Publications associées à A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

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

Predicting protein interactions using geometric deep learning on protein surfaces

Freyr Sverrisson

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

Microsecond Time-Resolved Cryo-Electron Microscopy

Oliver Florian Harder

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

EPFL2024

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

Ursula Röthlisberger, Justin Villard, Martin Peter Bircher

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, wit ...

Royal Soc Chemistry2024

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

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

Ion Spectroscopy Reveals Structural Difference for Proteins Microhydrated by Retention and Condensation of Water

Oleg Boyarkine, Andrei Zviagin

Protein ubiquitin in its +7 charge state microhydrated by 5 and 10 water molecules has been interrogated in the gas phase by cold ion UV/IR spectroscopy. The complexes were formed either by condensing water onto the unfolded bare proteins in a temperature- ...

Amer Chemical Soc2024

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Felix Naef, Pierre Vandergheynst, Cédric Gobet, Mohan Vamsi Nallapareddy, Francesco Craighero

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

Osmosis-driven stiffening of structured hydrogels

Esther Amstad, Ran Zhao, Alexandra Thoma

Plant cells harness osmotic pressures to stiffen their leaves through strong turgor pressures. Key to this osmosisdriven stiffening is the confinement of liquids within semipermeable membranes that can regulate the transport of water molecules and ions. In ...

Elsevier2024

Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Hydrostatic Pressure Stimuli

Yanheng Guo

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

EPFL2024

Development of tools and methods for protein identification: From single molecules to in vivo applications

Salome Riccarda Püntener

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

EPFL2024

FLO:RE – A new floor system made of reused reinforced concrete and steel elements

Maléna Bastien Masse, Numa Joy Bertola, Célia Marine Küpfer, Corentin Jean Dominique Fivet

Carefully extracting reinforced concrete (RC) elements from soon-to-be demolished structures and reusing them as load-bearing components is an emerging circular low-carbon alternative to building new structures. As floor construction typically accounts for ...

IABSE2024

Computational drug development for membrane protein targets

Henning Paul-Julius Stahlberg, Pierre Vogel, Shuguang Yuan, Dongchun Ni, Babatunde Edukpe Ekundayo

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

2024

A global framework for data-informed bridge examination

Eugen Brühwiler, Philippe Schiltz, Numa Joy Bertola

Examining the performance of an existing bridge requires information on several aspects, such as design choices, material properties, and ongoing degradation processes. It often happens that some critical information is not available. The traditional appro ...

2024

Verification of the Fourier-enhanced 3D finite element Poisson solver of the gyrokinetic full-f code PICLS

Stephan Brunner, Laurent Villard, Alberto Bottino, Moahan Murugappan

We introduce and derive the Fourier -enhanced 3D electrostatic field solver of the gyrokinetic full -f PIC code PICLS. The solver makes use of a Fourier representation in one periodic direction of the domain to make the solving of the system easily paralle ...

Elsevier2024

Microsecond time-resolved cryo-electron microscopy

Ulrich Lorenz

Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing protein dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide range of dynamics tha ...

2024

Monitoring an Emergent Pathogen at Low Incidence in Wastewater Using qPCR: Mpox in Switzerland

Tamar Kohn, Timothy R. Julian

Wastewater-based epidemiology offers a complementary approach to clinical case-based surveillance of emergent diseases and can help identify regions with infected people to prioritize clinical surveillance strategies. However, tracking emergent diseases in ...

2024

Dual-frame optimization for informationally complete quantum measurements

Ivano Tavernelli

Randomized measurement protocols such as classical shadows represent powerful resources for quantum technologies, with applications ranging from quantum state characterization and process tomography to machine learning and error mitigation. Recently, the n ...

2024

Influence of model uncertainty and long term deformations in action effects calculation in reinforced concrete structures

Xhemsi Malja

Most codes of practice adopt a semi probabilistic design approach for the dimensioning and assessment of structures. Accordingly, structural safety is ensured by performing limit state verifications using design values determined with adequately calibrated ...

EPFL2024