Publications associées à Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies

Palladium-based supramolecular assemblies: from complex structures to water-soluble anion-receptors

The combination of palladium salts and bipyridyl ligands can lead to the formation of a large variety of coordination complexes, with different shapes and sizes, displaying a very versatile host-guest chemistry. Increasing their structural complexity remai ...

EPFL2024

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Lucien Fabrice Krapp

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

EPFL2023

Antenna-coupled infrared nanospectroscopy of intramolecular vibrational interaction

Felipe Herrera, Hatice Altug, Aurélian Michel John-Herpin

Many photonic and electronic molecular properties, as well as chemical and biochemical reactivities are controlled by fast intramolecular vibrational energy redistribution (IVR). This fundamental ultrafast process limits coherence time in applications from ...

National Academy of Sciences2023

Targeting molecular surfaces to engineer novel protein-based immunogens and inhibitors

Sarah Wehrle

Proteins are the basic building blocks necessary for the operation and regulation of virtually all functions in living organisms. Over millions of years, evolution has created a vast repertoire of proteins finely tuned to execute their biological functions ...

EPFL2022

Phase Reconstruction of Low-Energy Electron Holograms of Individual Proteins

Klaus Kern, Stephan Rauschenbach, Sven Alexander Szilagyi, Hannah Julia Ochner

Low-energy electron holography (LEEH) is one of the few techniques capable of imaging large and complex three-dimensional molecules, such as proteins, on the single molecule level at subnanometer resolution. During the imaging process, the structural infor ...

AMER CHEMICAL SOC2022

A universal workflow for creation, validation and generalization of detailed neuronal models

Henry Markram, Srikanth Ramaswamy, Alexis Arnaudon, Werner Alfons Hilda Van Geit, Christian Andreas Rössert, Mustafa Anil Tuncel, Tanguy Pierre Louis Damart, Maria Reva, Darshan Mandge

Detailed single neuron modeling is widely used to study neuronal functions. While cellular and functional diversity across the mammalian cortex is vast, most of the available computational tools are dedicated to the reproduction of a small set of specific ...

Cambridge2023

New Methods for the Integrative Dynamic Modeling of Biomolecular Structures

Sylvain Träger

The true understanding of most cellular functions is only really achievable through the structural determination of their underlying macromolecular assemblies. However, their size, large number of individual components and metastable states make their eluc ...

EPFL2021

Half-clathrochelate Complexes as Versatile Links in Supramolecular Chemistry

Erica Giraldi

Clathrochelate complexes have been widely investigated with different size and shape and used as building blocks for the obtainment of discrete supramolecular architectures. These clathrochelate complexes are very stable and kinetically inert complexes. A ...

EPFL2021

Fast end-to-end learning on protein surfaces

Bruno Emanuel Ferreira De Sousa Correia, Freyr Sverrisson

Proteins' biological functions are defined by the geometric and chemical structure of their 3D molecular surfaces. Recent works have shown that geometric deep learning can be used on mesh-based representations of proteins to identify potential functional s ...

IEEE COMPUTER SOC2021

Structural and analytical identifications of biomolecules by cold ion spectroscopy of non-covalent complexes

Erik Saparbayev

Non-covalent interactions are ubiquitous in nature. The diversity and functionality of these interactions are employed by nature as a universal tool for building the molecular mechanism of life. Although weak, these interactions play a key role in both for ...

EPFL2021

Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly

Tatiana Favez, Pierre Gönczy, Virginie Hamel, Santiago Harald Andany, Georg Fantner, Oliver Hantschel, Georgios Hatzopoulos, Niccolo Banterle

Centrioles are evolutionarily conserved multi-protein organelles essential for forming cilia and centrosomes. Centriole biogenesis begins with self-assembly of SAS-6 proteins into 9-fold symmetrical ring polymers, which then stack into a cartwheel that sca ...

Nature Research2021

3D Structure From 2D Microscopy Images Using Deep Learning

Suliana Manley, Christian Sieben

Understanding the structure of a protein complex is crucial in determining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional. Recent advances i ...

Frontiers Media Sa2021

Structural Order of the Molecular Adlayer Impacts the Stability of Nanoparticle-on-Mirror Plasmonic Cavities

Magalí Alejandra Lingenfelder, Christophe Marcel Georges Galland, Fernando Pablo Cometto, Karla Banjac, Aqeel Ahmed, Sachin Suresh Verlekar

Immense field enhancement and nanoscale confinement of light are possible within nanoparticle-on-mirror (NPoM) plasmonic resonators, which enable novel optically activated physical and chemical phenomena and render these nanocavities greatly sensitive to m ...

AMER CHEMICAL SOC2021

Cyclic thermomechanical behaviour of pile-soil interface and design methods for energy pile foundations

Elena Ravera

Energy piles are shallow geothermal systems integrated into structures already required for structural functions of civil works that provide both geothermal energy supply and structural support to the built environments. This research work is driven by the ...

EPFL2021

Protein Structural Information and Evolutionary Landscape by In Vitro Evolution

Paolo De Los Rios

Protein structure is tightly intertwined with function according to the laws of evolution. Understanding how structure determines function has been the aim of structural biology for decades. Here, we have wondered instead whether it is possible to exploit ...

OXFORD UNIV PRESS2020

Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction?

Matteo Dal Peraro, Luciano Andres Abriata

Protein dynamics is undoubtedly a pervasive ingredient in all biological functions. However, structural biology has been strongly driven by a static-centered view of protein architecture. We argue that the recent advances of cryo-electron microscopy (EM) h ...

AMER CHEMICAL SOC2020

The role of xanthophylls in the supramolecular organization of the photosynthetic complex LHCII in lipid membranes studied by high-resolution imaging and nanospectroscopy

Giovanni Dietler, Serguei Sekatski, Jiangtao Zhou

The xanthophyll cycle is a regulatory mechanism operating in the photosynthetic apparatus of plants. It consists of the conversion of the xanthophyll pigment violaxanthin to zeaxanthin, and vice versa, in response to light intensity. According to the curre ...

ELSEVIER2020

Soft matter probed by nonlinear scattering: self-assembly, interfaces, hydration, and long-range order

Jan Dedic

All organisms are made to a large extent of soft matter - macromolecules such as proteins and polysaccharides, or assemblies of small molecules such as lipids embedded in an aqueous environment. Understanding the role of order in soft matter presents a cha ...

EPFL2020

The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards

Jeffrey David Jensen, Kristen Kay Irwin, Stefan Jean Laurent, Susanne Petra Pfeifer

By combining well-established population genetic theory with high-throughput sequencing data from natural populations, major strides have recently been made in understanding how, why, and when vertebrate populations evolve crypsis. Here, we focus on backgr ...

NATURE PUBLISHING GROUP2020

Functional de novo Protein Design for Targeted Vaccines and Synthetic Biology Applications

Che Yang

Evolution has created, selected and evolved large repertoires of proteins that operate in various biological systems. Nowadays biotechnological needs are coming up orders of magnitude faster than proteins naturally evolve. The emergence of de novo protein ...

EPFL2020