Publications associées à AFM Force Spectroscopy and Steered Molecular Dynamics Simulation of Protein Contactin 4

Publications associées (25)

Nonlinear Economic State Equilibria via van der Waals Modeling

The renowned van der Waals (VDW) state equation quantifies the equilibrium relationship between the pressure P, volume V, and temperature (Formula presented.) of a real gas. We assign new variable interpretations adapted to the economic context: (Formula p ...

2024

Ion Spectroscopy Reveals Structural Difference for Proteins Microhydrated by Retention and Condensation of Water

Oleg Boyarkine, Andrei Zviagin

Protein ubiquitin in its +7 charge state microhydrated by 5 and 10 water molecules has been interrogated in the gas phase by cold ion UV/IR spectroscopy. The complexes were formed either by condensing water onto the unfolded bare proteins in a temperature- ...

Amer Chemical Soc2024

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

Overexpression of transcription factor Foxa1 and target genes remediate therapeutic protein production bottlenecks in Chinese hamster ovary cells

Nicolas Mermod, Audrey Véronique Berger

Despite extensive research conducted to increase protein production from Chinese hamster ovary (CHO) cells, cellular bottlenecks often remain, hindering high yields. In this study, a transcriptomic analysis led to the identification of 32 genes that are co ...

WILEY2020

Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives

Chan Cao

In neurodegenerative diseases, a wide range of amyloid proteins or peptides such as amyloid-beta and alpha-synuclein fail to keep native functional conformations, followed by misfolding and self-assembling into a diverse array of aggregates. The aggregates ...

CAMBRIDGE UNIV PRESS2020

Early Stages of Precipitation In Aluminum Alloys by First-Principles and Machine-Learning Atomistic Simulations

Daniele Giofré

Age hardening induced by the formation of (semi)-coherent precipitate phases is crucial for the processing and final properties of the widely used Al-6000 alloys despite the early stages of precipitation are still far from being fully understood. This cruc ...

EPFL2018

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

Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD

Giovanni Dietler, Andrzej Kulik

Contactin-4 (CNTN4) is a complex cell adhesion molecule (CAM) localized at neuronal membranes, playing a key role in maintaining the mechanical integrity and signaling properties of the synapse. CNTN4 consists of six immunoglobulin C2 type (IgC2) domains a ...

Springer Nature2017

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

Active Conformation Control of Unfolded Proteins by Hyperthermal Collision with a Metal Surface

Klaus Kern, Stephan Rauschenbach, Gordon Rinke

The physical and chemical properties of macromolecules like proteins are strongly dependent on their conformation. The degrees of freedom of their chemical bonds generate a huge conformational space, of which, however, only a small fraction is accessible i ...

Amer Chemical Soc2014

Ultrafast Tryptophan-to-Heme Electron Transfer in Myoglobins Revealed by UV 2D Spectroscopy

Majed Chergui, Frank van Mourik, Gerald Auböck, Cristina Consani

Tryptophan is commonly used to study protein structure and dynamics, such as protein folding, as a donor in fluorescence resonant energy transfer (FRET) studies. By using ultra-broadband ultrafast two-dimensional (2D) spectroscopy in the ultraviolet (UV) a ...

American Association for the Advancement of Science2013

A single-molecule stretching method for lateral and normal AFM lever calibration

Giovanni Dietler, Andrzej Kulik, Fabrizio Benedetti

A novel method for quantitative lateral force measurement (LFM) calibration has been developed. Using a single-molecule spectroscopy approach it is possible to calibrate the AFM levers for both lateral and normal spring constants with a single image scan. ...

Institute of Physics2013

Statistical Study of the Unfolding of Multimodular Proteins and their Energy Landscape by Atomic Force Microscopy

Fabrizio Benedetti

The aim of the present thesis is to investigate several aspects of: the proteins mechanics, interprotein interactions and to study also new techniques, theoretical and technical, to obtain and analyze the force spectroscopy experiments. The first section i ...

EPFL2012

A Close Look at Proteins: Submolecular Resolution of Two- and Three-Dimensionally Folded Cytochrome c at Surfaces

Klaus Kern, Stephan Rauschenbach, Gordon Rinke

Imaging of individual protein molecules at the single amino acid level has so far not been possible due to the incompatibility of proteins with the vacuum environment necessary for high-resolution scanning probe microscopy. Here we demonstrate electrospray ...

American Chemical Society (ACS)2012

Lie Group and Lie Algebra Variational Integrators for Flexible Beam and Plate in R3

François Marie Alain Demoures

The purpose of this thesis is to develop variational integrators synchronous or asynchronous, which can be used as tools to study complex structures composed of plates and beams subjected to large deformations and stress. We consider the geometrically exac ...

EPFL2012

Electromechanical Coupling In Cardiac Dynamics: The Active Strain Approach

Alfio Quarteroni, Fabio Nobile

The coupling between cardiac mechanics and electric signaling is addressed in a nonstandard framework in which the electrical potential dictates the active strain (not stress) of the muscle. The physiological and mathematical motivations leading us to this ...

Society for Industrial and Applied Mathematics2011

Nonkinetic Modeling of the Mechanical Unfolding of Multimodular Proteins: Theory and Experiments

Giovanni Dietler, Serguei Sekatski, Fabrizio Benedetti

We introduce and discuss a novel approach called back-calculation for analyzing force spectroscopy experiments on multimodular proteins. The relationship between the histograms of the unfolding forces for different peaks, corresponding to a different numbe ...

Elsevier2011

Cold Ion Spectroscopy of Biological Molecules in the Gas Phase

Natalia Nagornova

The three-dimensional (3D) structures of proteins and peptides in vivo largely determine their biological functions. In vitro these native structures and their heterogeneity reflect a subtle balance between noncovalent intramolecular interactions and those ...

EPFL2011

Experimental strategies for studying transcription factor-DNA binding specificities

Sebastian Maerkl

Specific binding of transcription factors (TFs) determines in a large part the connectivity of gene regulatory networks as well as the quantitative level of gene expression. A multiplicity of both experimental and computational methods is currently used to ...

2010

The increase in protein contour length depends on mechanical unfolding conditions

László Forró, Andrzej Kulik

Many proteins in alive organisms have a domain structure providing them the possibility to reversible unfolding, which seems to play an essential role in those processes occurring in tissues which are controlled by mechanical cellular tension. In this work ...

2008