Publication
Methods to determine slow diffusion coefficients of biomolecules. Applications to Engrailed 2, a partially disordered protein
Publications associées (32)
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 ...
EPFL2024Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins
Scaffold-based protein libraries are designed to be both diverse and rich in functional/folded proteins. However, introducing an extended diversity while preserving stability of the initial scaffold remains a challenge. Here we developed an original approa ...
NATURE PORTFOLIO2023Fast viral dynamics revealed by microsecond time-resolved cryo-EM
Marcel Drabbels, Ulrich Lorenz, Sarah Victoria Barrass, Oliver Florian Harder
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 ...
2023Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions
The sheer size of the protein sequence space is massive: a protein of 100 residues can have 20^100 possible sequence combinations; and knowing that this exceeds the number of atoms in the universe, the chance of randomly discovering a stable new sequence w ...
EPFL2022A generic framework for hierarchical de novo protein design
Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Jaume Bonet Martinez, Fabian Sesterhenn, Stéphane Rosset, Che Yang
De novo protein design enables the exploration of novel sequences and structures absent from the natural protein universe. De novo design also stands as a stringent test for our understanding of the underlying physical principles of protein folding and may ...
NATL ACAD SCIENCES2022Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization
Matteo Dal Peraro, Luciano Andres Abriata
Continuous assessment of transferable forcefields for molecular simulations is essential to identify their weaknesses and direct improvement efforts. The latest efforts focused on better describing disordered proteins while retaining proper description of ...
2021Similarities and Differences among Protein Dynamics Studied by Variable Temperature Nuclear Magnetic Resonance Relaxation
David Lyndon Emsley, Jayasubba Reddy Yarava, Andrea Bertarello, Baptiste Busi, François Freymond
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 SOC2021MAS NMR Studies of Hierarchical Interplay in Protein Dynamics
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 ...
EPFL2021On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction
Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. We present RADI/raDIMod, a variation of the original DCA algorithm that grou ...
OXFORD UNIV PRESS2021Method for generating variants of a protein
The present relates to a method for generating variants of a protein based on a native protein regulated by allosteric pathway, the method comprising:- i) providing 3D structures of the native protein;- ii) identifying at least one pair of coupled alloster ...
2021