Publications related to Solution behavior of peptide and peptide-hybrid materials

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

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

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

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

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

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

Anthony Marchand

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 ...

EPFL2024

The Structural Dispersity of Oligoethylene Glycol-Containing Polymer Brushes Determines Their Interfacial Properties

Harm-Anton Klok, Alberto Ongaro, Irene Filipucci

Ought to their bioinert properties and facile synthesis, poly[(oligoethylene glycol)methacrylate]s (POEGMAs) have been raised as attractive alternatives to poly(ethylene glycols) (PEGs) in an array of (bio)material applications, especially when they are ap ...

Amer Chemical Soc2024

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

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

A Versatile Approach to Stabilize Liquid-Liquid Interfaces using Surfactant Self-Assembly

Julian Charles Shillcock

Stabilizing liquid-liquid interfaces, whether between miscible or immiscible liquids, is crucial for a wide range of applications, including energy storage, microreactors, and biomimetic structures. In this study, a versatile approach for stabilizing the w ...

Wiley-V C H Verlag Gmbh2024

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

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

Influence of Amino Acid Substitutions in Capsid Proteins of Coxsackievirus B5 on Free Chlorine and Thermal Inactivation

Tamar Kohn, Shotaro Torii, Aleksandar Antanasijevic, Kiruthika Kumar

The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, although the effect of individual substitutions remains unknown. Here, we employed reverse genetics to inv ...

2024

Controlled Formation of Nanoribbons and Their Heterostructures via Assembly of Mass-Selected Inorganic Ions

Klaus Kern

Control of nanomaterial dimensions with atomic precision through synthetic methods is essential to understanding and engineering of nanomaterials. For single-layer inorganic materials, size and shape controls have been achieved by self-assembly and surface ...

Wiley-V C H Verlag Gmbh2024

Methods for high-throughput synthesis and screening of peptide libraries

Zsolt Bognár

Macrocycles provide an attractive modality for drug development but the identification of ligands to targets of interest is hindered by the lack of large macrocyclic compound libraries for high-throughput screening. A strategy to efficiently synthesize lar ...

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

Nanogels with Metal‐Organic Cages as Functional Crosslinks

Kay Severin, Chaolei Hu

A dinuclear metal-organic cage with four acrylate side chains was prepared by self-assembly. Precipitation polymerization of the cage with N-isopropylacrylamide yielded a thermoresponsive nanogel. The host properties of the cage were retained within the ge ...

Wiley-VCH Verlag GmbH2024

Soft Mechanochemistry of Disulfide-Crosslinked Polymer Networks

Zhao Meng

Mechanochemistry harnesses mechanical force to facilitate chemical reactions. Traditionally, the field of polymer mechanochemistry has used methods to activate chemical bonds, which use forces that are larger than those that are required to break a covalen ...

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

Solid-phase peptide synthesis in 384-well plates

Christian Heinis, Gontran Sangouard, Mischa Schüttel, Sevan Mleh Habeshian, Edward Jeffrey Will, Alexander Lund Nielsen, Anne Sofie Luise Zarda

Newer solid-phase peptide synthesis and release strategies enable the production of short peptides with high purity, allowing direct screening for desired bioactivity without prior chromatographic purification. However, the maximum number of peptides that ...

2024