Publications associées à Long horizon input parameterisations to enlarge the region of attraction of MPC

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

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

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

Fast viral dynamics revealed by microsecond time-resolved cryo-EM

Marcel Drabbels, Ulrich Lorenz, Oliver Florian Harder, Sarah Victoria Barrass

Observing proteins as they perform their tasks has largely remained elusive, which has left our understanding of protein function fundamentally incom- plete. To enable such observations, we have recently proposed a technique that improves the time resoluti ...

Nature Research2023

Protein target highlights in CASP15: Analysis of models by structure providers

Bruno Lemaitre, Luciano Andres Abriata, Kuan-Lin Wu, Samuel Rommelaere, Han Xiao

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the su ...

WILEY2023

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

MAS NMR Studies of Hierarchical Interplay in Protein Dynamics

Baptiste Busi

The functionality of proteins is governed by the interplay between their structure and dynamics. Thus, understanding the mechanism and nature of protein motion is essential to understand their biological activity. Here we present and evaluate a novel metho ...

EPFL2021

Similarities and Differences among Protein Dynamics Studied by Variable Temperature Nuclear Magnetic Resonance Relaxation

François Freymond, David Lyndon Emsley, Jayasubba Reddy Yarava, Baptiste Busi, Andrea Bertarello

Understanding and describing the dynamics of proteins is one of the major challenges in biology. Here, we use multifield variable-temperature NMR longitudinal relaxation (R-1) measurements to determine the hierarchical activation energies of motions of fou ...

AMER CHEMICAL SOC2021

Rapid melting and revitrification as an approach to microsecond time-resolved cryo-electron microscopy

Marcel Drabbels, Ulrich Lorenz, Pavel Olshin, Jonathan Mark Voss, Oliver Florian Harder

Proteins typically undergo dynamics on the microsecond to millisecond timescale, which is much faster than the time resolution of cryo-electron microscopy. Here, we propose a novel approach for microsecond time-resolved cryo-electron microscopy that involv ...

Elsevier2021

Study of fast exchanging processes by NMR Spectroscopy

Estel Canet Martinez

Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful and informative methods to probe molecular dynamics. Specifically, chemical exchange is an important phenomenon and one of the earliest and most vigorously investigated in NMR spectr ...

EPFL2017

Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory

Luciano Andres Abriata

The understanding of protein evolution depends on the ability to relate the impact of mutations on molecular traits to organismal fitness. Biological activity and robustness have been regarded as important features in shaping protein evolutionary landscape ...

Oxford Univ Press2016

Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States

Alessandro Barducci

Molecular Dynamics (MD) plays a fundamental role in characterizing protein disordered states that are emerging as crucial actors in many biological processes. Here we assess the accuracy of three current force-fields in modeling disordered peptides by comb ...

Amer Chemical Soc2015

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

Matteo Dal Peraro, Luciano Andres Abriata

Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dime ...

Nature Publishing Group2015

Chromatin organization, transcription factor dynamics and gene expression in higher eukaryotes with superresolution imaging and single molecule tracking

Aleksandr Benke

Gene expression is dynamic and heterogeneous across all cell types. It serves several fundamental functions such as adaptation for changing environment and developing tissue specific phenotype and functionality during development and in adult organism. Con ...

EPFL2015

Real-Time Monitoring of Protein Conformational Changes Using a Nano-Mechanical Sensor

Giovanni Dietler, Paolo De Los Rios, Dusan Vobornik, Sandor Kasas, Livan Bladimir Alonso Sarduy, Fabrizio Benedetti, Giovanni Longo

Proteins can switch between different conformations in response to stimuli, such as pH or temperature variations, or to the binding of ligands. Such plasticity and its kinetics can have a crucial functional role, and their characterization has taken center ...

Public Library of Science2014

Multiscale simulations of protein dynamics

Enrico Spiga

Characteristic timescales associated with the function of biomolecules, like proteins, range from femtoseconds up to minutes, whereas their corresponding spatial extent ranges from few ̊A to μm when associating in large macromolecular complexes. Moreover, ...

EPFL2013

Mapping the Native Conformational Ensemble of Proteins from a Combination of Simulations and Experiments: New Insight into the src-SH3 Domain

Fabio Pietrucci

The biological function of a protein is strongly tied to the ensemble of three-dimensional conformations populated at physiological temperature, and dynamically transforming into each other. Experimental techniques such as nuclear magnetic resonance spectr ...

Amer Chemical Soc2013

Nanosecond Time Scale Motions in Proteins Revealed by High-Resolution NMR Relaxometry

Geoffrey Bodenhausen, Fabien Ferrage

Understanding the molecular determinants underlying protein function requires the characterization of both structure and dynamics at atomic resolution. Nuclear relaxation rates allow a precise characterization of protein dynamics at the Larmor frequencies ...

American Chemical Society2013

The allosteric communication pathways in KIX domain of CBP

Michele Parrinello, Alessandro Barducci

Allosteric regulation plays an important role in a myriad of bio-macromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the ...

National Academy of Sciences2013

Dynamic Studies through Control of Relaxation in NMR Spectroscopy

Nicola Salvi

In numerous biological processes that constitute the base of living organisms, protein function is fundamentally related to internal dynamics occurring on μs-ms time scales that can give rise to chemical exchange contributions to relaxation. In a heteronuc ...

EPFL2013

Insights into internal dynamics of 6-phosphogluconolactonase from Trypanosoma brucei studied by nuclear magnetic resonance and molecular dynamics

Geoffrey Bodenhausen, Daniel Abergel

Nuclear magnetic resonance is used to investigate the backbone dynamics in 6-phosphogluconolactonase from Trypanosoma brucei (Tb6PGL) with (holo-) and without (apo-) 6-phosphogluconic acid as ligand. Relaxation data were analyzed using the model-free appro ...

2012