Publications by Paolo De Los Rios

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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 ...

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 ...

The aggregation of proteins is central to many aspects of daily life, including food processing, blood coagulation, eye cataract formation disease and prion-related neurodegenerative infections[1–5]. However, the physical mechanisms responsible for amyloid ...

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, ...

The identification of cell cycle-related genes is still a difficult task, even for organisms with relatively few genes such as the fission yeast. Several gene expression studies have been published on S. pombe showing similarities but also discrepancies in ...

Although alcohols are well-known to be protein denaturants when present at high concentrations, their effect on proteins at low concentrations is much less well characterized. In this paper, we present a study of the effects of alcohols on protein stabilit ...

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 ...

Genome duplication, transcription, and translation are among many crucial cellular processes that need to be performed with high fidelity. However, those extremely low error rates cannot be explained with simple equilibrium thermodynamic considerations. Th ...

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 ...

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 ...

PDZ domains are typical examples of binding motifs mediating the formation of protein-protein assemblies in many different cells. A quantitative characterization of the mechanisms intertwining structure, chemistry, and dynamics with the PDZ function repres ...

The traditional node percolation map of directed networks is reanalyzed in terms of edges. In the percolated phase, edges can mainly organize into five distinct giant connected components, interfaces bridging the communication of nodes in the strongly conn ...

The configuration space network (CSN) of a dynamical system is an effective approach to represent the ensemble of configurations sampled during a simulation and their dynamic connectivity. To elucidate the connection between the CSN topology and the underl ...

Living systems are maintained out of equilibrium by external driving forces. At stationarity, they exhibit emergent selection phenomena that break equilibrium symmetries and originate from the expansion of the accessible chemical space due to nonequilibriu ...

Vibrational spectra of proteins and topologically disordered solids display a common anomaly at low frequencies, known as boson peak. We show that such feature in globular proteins can be deciphered in terms of an energy landscape picture, as it is for gla ...

Gel electrophoresis can be used to separate nicked circular DNA molecules of equal length but forming different knot types. At low electric fields, complex knots drift faster than simpler knots. However, at high electric field the opposite is the case and ...

Many approaches have been developed to characterize the heterogeneity of membranes in living cells. In this study, the elastic properties of specific membrane domains in living cells are characterized by atomic force microscopy. Our data reveal the existen ...

Cells rely on multiple protein quality control (PQC) pathways, including molecular chaperone-assisted folding and degradation systems, to maintain proteome integrity and functionality. These pathways work together to reduce the risk of toxic protein aggreg ...

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 ...

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, ...

Paolo De Los Rios

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

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

Understanding amyloid aggregation by statistical analysis of atomic force microscopy images

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

Bottleneck genes and community structure in the cell cycle network of S-pombe

Cold denaturation of yeast frataxin offers the clue to understand the effect of alcohols on protein stability

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

Individual and combined benefits of different nonequilibrium proofreading mechanisms

Universal Behavior in the Mesoscale Properties of Amyloid Fibrils

Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

Diffusion-limited unbinding of small peptides from PDZ domains

Interfaces and the edge percolation map of random directed networks

Uncovering the topology of configuration space networks

Thermodynamic Bounds on Symmetry Breaking in Linear and Catalytic Biochemical Systems

Glasslike structure of globular proteins and the boson peak

Simulations of electrophoretic collisions of DNA knots with gel obstacles

Elastic membrane heterogeneity of living cells revealed by stiff nanoscale membrane domains

Clearing the protein clutter in human cells: the role of protein disaggregases

Protein Structural Information and Evolutionary Landscape by In Vitro Evolution

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