Publications related to Protein-nanoparticle interactions: the effects of surface compositional and structural heterogeneity are scale dependent

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

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

Dilution versus fractionation: Separation technologies hyphenated with spICP-MS for characterizing metallic nanoparticles in aerosols

Andrea Testino, Christian Ludwig, Jian Wang, Tianyu Cen

The presence of metal salts has become one of the major limitations for measuring metallic nanoparticles (NPs) in single particle inductively coupled plasma mass spectrometry (spICP-MS). Their presence generates a background signal in spICP-MS that can be ...

2024

Second harmonic scattering of nanoparticles: A journey into the electrical double layer

Bingxin Chu

In aqueous solutions, a charged surface causes the redistribution of nearby ions. The ion layers formed are known as the electrical double layer (EDL), and are widespread in many systems involving electrochemistry, colloidal science, biomedicine, and energ ...

EPFL2024

Development of Hyphenated Analytical Techniques using spICP-MS for Online Characterization of Metallic Nanoparticles in Aerosols

Tianyu Cen

The presence of metallic nanoparticles (NPs) in aerosols has raised concern about their fate in the environment through natural processes and anthropological activities. The state-of-the-art technologies for direct aerosol characterization cannot reach rea ...

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

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

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

Long live(d) CsPbBr3 superlattices: colloidal atomic layer deposition for structural stability

Raffaella Buonsanti, Alexander Nicolas Chen, Philippe Benjamin Green, Victoria Lapointe

Superlattice formation afforded by metal halide perovskite nanocrystals has been a phenomenon of interest due to the high structural order induced in these self-assemblies, an order that is influenced by the surface chemistry and particle morphology of the ...

Royal Soc Chemistry2024

Palladium-based supramolecular assemblies: from complex structures to water-soluble anion-receptors

Sylvain Alexandre Marie Sudan

The combination of palladium salts and bipyridyl ligands can lead to the formation of a large variety of coordination complexes, with different shapes and sizes, displaying a very versatile host-guest chemistry. Increasing their structural complexity remai ...

EPFL2024

Plasmonic Nanostructures for Photocatalysis: Material, Photonic and Electronic Effects

Fateme Kiani Shahvandi

Plasmonic photochemistry has a large potential to replace energy-intensive chemical processes with low-temperature, low-pressure light-driven chemical reactions. Plasmonic nanostructures have emerged as promising photocatalysts with exceptional and tunable ...

EPFL2024

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

Plasmonically enhanced molecular junctions for investigation of atomic-scale fluctuations in self-assembled monolayers

Sakthi Priya Amirtharaj

Molecular junctions represent a fascinating frontier in the realm of nanotechnology and are one of the smallest optoelectronic devices possible, consisting of individual molecules or a group of molecules that serve as the active element sandwiched between ...

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

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

Effects of Hyporheic Exchange and Settlement on the Particle Size Distribution of Colloids

David Andrew Barry, Qihao Jiang

Colloid particle size plays an important role in contaminant adsorption and clogging in the hyporheic zone, but it remains unclear how the particle size changes during the transport of colloids. This study investigated the variation of the particle size of ...

Springer2024

The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation

Andrea Ablasser, Baptiste Claude André Guey, Jonathan Jean-Pierre Ricci, Pauline Ambre Melenec, Ying Liu, Pengbiao Xu, Chong Liu, Lingyun Li

Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2 ' 3 '-cyclic GMP-AMP (cGAMP)1-7. The indiscriminate activity of cGAS towards DNA d ...

Nature Portfolio2024

A chemical biology approach to decipher chromatin ubiquitylation by RNF168

Pauline Franz

DNA damage signaling following DNA double-strand breaks (DSBs) involves numerous regulating proteins, which dynamically recognize ('read') and alter ('write' or 'erase') histone post-translational modifications (PTMs). Among these PTMs, the ubiquitin syste ...

EPFL2024

Virucidal compounds and use thereof

Francesco Stellacci, Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui, Corey Alfred Stevens, Lukasz Richter, Francesca Olgiati, Chiara Medaglia

Disclosed herein are peptide-grafted compounds that irreversibly deactivate bacteriophages or influenza virus depending on the peptide and remain safe for bacteria and mammalian cells. The active compounds comprise a core (cyclodextrin or gold nanoparticle ...

2024