Unité du Prof. Dal Peraro

Laboratoire

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

STARD4 regulates cholesterol homeostasis by transferring cholesterol between the plasma membrane and endoplasmic reticulum. The STARD4 structure features a helix-grip fold surrounding a large hydrophobic cavity holding the sterol. Its access is controlled ...

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 ...

Over the past two decades, protein S-acylation (often referred to as S-palmitoylation) has emerged as an important regulator of vital signalling pathways. S-Acylation is a reversible post-translational modification that involves the attachment of a fatty a ...

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 ...

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, ...

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 ...

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 ...

The remarkable adaptability observed in marine ecosystems has often inspired researchers when developing new soft materials. The research undertaken in this thesis explores how ion chelator pair interactions influence the mechanical properties of bioinspir ...

Atomic force microscopy (AFM) is a widely used imaging tool for obtaining a variety of information for a range of samples. Although it was initially intended to serve as a method of observing very flat solid surfaces, its use expanded into several other fi ...

Cells have evolved endocytic pathways to internalize different molecules, to regulate intra-cellular communication and their interaction with external environment. Pathogens have co-evolved with cells to exploit these processes for infections. In particula ...

Patterned membranes prepared via spray-modified non -solvent induced phase separation (s-NIPS) have successfully shown enhanced fluxes and better fouling control, thanks to the increased surface area and high fluid shear at the membrane/feed interface. The ...

Macrocycles offer an attractive format for drug development due to their good binding properties and potential to cross cell membranes. To efficiently identify macrocyclic ligands for new targets, methods for the synthesis and screening of large combinator ...

Machine learning has provided a means to accelerate early-stage drug discovery by combining molecule generation and filtering steps in a single architecture that leverages the experience and design preferences of medicinal chemists. However, designing mach ...

Unité du Prof. Dal Peraro

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Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

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

Computational drug development for membrane protein targets

Predicting protein interactions using geometric deep learning on protein surfaces

Opportunities and challenges in design and optimization of protein function

Microsecond Time-Resolved Cryo-Electron Microscopy

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Membrane specificity of the human cholesterol transfer protein STARD4

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

Mechanisms and functions of protein S-acylation

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

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

Microsecond time-resolved cryo-electron microscopy

Structural heterogeneity of the ion and lipid channel TMEM16F

From Surfactants to 3D Printing: How Ion-Chelator Pair Interactions Affect the Mechanical Properties of Bioinspired Materials

Advancements in Nanomechanical Characterization and Biomolecular Imaging with Atomic force Microscopy

S-acylation and lipid exchange at the ER-Golgi membrane contact sites regulate pathogen entry in human cells

Influence of micro-patterned support properties and interfacial polymerization conditions on performance of patterned thin-film composite membranes

Large Libraries of Structurally Diverse Macrocycles Suitable for Membrane Permeation

Machine learning-aided generative molecular design