeling of supramolecular assemblies

Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo

Revealing the atomistic architecture of supramolecular complexes is a fundamental step toward a deeper understanding of cellular functioning. To date, this formidable task is facilitated by an emerging array of integrative modeling approaches that combine ...

Current Biology Ltd2015

A coiled coil switch mediates cold sensing by the thermosensory protein DesK

Thomas Lemmin, Matteo Dal Peraro, Luciano Andres Abriata

The thermosensor histidine kinase DesK from Bacillus subtilis senses changes in membrane fluidity initiating an adaptive response. Structural changes in DesK have been implicated in transmembrane signaling, but direct evidence is still lacking. On the basi ...

Wiley-Blackwell2015

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

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

Matteo Dal Peraro, Luciano Andres Abriata

Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dime ...

Nature Publishing Group2015

NAR Breakthrough Article Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination

Matteo Dal Peraro, Alexandra Styliani Kalantzi

In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex by a yet-unclear mechanism. Here, the crystal structure of Hop2-Mnd1 reveals that it form ...

Oxford University Press2015

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

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

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

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

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

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

Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics

Francesco Piazza, Matteo Dal Peraro, Enrico Spiga, Luciano Andres Abriata

We present herein a thorough description of the effects of high glucose concentrations on the diffusion, hydration and internal dynamics of ubiquitin, as predicted from extensive molecular dynamics simulations on several systems described at fully atomisti ...

Amer Chemical Soc2014

ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells

Aleksandra Radenovic, Matteo Dal Peraro, Melanie Blokesch, Patrick Martin Seitz, Hasan Pezeshgi Modarres, Lorenz Jan Steinbock, Roman Bulushev

The DNA uptake of naturally competent bacteria has been attributed to the action of DNA uptake machineries resembling type IV pilus complexes. However, the protein(s) for pulling the DNA across the outer membrane of Gram-negative bacteria remain speculativ ...

Public Library Science2014

New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly

Matteo Thomas Degiacomi, Matteo Dal Peraro, 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

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

A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP

Matteo Dal Peraro, Luciano Andres Abriata

CueP confers bacterial copper resistance in the periplasm, particularly under anaerobic conditions, through an unknown mechanism. The only available structure and limited solution data suggest that CueP forms noncovalent timers in solution, whereas sequenc ...

Elsevier Science Inc2014

HCV E2 core structures and mAbs: something is still missing

Matteo Dal Peraro, Matteo Castelli

The lack of structural information on hepatitis C virus (HCV) surface proteins has so far hampered the development of effective vaccines. Recently, two crystallographic structures have described the core portion (E2c) of E2 surface glycoprotein, the primar ...

Elsevier Sci Ltd2014

Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase

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

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

Thomas Lemmin, Matteo Dal Peraro, Anna Vestergaard

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

The Amyloid Precursor Protein Maintains an Ideal&Alpha-Helical Conformation in the Lipid Bilayer

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

Cell Press2014

A Computational Study of Ligand Binding in Chemosensory Ionotropic Glutamate Receptors

Matteo Dal Peraro, Benoîte Bargeton

Cell Press2014

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

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

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

In situ structural analysis of the Yersinia enterocolitica injectisome

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

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

Peptide-Based Vaccinology: Experimental and Computational Approaches to Target Hypervariable Viruses through the Fine Characterization of Protective Epitopes Recognized by Monoclonal Antibodies and the Identification of T-Cell-Activating Peptides

Matteo Dal Peraro, Matteo Castelli

Defining immunogenic domains of viral proteins capable of eliciting a protective immune response is crucial in the development of novel epitope-based prophylactic strategies. This is particularly important for the selective targeting of conserved regions s ...

Hindawi Publishing Corporation2013

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