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Paolo De Los Rios

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Publications associées (93)

The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase

Paolo De Los Rios, Pierre Goloubinoff

Hsp70-Hsp40-NEF and possibly Hsp100 are the only known molecular chaperones that can use the energy of ATP to convert stably pre-aggregated polypeptides into natively refolded proteins. However, the kinetic parameters and ATP costs have remained elusive be ...

Nature Publishing Group2010

Understanding amyloid aggregation by statistical analysis of atomic force microscopy images

Raffaele Mezzenga, Giovanni Dietler, Paolo De Los Rios, Jérôme Flakowski

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 ...

Nature Publishing Group2010

Vibrational entropy and the structural organization of proteins

Paolo De Los Rios, Francesco Piazza

In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic heterogeneity of force c ...

2010

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

Extended Navigability of Small World Networks: Exact Results and New Insights

Paolo De Los Rios, Cécile Caretta Cartozo

Navigability of networks, that is, the ability to find any given destination vertex starting from any other vertex, is crucial to their usefulness. In 2000 Kleinberg showed that optimal navigability could be achieved in small world networks provided that a ...

American Physical Society2009

Spectral coarse graining and synchronization in oscillator networks

Paolo De Los Rios, David Gfeller

Coarse graining techniques offer a promising alternative to large-scale simulations of complex dynamical systems, as long as the coarse-grained system is truly representative of the initial one. Here, we investigate how the dynamical properties of oscillat ...

American Physical Society2008

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

Charles Roduit, Giovanni Dietler, Paolo De Los Rios, Sandor Kasas, Pascal Steiner, Alexandre Yersin, Françoise Gisou van der Goot Grunberg

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 ...

Elsevier2008

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

Paolo De Los Rios

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 ...

American Chemical Society2008

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

Discrete Breathers in Nonlinear Network Models of Proteins

Paolo De Los Rios, Francesco Piazza

American Physical Society2007

A dynamical study of antibody-antigen encounter reactions

Paolo De Los Rios, Francesco Piazza

The effects of internal dynamics in diffusion-driven encounters between macro-molecules represent a problem of broad relevance in molecular biology. In this view, we investigate a typical antigen-antibody reaction chain, based on a coarse-grained mechanica ...

2007

On the origin of the boson peak in globular proteins

Paolo De Los Rios, Francesco Piazza

We study the boson peak phenomenology experimentally observed in globular proteins by means of elastic network models. These models are suitable for an analytic treatment in the framework of Euclidean random matrix theory, whose predictions can be numerica ...

Taylor & Francis2007

Uncovering the topology of configuration space networks

David Sébastien Morton de Lachapelle, Paolo De Los Rios, David Gfeller

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 ...

2007

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

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

Paolo De Los Rios, Francesco Piazza, Cécile Caretta Cartozo

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 ...

Public Library of Science2007

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

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

The mechanism of Hsp70 chaperones: (entropic) pulling the models together

Paolo De Los Rios, Pierre Goloubinoff

Elsevier2007

Diffusion-limited unbinding of small peptides from PDZ domains

Paolo De Los Rios, Francesco Piazza

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 ...

2007

Interfaces and the edge percolation map of random directed networks

Paolo De Los Rios

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 ...

2007

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

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