Publications de Matteo Thomas Degiacomi

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

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

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

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

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

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

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

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

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

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

Molecular Modeling of Bacterial Nanomachineries

Matteo Thomas Degiacomi

Proteins have the ability to assemble in multimeric states to perform their specific biological function. Unfortunately, characterizing experimentally these structures at atomistic resolution is usually difficult. For this reason, in silico methodologies a ...

EPFL2012

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

The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome

Matteo Thomas Degiacomi, Matteo Dal Peraro

The length of the Yersinia injectisome needle is determined by the protein YscP, which could act as a molecular ruler. The analysis of the correlation between the size of YscP and the needle length in seven wild-type strains of Yersinia enterocolitica rein ...

2009