Publications related to AFM Force Spectroscopy and Steered Molecular Dynamics Simulation of Protein Contactin 4

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

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, Iris Bodenmann

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

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

Andrzej Kulik, Giovanni Dietler, Karolina Anna Mikulska Ruminska

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, Andrea Cerreta, Francesco Simone Ruggeri

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, Cristina Consani, Gerald Auböck

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

Andrzej Kulik, Giovanni Dietler, 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, Nicha Thontasen, 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

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

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

Amyloid ß-derived switch-peptides as tool to study conformational changes relevant in degenerative diseases

Marie-Stéphanie Camus

The rapid growing number of patients diagnosed with a neurodegenerative disease and more particularly with Alzheimer's disease (AD) has stimulated intensive research in determining and understanding biological phenomena causing such devastating diseases an ...

EPFL2008

Solvent effects on the ultrafast dynamics of the retinal chromophore of bacteriorhodopsin

Goran Zgrablic

Photo-induced excited-state reactions stand in the center of function of the photosensitive biological systems. These reactions can be accompanied by structural changes of the chromophore (for example isomerization) which are influenced by the nearest envi ...

EPFL2006

Influence of the protein environment on spectroscopy and ultrafast dynamics of retinal in bacteriorhodopsin

Selma Schenkl

The environment is important for the exact course of a chemical reaction. As an example of the strong influence of the environment on the reaction, this work studies the isomerization reaction of the chromophore retinal in the binding pocket of the protein ...

EPFL2004