Skip to main content

Research Repository

Advanced Search

All Outputs (51)

New strategies for integrative dynamic modeling of macromolecular assembly (2014)
Journal Article
Spiga, E., Degiacomi, M., & Dal Peraro, M. (2014). New strategies for integrative dynamic modeling of macromolecular assembly. Advances in protein chemistry and structural biology, 96, 77-111. https://doi.org/10.1016/bs.apcsb.2014.06.008

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 controll... Read More about New strategies for integrative dynamic modeling of macromolecular assembly.

Reaction mechanism and catalytic fingerprint of allantoin racemase (2014)
Journal Article
Bovigny, C., Degiacomi, M., Lemmin, T., Dal Peraro, M., & Stenta, M. (2014). Reaction mechanism and catalytic fingerprint of allantoin racemase. Journal of Physical Chemistry B (Soft Condensed Matter and Biophysical Chemistry), 118(27), 7457-7466. https://doi.org/10.1021/jp411786z

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 (... Read More about Reaction mechanism and catalytic fingerprint of allantoin racemase.

Membrane proteins bind lipids selectively to modulate their structure and function. (2014)
Journal Article
Laganowsky, A., Reading, E., Allison, T., Ulmschneider, M., Degiacomi, M., Baldwin, A., & Robinson, C. (2014). Membrane proteins bind lipids selectively to modulate their structure and function. Nature, 510(7503), 172-175. https://doi.org/10.1038/nature13419

Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments1, 2, 3, 4, 5, 6, 7 and that lipids can bind to specific sites, for example, in potassium channels8. Fundamental... Read More about Membrane proteins bind lipids selectively to modulate their structure and function..

Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism (2013)
Journal Article
Degiacomi, M., Iacovache, I., Pernot, L., Chami, M., Kudryashev, M., Stahlberg, H., …Dal Peraro, M. (2013). Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism. Nature Chemical Biology, 9(10), 623-629. https://doi.org/10.1038/nchembio.1312

Aerolysin is the founding member of a superfamily of β-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 mutant... Read More about Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism.

In situ structural analysis of the Yersinia enterocolitica injectisome (2013)
Journal Article
Kudryashev, M., Stenta, M., Schmelz, S., Amstutz, M., Wiesand, U., Castaño-Díez, D., …Stahlberg, H. (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2013(2), Article e00792. https://doi.org/10.7554/elife.00792

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 enteroco... Read More about In situ structural analysis of the Yersinia enterocolitica injectisome.

Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling (2013)
Journal Article
Degiacomi, M., & Dal Peraro, M. (2013). Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling. Structure, 21(7), 1097-1106. https://doi.org/10.1016/j.str.2013.05.014

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 gr... Read More about Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling.

Electrostatic-consistent coarse-grained potentials for molecular simulations of proteins. (2013)
Journal Article
Spiga, E., Alemani, D., Degiacomi, M., Cascella, M., & Peraro, M. (2013). Electrostatic-consistent coarse-grained potentials for molecular simulations of proteins. Journal of Chemical Theory and Computation, 9(8), 3515-3526. https://doi.org/10.1021/ct400137q

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 prote... Read More about Electrostatic-consistent coarse-grained potentials for molecular simulations of proteins..

Arranged sevenfold: Structural insights into the C-terminal oligomerization domain of human C4b-binding protein. (2012)
Journal Article
Hofmeyer, T., Schmelz, S., Degiacomi, M., Dal Peraro, M., Daneschdar, M., Scrima, A., …Kolmar, H. (2013). Arranged sevenfold: Structural insights into the C-terminal oligomerization domain of human C4b-binding protein. Journal of Molecular Biology, 425(8), 1302-1317. https://doi.org/10.1016/j.jmb.2012.12.017

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 re... Read More about Arranged sevenfold: Structural insights into the C-terminal oligomerization domain of human C4b-binding protein..

Dual chaperone role of the c-terminal propeptide in folding and oligomerization of the pore-forming toxin aerolysin (2011)
Journal Article
Iacovache, I., Degiacomi, M., Pernot, L., Ho, S., Schiltz, M., Dal Peraro, M., & van der Goot, F. (2011). Dual chaperone role of the c-terminal propeptide in folding and oligomerization of the pore-forming toxin aerolysin. PLoS Pathogens, 7(7), Article e1002135. https://doi.org/10.1371/journal.ppat.1002135

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... Read More about Dual chaperone role of the c-terminal propeptide in folding and oligomerization of the pore-forming toxin aerolysin.

The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome. (2008)
Journal Article
Wagner, S., Sorg, I., Degiacomi, M., Journet, L., Peraro, M., & Cornelis, G. (2009). The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome. Molecular Microbiology, 71(3), 692-701. https://doi.org/10.1111/j.1365-2958.2008.06556.x

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 enterocolitic... Read More about The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome..