Publication

Mapping and classifying molecules from a high-throughput structural database

Publications associées (30)

Influence of Amino Acid Substitutions in Capsid Proteins of Coxsackievirus B5 on Free Chlorine and Thermal Inactivation

Tamar Kohn, Shotaro Torii, Aleksandar Antanasijevic, Kiruthika Kumar

The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, although the effect of individual substitutions remains unknown. Here, we employed reverse genetics to inv ...

2024

Insights from an extensive triaxial testing campaign on a shale for comparative site characterization of a deep geological repository

Lyesse Laloui, Alessio Ferrari, Eleonora Crisci

Several boreholes were drilled for site comparison of a deep geological repository (DGR) in Northern Switzerland. The main target of the exploration program was the >100m thick Opalinus Clay, the designated host rock encountered at approximately 450 to 100 ...

Elsevier2024

Fluorescent fatty acid conjugates for live cell imaging of peroxisomes

Luc Reymond, Manon Sandra Bardyn, Fabien Kuttler, Daria Korotkova, Triana Amen, Milena Maria Schuhmacher

Peroxisomes are eukaryotic organelles that are essential for multiple metabolic pathways, including fatty acid oxidation, degradation of amino acids, and biosynthesis of ether lipids. Consequently, peroxisome dysfunction leads to pediatric-onset neurodegen ...

Nature Research2024

Computational Homogenization for Inverse Design of Surface-based Inflatables

Mark Pauly, Francis Julian Panetta, Uday Kusupati, Yingying Ren, Florin Isvoranu, Seiichi Eduardo Suzuki Erazo

Surface-based inflatables are composed of two thin layers of nearly inextensible sheet material joined together along carefully selected fusing curves. During inflation, pressure forces separate the two sheets to maximize the enclosed volume. The fusing c ...

2024

A Biallelic Truncating Variant in the TPR Domain of GEMIN5 Associated with Intellectual Disability and Cerebral Atrophy

Nicolas Jean Philippe Guex

GEMIN5 is a multifunctional RNA-binding protein required for the assembly of survival motor neurons. Several bi-allelic truncating and missense variants in this gene are reported to cause a neurodevelopmental disorder characterized by cerebellar atrophy, i ...

2023

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Hamed Khakzad

Author summaryIn recent years, the application of deep learning represented a breakthrough in the mass spectrometry (MS) field by improving the assignment of the correct sequence of amino acids from observable MS spectra without prior knowledge, also known ...

PUBLIC LIBRARY SCIENCE2023

Hypervalent Iodine: New Reagents and Functionalization of Peptides

Eliott Hugo Joran Le Du

Alkynes are found in a multitude of natural or synthetic bioactive compounds. In addition to the capacity of these chemical motifs to impact the physicochemical properties of a molecule of interest, the well-established reactivity of alkynes makes them ide ...

EPFL2023

Computational Studies for the Design of Metalloenzyme Mimics

Guido Frisari

At present, there is no general standard automated method for engineering metalloenzymes, industrially-relevant systems able to catalyze environmentally friendly reactions. One of the most studied natural metalloenzymes is the second isoform of human carbo ...

EPFL2023

Single-Molecule Peptide Identification Using Fluorescence Blinking Fingerprints

Pablo Rivera Fuentes, Salome Riccarda Püntener

The ability to identify peptides with single-molecule sensitivity would lead to next-generation proteomics methods for basic research and clinical applications. Existing single-molecule peptide sequencing methods can read some amino acid sequences, but the ...

AMER CHEMICAL SOC2023

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

Molecular sensitised probe for amino acid recognition within peptide sequences

Klaus Kern, Stephan Rauschenbach, Uta Schlickum, Daniel Pablo Rosenblatt, Sabine Abb, Sebastian Koslowski

The combination of low-temperature scanning tunnelling microscopy with a mass-selective electro-spray ion-beam deposition established the investigation of large biomolecules at nanometer and sub-nanometer scale. Due to complex architecture and conformation ...

Nature Portfolio2023

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

Dissecting the role of the asparagine synthesis in acute liver injury

Yu Sun

Amino acids are some of the main building stones of life used in a variety of biological processes, such as protein synthesis, energy metabolism or even as precursors for hormone synthesis. How-ever, some of them also participate and coordinate certain cel ...

EPFL2022

Ring-Opening Reactions of Aminocyclopropanes and Aminocyclobutanes

Mingming Wang

Nitrogen-containing compounds are an important class of molecules in medicinal chemistry, chemical biology, biochemistry, material sciences or environmental sciences. Organic nitrogen occurs in many forms, ranging from small building blocks such as urea, a ...

EPFL2022

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

Reactions of amines with ozone and chlorine: Two novel oxidative methods to evaluate the N-DBP formation potential from dissolved organic nitrogen

Karim-Alexandre Essaied, Urs von Gunten, Lucy Victoria Brown

The composition of oxidant-reactive dissolved organic nitrogen (DON) is poorly characterized, although its ozonation is likely to form a great variety of disinfection by-products containing a nitrogen-oxygen bond (NDBPs). In this study, two chemical oxidat ...

PERGAMON-ELSEVIER SCIENCE LTD2022

N-Terminal Selective C-H Azidation of Proline-Containing Peptides: a Platform for Late-Stage Diversification

Jérôme Waser, Raphaël Michel Henri Simonet-Davin, Emmanuelle Madeline Dominique Allouche

A methodology for the C-H azidation of N-terminal proline-containing peptides was developed employing only commercially available reagents. Peptides bearing a broad range of functionalities and containing up to 6 amino acids were selectively azidated at th ...

2022

The capture technology matters: Composition of municipal wastewater solids drives complexity of microbial community structure and volatile fatty acid profile during anaerobic fermentation

Pierre Rossi, Arnaud Michel Gelb

The production of volatile fatty acids (VFAs) represents a relevant option to valorize municipal wastewater (MWW). In this context, different capture technologies can be used to recover organic carbon from wastewater in form of solids, while pre-treatment ...

2022

Small peptide diversification through photoredox-catalyzed oxidative C-terminal modification

Jérôme Waser, Eliott Hugo Joran Le Du, Marion Marie-Agnès Garreau

A photoredox-catalyzed oxidative decarboxylative coupling of small peptides is reported, giving access to a variety of N,O-acetals. They were used as intermediates for the addition of phenols and indoles, leading to novel peptide scaffolds and bioconjugate ...

2021

Novel inhibitors of kallikrein proteases and uses thereof

Christian Heinis, Alessandro Zorzi, Patrick Andreas Gonschorek

The present invention relates to a cyclic inhibitor of a kallikrein protease comprising or consisting of (I) the peptide (X1 (X2)(X3)R(X4)(X5)(X6)(X7)(X8)(X9)(X10)(X11) (Formula (X)), wherein (X1) is present or absent and, is preferably present, and if pre ...

2021