Publications de Fabrizio Benedetti

Unsupervised Analysis of Flow Cytometry Data in a Clinical Setting Captures Cell Diversity and Allows Population Discovery

Nicolas Jean Philippe Guex, Fabrizio Benedetti, George Coukos, Ioannis Xenarios, Alexandre Harari

2021

Identification and nanomechanical characterization of the fundamental single-strand protofilaments of amyloid α-synuclein fibrils

Giovanni Dietler, Hilal Lashuel, Fabrizio Benedetti, Francesco Simone Ruggeri

National Academy of Sciences2018

Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S-pombe

Yannis Burnier, Andrzej Stasiak, Julien Dorier, Fabrizio Benedetti

The question of how self-interacting chromatin domains in interphase chromosomes are structured and generated dominates current discussions on eukaryotic chromosomes. Numerical simulations using standard polymer models have been helpful in testing the vali ...

Oxford University Press (OUP)2017

Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization

Giovanni Dietler, Paolo De Los Rios, Fabrizio Benedetti, Giovanni Longo, Aleksandre Japaridze

Bacterial chromosome has a compact structure that dynamically changes its shape in response to bacterial growth rate and growth phase. Determining how chromatin remains accessible to DNA binding proteins, and transcription machinery is crucial to understan ...

American Chemical Society2017

Can Dissipative Properties of Single Molecules Be Extracted from a Force Spectroscopy Experiment?

Andrzej Kulik, Giovanni Dietler, Serguei Sekatski, Dmitry Klinov, Fabrizio Benedetti

We performed dynamic force spectroscopy of single dextran and titin 127 molecules using small-amplitude and low-frequency (40-240 Hz) dithering of an atomic force microscope tip excited by a sine wave voltage fed onto the tip-carrying piezo. We show that f ...

Elsevier2016

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

Yannis Burnier, Giovanni Dietler, Andrzej Stasiak, Julien Dorier, Fabrizio Benedetti, Aleksandre Japaridze, Robert Sebastian Kwapich

DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from ...

Oxford University Press2015

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

Yannis Burnier, Andrzej Stasiak, Julien Dorier, Fabrizio Benedetti

Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput DNA sequencing expanded the power of chromosome conformation capture (3C) methods that provide in ...

Oxford University Press2014

Force-induced globule-coil transition in laminin binding protein and its role for viral-cell membrane fusion

Giovanni Dietler, Serguei Sekatski, Andrey Mikhaylov, Fabrizio Benedetti, Tatyana Karakouz, Denis Korneev

The specific interactions of the pairs laminin binding protein (LBP)-purified tick-borne encephalitis viral surface protein E and certain recombinant fragments of this protein, as well as West Nile viral surface protein E and certain recombinant fragments ...

Wiley-Blackwell2014

Real-Time Monitoring of Protein Conformational Changes Using a Nano-Mechanical Sensor

Giovanni Dietler, Paolo De Los Rios, Dusan Vobornik, Sandor Kasas, Livan Bladimir Alonso Sarduy, Fabrizio Benedetti, Giovanni Longo

Proteins can switch between different conformations in response to stimuli, such as pH or temperature variations, or to the binding of ligands. Such plasticity and its kinetics can have a crucial functional role, and their characterization has taken center ...

Public Library of Science2014

Dependence of the most probable and average bond rupture force on the force loading rate: First order correction to the Bell-Evans model

Giovanni Dietler, Serguei Sekatski, Fabrizio Benedetti

The Bell-Evans model which predicts the linear dependence of the most probable intermolecular bond rupture force on the logarithm of stretching force loading rate is usually used to discuss the dynamic force spectroscopy experiment data. This model is cons ...

American Institute of Physics2013

Dependence of the Most Probable and Average Bond Rupture Forces on the Force Loading Rate in Single Molecule Dynamic Force Spectroscopy Experiment: First Order Correction to the Bell-Evans Model

Giovanni Dietler, Serguei Sekatski, Fabrizio Benedetti

Cell Press2013

A single-molecule stretching method for lateral and normal AFM lever calibration

Andrzej Kulik, Giovanni Dietler, Fabrizio Benedetti

A novel method for quantitative lateral force measurement (LFM) calibration has been developed. Using a single-molecule spectroscopy approach it is possible to calibrate the AFM levers for both lateral and normal spring constants with a single image scan. ...

Institute of Physics2013

Statistical Study of the Unfolding of Multimodular Proteins and their Energy Landscape by Atomic Force Microscopy

Fabrizio Benedetti

The aim of the present thesis is to investigate several aspects of: the proteins mechanics, interprotein interactions and to study also new techniques, theoretical and technical, to obtain and analyze the force spectroscopy experiments. The first section i ...

EPFL2012

A Nanoscale Force Probe for Gauging Intermolecular Interactions

Fabrizio Benedetti

Wiley-VCH Verlag GmbH2012

Nonkinetic Modeling of the Mechanical Unfolding of Multimodular Proteins: Theory and Experiments

Giovanni Dietler, Serguei Sekatski, Fabrizio Benedetti

We introduce and discuss a novel approach called back-calculation for analyzing force spectroscopy experiments on multimodular proteins. The relationship between the histograms of the unfolding forces for different peaks, corresponding to a different numbe ...

Elsevier2011