Publications de Matteo Thomas Degiacomi

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

Dario Floreano, Matteo Dal Peraro, Matteo Thomas Degiacomi, Andrea Maesani, Giorgio Elikem Tamo, 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 Publishing Group2017

New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly

Matteo Dal Peraro, Matteo Thomas Degiacomi, 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

Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase

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

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

Matteo Dal Peraro, Matteo Thomas Degiacomi

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

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

Matteo Dal Peraro, Michele Cascella, Matteo Thomas Degiacomi, Davide Alemani, Enrico Spiga

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

Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling

Matteo Dal Peraro, Matteo Thomas Degiacomi

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

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

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

In situ structural analysis of the Yersinia enterocolitica injectisome

Henning Paul-Julius Stahlberg, Matteo Dal Peraro, 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

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

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

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

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Matteo Thomas Degiacomi

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

New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly

Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase

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

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

Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling

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

In situ structural analysis of the Yersinia enterocolitica injectisome

Molecular Modeling of Bacterial Nanomachineries

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

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

Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling

New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly

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

Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase

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

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

In situ structural analysis of the Yersinia enterocolitica injectisome

Molecular Modeling of Bacterial Nanomachineries

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