Publications associées à The effect of crowding and confinement: a comparison of Yfh1 stability in different environments

Publications associées (27)

Discontinuous Galerkin methods for Fisher-Kolmogorov equation with application to a-synuclein spreading in Parkinson's disease

This spreading of prion proteins is at the basis of brain neurodegeneration. This paper deals with the numerical modelling of the misfolding process of a-synuclein in Parkinson's disease. We introduce and analyse a discontinuous Galerkin method for the sem ...

Elsevier Science Sa2023

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

Andrei Zviagin

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

EPFL2023

Molten globule-like transition state of protein barnase measured with calorimetric force spectroscopy

Sebastian James Davis

Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native conformation of glob ...

National Academy of Sciences2022

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

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

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

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

Thioredoxin-Related Transmembrane Proteins: TMX1 and Little Brothers TMX2, TMX3, TMX4 and TMX5

Maurizio Molinari

The endoplasmic reticulum (ER) is site of synthesis and maturation of membrane and secretory proteins in eukaryotic cells. The ER contains more than 20 members of the Protein Disulfide Isomerase (PDI) family. These enzymes regulate formation, isomerization ...

2020

A smart low molecular weight gelator for the triple detection of copper (II), mercury (II), and cyanide ions in water resources

Rosario Scopelliti

Novel supramolecular gelators based on quinoline-indolin-2-one structure were synthesized. These gelators formed stable organogels in a mixture of DMSO/H2O (1:1). The scanning electron microscopy (SEM), IR and NMR spectroscopies, and rheological measuremen ...

ELSEVIER2020

Influence of curing temperature on cement paste microstructure measured by H-1 NMR relaxometry

Karen Scrivener, Arnaud Charles Albert Muller

H-1 nuclear magnetic resonance (NMR) relaxometry, supported by X-Ray diffraction and thermogravimetric analysis, has been used to characterise microstructure of white cement pastes underwater cured at temperatures in the range 10 degrees C to 60 degrees C. ...

Pergamon-Elsevier Science Ltd2019

Water Redistribution-Microdiffusion in Cement Paste under Mechanical Loading Evidenced by H-1 NMR

Karen Scrivener

The mobility of water within the microstructure of hardened cement paste has been at the center of a long-lasting debate, motivated by the need to understand the fundamental mechanisms that play a role in drying, shrinkage, creep, and thermal expansion. Ou ...

2019

Equilibrium and Out-of-Equilibrium Adherence of Hydrogels against Polymer Brushes

Jennifer Mary Adrienne Alice Macron

At low pH, underwater adherence between poly(N,N-dimethylacrylamide) hydrogels and poly(acrylic acid) brushes is due to the formation of multiple hydrogen bonds. The effect of the key parameters controlling the formation of these interactions (contact time ...

American Chemical Society2018

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

Three branches to rule them all? UPR signalling in response to chemically versus misfolded proteins-induced ER stress

Maurizio Molinari

Study of the unfolded protein responses (UPR) is mainly addressed by challenging eukaryotic cells with chemical compounds that impair calcium, redox or glycan homeostasis. These dramatically alter the endoplasmic reticulum (ER) environment and function, bu ...

2018

Non equilibrium thermodynamics of protein organization

Alberto Stefano Sassi

Three quarters of the thesis will be devoted to the discussion of non equilibrium systems. We show how certain biological systems cannot be described by standard thermodynamics. The reason is that the energy consumption due to the hydrolysis of ATP imposes ...

EPFL2018

A discussion on the paper "Role of porosity on the stiffness and stability of (001) surface of the nanogranular C-S-H gel"

Paul Bowen, Aslam Kunhi Mohamed

This paper is a discussion of a recent publication by Sekkal and coworkers, which investigated the elasticity, cohesion, and stability of the C-S-H (001) surface as a function of porosity using molecular dynamics simulations. In our discussion, we highligh ...

Pergamon-Elsevier Science Ltd2017

Decoding urban development dynamics through actor-network methodological approach

Jean-Claude Bolay, Marija Cvetinovic

Due to growing social and physical transformations, contemporary cities reveal the profound necessity of proper scientific approaches that are adjusted to conditions of global complexity and dynamic patterns of development. Predominance of an overall marke ...

2017

AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species

Giovanni Dietler, Francesco Simone Ruggeri, Andrea Cerreta

Background: A wide class of human diseases and neurodegenerative disorders, such as Alzheimer's disease, is due to the failure of a specific peptide or protein to keep its native functional conformational state and to undergo a conformational change into a ...

Bentham Science Publishers2016

Experimental Milestones in the Discovery of Molecular Chaperones as Polypeptide Unfolding Enzymes

Andrija Finka

Molecular chaperones control the cellular folding, assembly, unfolding, disassembly, translocation, activation, inactivation, disaggregation, and degradation of proteins. In 1989, groundbreaking experiments demonstrated that a purified chaperone can bind a ...

Annual Reviews2016

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

Matteo Dal Peraro, Luciano Andres Abriata

Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dime ...

Nature Publishing Group2015

Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map

Michele Ceriotti

This work examines the conformational ensemble involved in beta-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent molecules is used, an ...

2015

Modeling and Engineering Proteins Thermostability

Hasan Pezeshgi Modarres

Enzymes have evolved during millions of years to become efficient catalysts for specific biochemical reactions within a specific range of working conditions in the cellular environment. The activity of an enzyme is directly related to its folded structure ...

EPFL2015