Publications related to Vibrational coherences of the protonated Schiff base of all-trans-retinal in solution

Predicting protein interactions using geometric deep learning on protein surfaces

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

EPFL2024

Processing factors affecting roughness, optical and mechanical properties of nanocellulose films for optoelectronics

Tiffany Abitbol

This work aims to understand how nanocellulose (NC) processing can modify the key characteristics of NC films to align with the main requirements for high-performance optoelectronics. The performance of these devices relies heavily on the light transmittan ...

Elsevier Sci Ltd2024

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Zhidian Zhang

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

EPFL2024

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Anthony Marchand

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

Size dependence of second-harmonic scattering from nanoparticles: Disentangling surface and electrostatic contributions

Arianna Marchioro, Sylvie Roke, Bingxin Chu

Polarimetric angle-resolved second-harmonic scattering (AR-SHS) is an all-optical tool enabling the study of unlabeled interfaces of nano-sized particles in an aqueous solution. As the second harmonic signal is modulated by interference between nonlinear c ...

AIP Publishing2023

De novo designed proteins: a study in engineering novel folds and functions

Alexandra Krina Van Hall-Beauvais

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

EPFL2023

Synthesis and application of bifunctional hypervalent iodine reagents for peptide modification

Elija Grinhagena

Protein-protein interactions (PPIs) are responsible for regulating many biological processes in human bodies. PPIs often have a large binding site and often interact through an alpha helical segment. Therefore, the inhibition of PPIs can be difficult using ...

EPFL2023

A new age in protein design empowered by deep learning

Bruno Emanuel Ferreira De Sousa Correia, Michael Bronstein, Casper Alexander Goverde, Ilia Igashov, Arne Schneuing, Hamed Khakzad

The rapid progress in the field of deep learning has had a significant impact on protein design. Deep learning methods have recently produced a breakthrough in protein structure prediction, leading to the availability of high-quality models for millions of ...

Cell Press2023

Generative power of a protein language model trained on multiple sequence alignments

Umberto Lupo, Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

eLIFE SCIENCES PUBL LTD2023

Bioaccumulation and molecular effects of carbamazepine and methylmercury co-exposure in males of Dreissena polymorpha

Dominique Grandjean, Florian Frédéric Vincent Breider, Claudia Cosio, Nguyên Thiên Kim Lê

Dreissena polymorpha is a bivalve promising for biomonitoring in freshwater ecosystems thanks to its abundance and high filtration activity allowing rapid uptake of toxicants and identification of their negative effects. Nonetheless, we still lack knowledg ...

2023

De novo protein design by inversion of the AlphaFold structure prediction network

Bruno Emanuel Ferreira De Sousa Correia, Stéphane Rosset, Casper Alexander Goverde, Benedict Dieter Gregor Wolf, Hamed Khakzad

De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in comp ...

2023

On the durability of surgical masks after simulated handling and wear

Véronique Michaud, Vincent Marc Varanges, Jian Wang, Baris Çaglar, Yann Albert Gérard Lebaupin, René M. Rossi

After the spread of COVID-19, surgical masks became highly recommended to the public. They tend to be handled and used multiple times, which may impact their performance. To evaluate this risk, surgical masks of Type IIR were submitted to four simulated tr ...

Nature Research2022

Azide-Containing Hypervalent Iodine Reagents for Biomolecules Functionalization

Raphaël Michel Henri Simonet-Davin

The goal of my PhD was the development of a new method for unselective surface labeling, not substrate-specific, that would give access to direct visualization of any surface interactions. In order to achieve this challenging goal, we wanted to develop a g ...

EPFL2022

Electrokinetic, electrochemical, and electrostatic surface potentials of the pristine water liquid-vapor interface

Philip Robin Loche

Although conceptually simple, the air-water interface displays rich behavior and is subject to intense experimental and theoretical investigations. Different definitions of the electrostatic surface potential as well as different calculation methods, each ...

AIP Publishing2022

Amplitude and phase reconstruction for Low-Energy Electron Holography of individual proteins

Hannah Julia Ochner

Single-molecule imaging methods are of importance in structural biology, and specifically in the imaging of proteins, since they can elucidate conformational variability and structural changes that might be lost in imaging methods relying on averaging proc ...

EPFL2022

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

Zander Harteveld

The sheer size of the protein sequence space is massive: a protein of 100 residues can have 20^100 possible sequence combinations; and knowing that this exceeds the number of atoms in the universe, the chance of randomly discovering a stable new sequence w ...

EPFL2022

Organic semiconductors for light-mediated neuromodulation

Diego Ghezzi, Danashi Imani Medagoda

There is growing interest in organic semiconductor devices for light-mediated neuromodulation, such as for retinal stimulation. Here, the key working principles of these devices are discussed, as well as promising applications and outstanding challenges fo ...

SPRINGERNATURE2021

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions

Jaume Bonet Martinez

BackgroundStatistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we deco ...

2021

Method for generating variants of a protein

Patrick Daniel Barth

The present relates to a method for generating variants of a protein based on a native protein regulated by allosteric pathway, the method comprising: - i) providing 3D structures of the native protein; - ii) identifying at least one pair of coupled allost ...

2021

Method for generating variants of a protein

Patrick Daniel Barth

The present relates to a method for generating variants of a protein based on a native protein regulated by allosteric pathway, the method comprising:- i) providing 3D structures of the native protein;- ii) identifying at least one pair of coupled alloster ...

2021