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

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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. ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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

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Nonlinear Economic State Equilibria via van der Waals Modeling

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

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

Non equilibrium thermodynamics of protein organization

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

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

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

Electromechanical Coupling In Cardiac Dynamics: The Active Strain Approach

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

Cold Ion Spectroscopy of Biological Molecules in the Gas Phase

Experimental strategies for studying transcription factor-DNA binding specificities

The increase in protein contour length depends on mechanical unfolding conditions

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