Publications de Stefano Zamuner

ABC transporters are billion-year-old Maxwell Demons

Paolo De Los Rios, Solange Marie Flatt, Stefano Zamuner, Daniel Maria Busiello

ATP-Binding Cassette (ABC) transporters are a broad family of biological machines, found in most prokaryotic and eukaryotic cells, performing the crucial import or export of substrates through both plasma and organellar membranes, and maintaining a steady ...

NATURE PORTFOLIO2023

Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins

Paolo De Los Rios, Duccio Malinverni, Alessandro Barducci, Stefano Zamuner, Mathieu Rebeaud

The 70-kD heat shock protein (Hsp70) chaperone system is a central hub of the proteostasis network that helps maintain protein homeostasis in all organisms. The recruitment of Hsp70 to perform different and specific cellular functions is regulated by the J ...

National Academy of Sciences2023

Individual and combined benefits of different nonequilibrium proofreading mechanisms

Paolo De Los Rios, Adélaïde Alice Mohr, Stefano Zamuner, Daniel Maria Busiello

Genome duplication, transcription, and translation are among many crucial cellular processes that need to be performed with high fidelity. However, those extremely low error rates cannot be explained with simple equilibrium thermodynamic considerations. Th ...

Amer Physical Soc2023

CERT1 mutations perturb human development by disrupting sphingolipid homeostasis

Paolo De Los Rios, Bruno Lemaitre, Evelyne Ruchti, Sylvia Ho, Anthony Vocat, Samuel Rommelaere, Greta Limoni, Stefano Zamuner, Giovanni D'Angelo, Laura Capolupo, Charlotte Julie Caroline Gehin, Huixin Guo

Neural differentiation, synaptic transmission, and action potential propagation depend on membrane sphingolipids, whose metabolism is tightly regulated. Mutations in the ceramide transporter CERT (CERT1), which is involved in sphingolipid biosynthesis, are ...

American Society for Clinical Investigation2023

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

Stefano Zamuner

Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference ...

PUBLIC LIBRARY SCIENCE2022

Light‐switchable buffers

Kay Severin, Rosario Scopelliti, Cristian Pezzato, Farzaneh Fadaei Tirani, Stefano Zamuner, Cesare Berton, Daniel Maria Busiello

A visible light-switchable buffer system based on a protonated merocyanine photoacid is presented. Para -substitution of the indolium side with a methoxy group affords a compound suitable for making hydrolytically stable aqueous buffers whose pH can be tun ...

Wiley-VCH Verlag GmbH2021

Relief of ParB autoinhibition by parS DNA catalysis and recycling of ParB by CTP hydrolysis promote bacterial centromere assembly

Paolo De Los Rios, Stefano Zamuner

Three-component ParABS systems are widely distributed factors for plasmid partitioning and chromosome segregation in bacteria. ParB acts as adaptor protein between the 16-base pair centromeric parS DNA sequences and the DNA segregation proteins ParA and Sm ...

AMER ASSOC ADVANCEMENT SCIENCE2021

Thermodynamics and kinetics of protonated merocyanine photoacids in water

Kay Severin, Rosario Scopelliti, Euro Solari, Cristian Pezzato, Farzaneh Fadaei Tirani, Stefano Zamuner, Cesare Berton, Daniel Maria Busiello

Metastable-state photoacids (mPAHs) are chemical species whose photo-activated state is long-lived enough to allow for proton diffusion. Liao's photoacid (1) represents the archetype of mPAHs, and is being widely used on account of its unique capability to ...

2020

Computational pipeline to probe NaV1.7 gain-of-function variants in neuropathic painful syndromes

Margherita Marchi, Stefano Zamuner

Applications of machine learning and graph theory techniques to neuroscience have witnessed an increased interest in the last decade due to the large data availability and unprecedented technology developments. Their employment to investigate the effect of ...

NATURE RESEARCH2020

Self-organization of parS centromeres by the ParB CTP hydrolase

Paolo De Los Rios, Stefano Zamuner

ParABS systems facilitate chromosome segregation and plasmid partitioning in bacteria and archaea. ParB protein binds centromeric parS DNA sequences and spreads to flanking DNA. We show that ParB is an enzyme that hydrolyzes cytidine triphosphate (CTP) to ...

American Association for the Advancement of Science2019

Mechanics of Allostery: Contrasting the Induced Fit and Population Shift Scenarios

Solange Marie Flatt, Matthieu Wyart, Stefano Zamuner, Riccardo Ravasio, Carolina Brito Carvalho dos Santos

In allosteric proteins, binding a ligand can affect function at a distant location, for example, by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed number of stable c ...

CELL PRESS2019

Vibrational entropy estimation can improve binding affinity prediction for non-obligatory protein complexes

Stefano Zamuner

2018

Toward a unified scoring function for native state discrimination and drug-binding pocket recognition

Stefano Zamuner

Protein folding and receptor–ligand recognition are fundamental processes for any living organism. Although folding and ligand recognition are based on the same chemistry, the existing empirical scoring functions target just one problem: predicting the cor ...

2018

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

Bruno Emanuel Ferreira De Sousa Correia, Stefano Zamuner

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based ...

Wiley-Blackwell2016