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Paolo De Los Rios

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Related publications (89)

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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

Physical realizability of small-world networks

Paolo De Los Rios, Thomas Petermann

Supplementing a lattice with long-range connections effectively models small-world networks characterized by a high local and global interconnectedness observed in systems ranging from society to the brain. If the links have a wiring cost associated with t ...

2006

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

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

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

Temperature Dependence of Normal Mode Reconstructions of Protein Dynamics

Paolo De Los Rios, Francesco Piazza

Normal mode (NM) analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent NMs capture the salient features of the dynamics over a range ...

American Physical Society2009

A fluorescent multi-domain protein reveals the unfolding mechanism of Hsp70

Paolo De Los Rios, Bruno Claude Daniel Fauvet, Salvatore Assenza, Satyam Tiwari

Detailed understanding of the mechanism by which Hsp70 chaperones protect cells against protein aggregation is hampered by the lack of a comprehensive characterization of the aggregates, which are typically heterogeneous. Here we designed a reporter chaper ...

Nature Research2023

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

Paolo De Los Rios

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

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

Paolo De Los Rios, Alessandro Barducci, Duccio Malinverni

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

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

Paolo De Los Rios, Alessandro Barducci, Duccio Malinverni

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

The cold denaturation of IscU highlights structure–function dualism in marginally stable proteins

Paolo De Los Rios

Proteins undergo both cold and heat denaturation, but often cold denaturation cannot be detected because it occurs at temperatures below water freezing. Proteins undergoing detectable cold as well as heat denaturation yield a reliable curve of protein stab ...

2018

J-domain protein chaperone circuits in proteostasis and disease

Paolo De Los Rios, Duccio Malinverni

The J-domain proteins (JDP) form the largest protein family among cellular chaperones. In cooperation with the Hsp70 chaperone system, these co-chaperones orchestrate a plethora of distinct functions, including those that help maintain cellular proteostasi ...

ELSEVIER SCIENCE LONDON2022

Complex network analysis of free-energy landscapes

Paolo De Los Rios, David Gfeller

The kinetics of biomolecular isomerization processes, such as protein folding, is governed by a free-energy surface of high dimensionality and complexity. As an alternative to projections into one or two dimensions, the free-energy surface can be mapped in ...

National Academy of Sciences2007

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

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

Paolo De Los Rios

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

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

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

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

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, Vishal Sood, Andrija Finka

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

Anti-cooperativity in diffusion-controlled reactions with pairs of anisotropic domains: a model for the antigen-antibody encounter

Paolo De Los Rios, Francesco Piazza

The encounter between anisotropic agents in diffusion-controlled reactions is a topic of very general relevance in chemistry and biology. Here we introduce a simplified model of encounter of an isotropic molecule with a pair of partially reacting agents an ...

Springer-Verlag2005

Membraneless organelles: phasing out of equilibrium

Paolo De Los Rios

Over the past years, liquid-liquid phase separation (LLPS) has emerged as a ubiquitous principle of cellular organization implicated in many biological processes ranging from gene expression to cell division. The formation of biological condensates, like t ...

PORTLAND PRESS LTD2020

Mechanisms of Quantum Dot Energy Engineering by Metalorganic Vapor Phase Epitaxy on Patterned Nonplanar Substrates

Elyahou Kapon, Benjamin Dwir, Paolo De Los Rios, Klaus Leifer, Qing Zhu

A novel technique for tuning the strength of quantum confinement in site-controlled semiconductor quantum dots (QDs) is introduced and investigated theoretically and experimentally. The method makes use of controlled local growth rates during metalorganic ...

American Chemical Society2007

Autorepression of yeast Hsp70 cochaperones by intramolecular interactions involving their J-domains

Paolo De Los Rios, Bruno Claude Daniel Fauvet, Adélaïde Alice Mohr, Mathieu Rebeaud, Satyam Tiwari

The 70 kDa heat shock protein (Hsp70) chaperones control protein homeostasis in all ATP-containing cellular compartments. J-domain proteins (JDPs) coevolved with Hsp70s to trigger ATP hydrolysis and catalytically upload various substrate polypeptides in ne ...

Elsevier Science Inc2024