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Related publications (23)

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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

First paleoproteome study of fossil fish otoliths and the pristine preservation of the biomineral crystal host

Anders Meibom, Jaroslaw Hubert Stolarski, Jinming Guo

Otoliths are calcium carbonate components of the stato-acoustical organ responsible for hearing and maintenance of the body balance in teleost fish. During their formation, control over, e.g., morphology and carbonate polymorph is influenced by complex ins ...

Nature Portfolio2023

Structure of a membrane-bound menaquinol:organohalide oxidoreductase

Christof Holliger, Henning Paul-Julius Stahlberg, Julien Maillard, Dongchun Ni, Lorenzo Cimmino, Babatunde Edukpe Ekundayo

Organohalide-respiring bacteria are key organisms for the bioremediation of soils and aquifers contaminated with halogenated organic compounds. The major players in this process are respiratory reductive dehalogenases, corrinoid enzymes that use organohali ...

Nature Research2023

Biological nanopores for single-molecule sensing

Matteo Dal Peraro, Chan Cao, Simon Finn Mayer

Evolution has found countless ways to transport material across cells and cellular compartments separated by membranes. Protein assemblies are the cornerstone for the formation of channels and pores that enable this regulated passage of molecules in and ou ...

Cell Press2022

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Anne-Florence Raphaëlle Bitbol

Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...

Nature Portfolio2022

High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica

Henning Paul-Julius Stahlberg

Urease converts urea into ammonia and carbon dioxide and makes urea available as a nitrogen source for all forms of life except animals. In human bacterial pathogens, ureases also aid in the invasion of acidic environments such as the stomach by raising th ...

Nature Research2020

The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase

Yimon Aye, Alexandra Krina Van Hall-Beauvais

Stereotyped as a nexus of dNTP synthesis, the dual-subunit enzyme - ribonucleotide reductase (RNR) - is coming into view as a paradigm of oligomerization and moonlighting behavior. In the present issue of `omics', we discuss what makes the larger subunit o ...

ELSEVIER SCI LTD2020

Photons in - numbers out: perspectives in quantitative fluorescence microscopy for in situ protein counting

Kristin Stefanie Grussmayer

The full understanding of cellular functions requires information about protein numbers for various biomolecular assemblies and their dynamics, which can be partly accessed by super-resolution fluorescence microscopy. Yet, many protein assemblies and cellu ...

2019

A ligand-based system for receptor-specific delivery of proteins

Kai Johnsson, Luc Reymond

Gene delivery using vector or viral-based methods is often limited by technical and safety barriers. A promising alternative that circumvents these shortcomings is the direct delivery of proteins into cells. Here we introduce a non-viral, ligand-mediated p ...

Springer Nature2019

In situ Studies of Peptide and Protein Assemblies at the Solid-Liquid Interface : Hierarchical Self-Assembly, Dynamics and Functional Properties

Bart Willem Stel

At the interface between science and engineering, there is the field of biomimicry: Innovations inspired by the observation of natural, evolutionary optimized biological structures and processes. To understand the challenges of biomimicry, the concept of â ...

EPFL2018

Nuclear RNR-alpha antagonizes cell proliferation by directly inhibiting ZRANB3

Since the origins of DNA-based life, the enzyme ribonucleotide reductase (RNR) has spurred proliferation because of its rate-limiting role in de novo deoxynucleoside-triphosphate (dNTP) biosynthesis. Paradoxically, the large subunit, RNR-alpha, of this obl ...

2018

PdII2L4-type coordination cages up to three nanometers in size

Rosario Scopelliti, Kay Severin, Suzanne Maria Jansze, Matthew David Wise

The utilization of large ligands in coordination-based self-assembly represents an attractive strategy for the construction of supramolecular assemblies more than two nanometers in size. However, the implementation of this strategy is hampered by the fact ...

2017

Computational Investigation of Intracellular Signalling Cascades : from G-Protein-Coupled Receptors to Adenylyl Cyclase

Siri Camee van Keulen

In order to adjust to changes in the environment, cells can communicate via signalling cascades. A common pathway for intercellular communication is the G-protein-coupled- receptor (GPCR) signal transduction cascade which is triggered by a (chemical or phy ...

EPFL2017

An Intein-based Strategy for the Production of Tag-free Huntingtin Exon 1 Proteins Enables New Insights into the Polyglutamine Dependence of Httex1 Aggregation and Fibril Formation

Hilal Lashuel, Annalisa Ansaloni, Sophie Vieweg, John Blaine Warner IV

The first exon of the Huntingtin protein (Httex1) is one of the most actively studied Htt fragments because its overexpression in R6/2 transgenic mice has been shown to recapitulate several key features of Huntington disease. However, the majority of bioph ...

Amer Soc Biochemistry Molecular Biology Inc2016

The centriolar protein CPAP G-box: an amyloid fibril in a single domain

Georgios Hatzopoulos

Centrioles are evolutionarily conserved cylindrical cell organelleswith characteristic radial symmetry. Despite their considerable size (400 nm x 200 nm, in humans), genetic studies suggest that relatively few protein components are involved in their assem ...

Portland Press Ltd2015

PDB-Explorer: a web-based interactive map of the protein data bank in shape space

Luc Patiny, Michaël Giuseppe Zasso, Daniel Kostro

Background: The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the ...

Biomed Central Ltd2015

Viability evolutionary algorithms and applications to neuroscience and biology

Evolutionary algorithms are heuristic methods that operate on a population of individuals, which represent candidate solutions to optimization problems. Individuals with better quality, or fitness, are reproduced at a higher rate than less fit individuals ...

EPFL2015

The mitochondrial unfolded protein response - synchronizing genomes

Johan Auwerx, Virginija Jovaisaite

Maintenance of the mitochondrial proteome is performed primarily by chaperones, which fold and assemble proteins, and by proteases, which degrade excess damaged proteins. Upon various types of mitochondrial stress, triggered genetically or pharmacologicall ...

Current Biology Ltd2015

Peptide-Polymer Conjugates for Therapeutic Applications

Ana Maria Raduta

Over the last ten years the attention of the pharmaceutical industry has shifted away from small molecules to focus on new biologics such as antibodies, proteins and therapeutic peptides. Herein, peptides have emerged as a particularly interesting category ...

EPFL2015

Revealing GPCR oligomerization at the single-molecule level through a nanoscopic lens: methods, dynamics and biological function

Aleksandra Radenovic, Paolo Annibale, Marco Scarselli

The introduction of super-resolution fluorescence microscopy has allowed the visualization of single proteins in their biological environment. Recently, these techniques have been applied to determine the organization of class A G-protein-coupled receptors ...

Wiley-Blackwell2015