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Paolo De Los Rios

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Related publications (93)

New Techniques for Ancient Proteins: Direct Coupling Analysis Applied on Proteins Involved in Iron Sulfur Cluster Biogenesis

Direct coupling analysis (DCA) is a powerful statistical inference tool used to study protein evolution. It was introduced to predict protein folds and protein-protein interactions, and has also been applied to the prediction of entire interactomes. Here, ...

2017

ScienceWISE: Topic Modeling over Scientific Literature Networks

Paolo De Los Rios, Andrea Martini, Alessio Vincenzo Cardillo

We provide an up-to-date view on the knowledge management system ScienceWISE (SW) and address issues related to the automatic assignment of articles to research topics. So far, SW has been proven to be an effective platform for managing large volumes of te ...

2017

Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes

Paolo De Los Rios, Duccio Malinverni, Alessandro Barducci

Hsp70 participates in a broad spectrum of protein folding processes extending from nascent chain folding to protein disaggregation. This versatility in function is achieved through a diverse family of J-protein cochaperones that select substrates for Hsp70 ...

Elife Sciences Publications Ltd2017

Thermodynamic bounds on the ultra- and infra-affinity of Hsp70 for its substrates

Paolo De Los Rios, Basile Nguyen

The 70 kDa Heat Shock Proteins Hsp70 have several essential functions in living systems, such as protecting proteins against protein aggregation, assisting protein folding, remodeling protein complexes and driving the translocation into organelles. These f ...

2017

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

Paolo De Los Rios, Pierre Goloubinoff

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. ...

2016

Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces

Paolo De Los Rios, Francesco Piazza, Giuseppe Foffi

In this paper we introduce a fully flexible coarse-grained model of immunoglobulin G (IgG) antibodies parametrized directly on cryo-EM data and simulate the binding dynamics of many IgGs to antigens adsorbed on a surface at increasing densities. Moreover, ...

Public Library Science2016

Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs

Paolo De Los Rios, Andrija Finka, Vishal Sood, Pierre Goloubinoff

Classic semiquantitative proteomic methods have shown that all organisms respond to a mild heat shock by an apparent massive accumulation of a small set of proteins, named heat-shock proteins (HSPs) and a concomitant slowing down in the synthesis of the ot ...

Springer2015

Quantifying the role of chaperones in protein translocation by computational modeling

Paolo De Los Rios, Salvatore Assenza, Alessandro Barducci

2015

Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones

Paolo De Los Rios, Duccio Malinverni, Alessandro Barducci

Hsp70s are a class of ubiquitous and highly conserved molecular chaperones playing a central role in the regulation of proteostasis in the cell. Hsp70s assist a myriad of cellular processes by binding unfolded or misfolded substrates during a complex bioch ...

Public Library Science2015

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

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

Hsp70 chaperones are non-equilibrium machines that achieve ultra-affinity by energy consumption

Paolo De Los Rios, Alessandro Barducci

70-kDa Heat shock proteins are ATP-driven molecular chaperones that perform a myriad of essential cellular tasks. Although structural and biochemical studies have shed some light on their functional mechanism, the fundamental issue of the role of energy co ...

Elife Sciences Publications Ltd2014

Universal Behavior in the Mesoscale Properties of Amyloid Fibrils

Raffaele Mezzenga, Paolo De Los Rios, Salvatore Assenza

Amyloid fibrils are ubiquitous proteinaceous aggregates occurring in vivo and in vitro, with an invariant structural fingerprint at the molecular length scale. However, interpretation of their mesoscopic architectures is complicated by diverse observable p ...

2014

Hydrophobic hydration of poly-N-isopropyl acrylamide: a matter of the mean energetic state of water

Paolo De Los Rios

The enthalpically favoured hydration of hydrophobic entities, termed hydrophobic hydration, impacts the phase behaviour of numerous amphiphiles in water. Here, we show experimental evidence that hydrophobic hydration is strongly determined by the mean ener ...

Nature Publishing Group2014

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

Stochastic fluctuations and the detectability limit of network communities

Paolo De Los Rios, Jonas Liechti, 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

Explaining the length threshold of polyglutamine aggregation

Marc Hafner, Paolo De Los Rios

The existence of a length threshold, of about 35 residues, above which polyglutamine repeats can give rise to aggregation and to pathologies, is one of the hallmarks of polyglutamine neurodegenerative diseases such as Huntington's disease. The reason why s ...

2012

First-order coil-globule transition driven by vibrational entropy

Paolo De Los Rios, Francesco Piazza, Carlo Maffi

By shifting the balance between conformational entropy and internal energy, polymers modify their shape under external stimuli, such as changes in temperature. Prominent among such transformations is the coil-globule transition, whereby a polymer can switc ...

Nature Publishing Group2012

Protein folding: Chaperoning protein evolution

Paolo De Los Rios, Pierre Goloubinoff

2012

Probing the different chaperone activities of the bacterial HSP70-HSP40 system using a thermolabile luciferase substrate

Paolo De Los Rios, Pierre Goloubinoff

During mild heat-stress, a native thermolabile polypeptide may partially unfold and transiently expose water-avoiding hydrophobic segments that readily tend to associate into a stable misfolded species, rich in intra-molecular non-native beta-sheet structu ...

2011

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