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Paolo De Los Rios

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Related publications (93)

Repair or Degrade: the Thermodynamic Dilemma of Cellular Protein Quality-Control

Paolo De Los Rios, Bruno Claude Daniel Fauvet, Satyam Tiwari, Mathieu Rebeaud, Pierre Goloubinoff

Life is a non-equilibrium phenomenon. Owing to their high free energy content, the macromolecules of life tend to spontaneously react with ambient oxygen and water and turn into more stable inorganic molecules. A similar thermodynamic picture applies to th ...

FRONTIERS MEDIA SA2021

Bidirectional propagation of low frequency oscillations over the human hippocampal surface

Paolo De Los Rios, Shiling Liang, Daniel Maria Busiello

The hippocampus is diversely interconnected with other brain systems along its axis. Cycles of theta-frequency activity are believed to propagate from the septal to temporal pole, yet it is unclear how this one-way route supports the flexible cognitive cap ...

Nature Research2021

Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network

Paolo De Los Rios, Francesco Piazza, Shiling Liang, Daniel Maria Busiello

The exclusive presence of beta -D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fra ...

Nature Research2021

Dissipation-Driven Selection under Finite Diffusion: Hints from Equilibrium and Separation of Time Scales

Paolo De Los Rios, Shiling Liang, Daniel Maria Busiello

When exposed to a thermal gradient, reaction networks can convert thermal energy into the chemical selection of states that would be unfavourable at equilibrium. The kinetics of reaction paths, and thus how fast they dissipate available energy, might be do ...

MDPI2021

A gyrokinetic model for the plasma periphery of tokamak devices

Paolo De Los Rios, Paolo Ricci, Baptiste Jimmy Frei, Rogério Manuel Cabete De Jesus Jorge

A gyrokinetic model is presented that can properly describe large and small amplitude electromagnetic fluctuations occurring on scale lengths ranging from the electron Larmor radius to the equilibrium perpendicular pressure gradient scale length, and the a ...

Cambridge University Press2020

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

Molecular dissection of amyloid disaggregation by human HSP70

Paolo De Los Rios, Alessandro Barducci

The molecular steps that lead to the disaggregation of amyloid fibrils are shown to involve the synergistic action of HSP70 and its co-chaperones DNAJB1 and HSP110. ...

NATURE RESEARCH2020

Protein Structural Information and Evolutionary Landscape by In Vitro Evolution

Paolo De Los Rios

Protein structure is tightly intertwined with function according to the laws of evolution. Understanding how structure determines function has been the aim of structural biology for decades. Here, we have wondered instead whether it is possible to exploit ...

OXFORD UNIV PRESS2020

How Complex Molecules Could Possibly be Stable at the Dawn of Life: Out of Equilibrium Dissipation Shapes Selection

Paolo De Los Rios, Shiling Liang, Daniel Maria Busiello

CELL PRESS2020

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

Paolo De Los Rios, Alessandro Barducci

Cells possess remarkable control of the folding and entanglement topology of long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs i ...

2019

Function, evolution, and structure of J-domain proteins

Paolo De Los Rios, Alessandro Barducci, Pierre Goloubinoff

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

Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

Paolo De Los Rios, Salvatore Assenza, Alessandro Barducci, Alberto Stefano Sassi

Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here, we combine complementary theoretical approaches to elucidate the struct ...

2019

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

Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins

Paolo De Los Rios, Bruno Claude Daniel Fauvet, Alessandro Barducci, Alberto Stefano Sassi, Pierre Goloubinoff

During and after protein translation, molecular chaperones require ATP hydrolysis to favor the native folding of their substrates and, under stress, to avoid aggregation and revert misfolding. Why do some chaperones need ATP, and what are the consequences ...

2018

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

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

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

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

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

Paolo De Los Rios, Duccio Malinverni, Alessandro Barducci

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

Molecular chaperones inject energy from ATP hydrolysis into the non-equilibrium stabilisation of native proteins

Paolo De Los Rios, Bruno Claude Daniel Fauvet, Alessandro Barducci, Alberto Stefano Sassi, Pierre Goloubinoff

Protein homeostasis, namely the ensemble of cellular mechanisms collectively controlling the activity, stability and conformational states of proteins, depends on energy-consuming processes. De novo protein synthesis requires ATP hydrolysis for peptide bon ...

2017

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