Publications associées à Protein dynamics

Structural heterogeneity of the ion and lipid channel TMEM16F

Transmembrane protein 16 F (TMEM16F) is a Ca2+-activated homodimer which functions as an ion channel and a phospholipid scramblase. Despite the availability of several TMEM16F cryogenic electron microscopy (cryo-EM) structures, the mechanism of activation ...

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

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

Fast 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 ...

Nature Research2023

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

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

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

Systems and methods for de novo design of protein interactions with learned surface fingerprints

Andreas Scheck, Michael Bronstein, Anthony Marchand, Pablo Gainza Cirauqui, Zander Harteveld, Sarah Wehrle, Freyr Sverrisson, Alexandra Krina Van Hall-Beauvais

The present application relates to a computer-implemented systems and methods for protein interaction design using surface fingerprints. The method comprises predicting at least one target interface site with high binding propensity, wherein, optionally, t ...

2023

Deep learning approaches for conformational flexibility and switching properties in protein design

Patrick Daniel Barth, Lucas Sebastian Powell-Rudden, Mahdi Hijazi

Following the hugely successful application of deep learning methods to protein structure prediction, an increasing number of design methods seek to leverage generative models to design proteins with improved functionality over native proteins or novel str ...

2022

J-domain protein chaperone circuits in proteostasis and disease

Paolo De Los Rios, Duccio Malinverni, Ruobing Zhang

The J-domain proteins (JDP) form the largest protein family among cellular chaperones. In cooperation with the Hsp70 chaperone system, these co-chaperones orchestrate a plethora of distinct functions, including those that help maintain cellular proteostasi ...

ELSEVIER SCIENCE LONDON2022

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Andonis Samuel Rene Gerardos

Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families ...

Public Library Science2022