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Paolo De Los Rios

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Publications associées (89)

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Stochastic fluctuations and the detectability limit of network communities

Paolo De Los Rios, Lucio Floretta

We have analyzed the detectability limits of network communities in the framework of the popular Girvan and Newman benchmark. By carefully taking into account the inevitable stochastic fluctuations that affect the construction of each and every instance of ...

American Physical Society2013

Fractal dimension and localization of DNA knots

Giovanni Dietler, Paolo De Los Rios, Guillaume Witz, Erika Ercolini

The scaling properties of DNA knots of different complexities were studied by atomic force microscope. Following two different protocols DNA knots are adsorbed onto a mica surface in regimes of (i) strong binding, that induces a kinetic trapping of the thr ...

American Physical Society2007

The effect of crowding and confinement: a comparison of Yfh1 stability in different environments

Paolo De Los Rios

Crowding and confinement can affect protein stability, favouring the more compact species amongst the folded and unfolded conformations. An unbiased assessment of the relative efficacy of crowded and confined environments has been hampered so far by the pa ...

Institute of Physics2013

Quantifying the role of chaperones in protein translocation by computational modeling

Paolo De Los Rios, Alessandro Barducci, Salvatore Assenza

2015

J-domain proteins: From molecular mechanisms to diseases

Paolo De Los Rios, Mathieu Rebeaud

Here, we report on the latest findings related to JDP functions presented at a dedicated JDP workshop in Gdansk, Poland. The report does not include all (details) of what was shared and discussed at the meeting, because some of these original data have not ...

2024

Interplay between cost and benefits triggers nontrivial vaccination uptake

Paolo De Los Rios, Alessio Vincenzo Cardillo

The containment of epidemic spreading is a major challenge in science. Vaccination, whenever available, is the best way to prevent the spreading, because it eventually immunizes individuals. However, vaccines are not perfect, and total immunization is not ...

2018

Second Virtual International Symposium on Cellular and Organismal Stress Responses, September 8-9, 2022

Paolo De Los Rios

The Second International Symposium on Cellular and Organismal Stress Responses took place virtually on September 8-9, 2022. This meeting was supported by the Cell Stress Society International (CSSI) and organized by Patricija Van OostenHawle and Andrew Tru ...

SPRINGER2023

Emergent thermophoretic behavior in chemical reaction systems

Paolo De Los Rios, Daniel Maria Busiello, Shiling Liang

Exposing a solution to a temperature gradient can lead to the accumulation of particles on either the cold or warm side. This phenomenon is known as thermophoresis, and its microscopic origin is still debated. Here, we show that thermophoresis can be obser ...

IOP Publishing Ltd2022

Effective interactions between chaotropic agents and proteins

Paolo De Los Rios

Chaotropic agents are cosolutes that can disrupt the hydrogen bonding network between water molecules and reduce the stability of the native state of proteins by weakening the hydrophobic effect. In this work, we represent the chaotropic agent as a factor ...

2005

Function, evolution, and structure of J-domain proteins

Paolo De Los Rios, Alessandro Barducci

Hsp70 chaperone systems are very versatile machines present in nearly all living organisms and in nearly all intracellular compartments. They function in many fundamental processes through their facilitation of protein (re)folding, trafficking, remodeling, ...

2019

Hsp70 chaperones use ATP to remodel native protein oligomers and stable aggregates by entropic pulling

Paolo De Los Rios

Forceful unfolding by entropic pulling is the general mechanism by which Hsp70 and Hsp110 chaperones control the oligomeric states, structures and activities of cellular proteins. ...

Nature Research2016

An outmoded in vitro-inferred mechanism for chaperonin-accelerated protein refolding is confirmed in cells by cryo-electron tomography

Paolo De Los Rios, Mathieu Rebeaud

ELSEVIER SCIENCE INC2024

Structural Efficiency of Percolated Landscapes in Flow Networks

Paolo De Los Rios

The large-scale structure of complex systems is intimately related to their functionality and evolution. In particular, global transport processes in flow networks rely on the presence of directed pathways from input to output nodes and edges, which organi ...

Public Library of Science2008

Single-molecule evidence of Entropic Pulling by Hsp70 chaperones

Paolo De Los Rios, Chan Cao, Verena Rukes, Mathieu Rebeaud

Hsp70 chaperones are central components of the cellular network that ensures the structural quality of proteins. Despite crucial roles in processes such as protein disaggregation and protein translocation into organelles, their physical mechanism of action ...

Nature Research2024

Non-equilibrium conformational dynamics in the function of molecular chaperones

Paolo De Los Rios, Alessandro Barducci

Why do chaperones need ATP hydrolysis to help proteins reach their native, functional states? In this review, we highlight the most recent experimental and theoretical evidences suggesting that ATP hydrolysis allows molecular chaperones to escape the bound ...

Elsevier2015

The Shape of a Stretched Polymer

Paolo De Los Rios, Salvatore Assenza, Alberto Stefano Sassi

The shape of a polymer plays an important role in determining its interactions with other molecules and with the environment, and is in turn affected by both of them. As a consequence, in the literature the shape properties of a chain in many different con ...

2017

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis

Paolo De Los Rios, Alessandro Barducci, Duccio Malinverni

The interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of the interaction are still elusive and contrasting models hav ...

Elife Sciences Publications Ltd2017

Paolo De Los Rios

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Stochastic fluctuations and the detectability limit of network communities

Fractal dimension and localization of DNA knots

The effect of crowding and confinement: a comparison of Yfh1 stability in different environments

Quantifying the role of chaperones in protein translocation by computational modeling

J-domain proteins: From molecular mechanisms to diseases

Interplay between cost and benefits triggers nontrivial vaccination uptake

Second Virtual International Symposium on Cellular and Organismal Stress Responses, September 8-9, 2022

Emergent thermophoretic behavior in chemical reaction systems

Effective interactions between chaotropic agents and proteins

Function, evolution, and structure of J-domain proteins

Hsp70 chaperones use ATP to remodel native protein oligomers and stable aggregates by entropic pulling

An outmoded in vitro-inferred mechanism for chaperonin-accelerated protein refolding is confirmed in cells by cryo-electron tomography

Structural Efficiency of Percolated Landscapes in Flow Networks

Single-molecule evidence of Entropic Pulling by Hsp70 chaperones

Non-equilibrium conformational dynamics in the function of molecular chaperones

The Shape of a Stretched Polymer

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis

Slow Energy Relaxation of Macromolecules and Nanoclusters in Solution

Hsp70 chaperones accelerate protein translocation and the unfolding of stable protein aggregates by entropic pulling

Numerical simulation of gel electrophoresis of DNA knots in weak and strong electric fields