Publications related to Broad-Band Ultraviolet CD Spectroscopy of Ultrafast Peptide Backbone Conformational Dynamics

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 ...

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

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

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

Indication of 310-Helix Structure in Gas-Phase Neutral Pentaalanine

Vasyl Yatsyna

We investigate the gas-phase structure of the neutral pentaalanine peptide. The IR spectrum in the 340-1820 cm-1 frequency range is obtained by employing supersonic jet cooling, infrared multiphoton dissociation, and vacuum-ultraviolet action spectroscopy. ...

AMER CHEMICAL SOC2023

Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis

Andreas Füglistaler, Aurélien Laurent Jean-Charles Oggier, Mahdi Hijazi, Patrick Daniel Barth, Robert Everett Jefferson, Ana Paola Rico Villarreal

Engineering protein biosensors that sensitively respond to specific biomolecules by triggering precise cellular responses is a major goal of diagnostics and synthetic cell biology. Previous biosensor designs have largely relied on binding structurally well ...

Nature Research2023

Dielectric Tetramer Nanoresonators Supporting Strong Superchiral Fields for Vibrational Circular Dichroism Spectroscopy

Hatice Altug, Yasaman Jahani, Bang Hyun Lee, Ming-Lun Tseng, Rui Lu, Longfang Ye, Felix Ulrich Richter

Chirality (C) is a fundamental property of objects, in terms of symmetry. It is extremely important to sense and distinguish chiral molecules in the fields of biochemistry, science, and medicine. Vibrational circular dichroism (VCD) spectroscopy, obtained ...

Amer Chemical Soc2023

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

Andrei Zviagin

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

EPFL2023

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

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

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

Hard X-ray helical dichroism of disordered molecular media

Majed Chergui, Jérôme Lacour, Christian David, Giulia Fulvia Mancini, Malte Oppermann, Dominik Kinschel, Oliviero Cannelli, Camila Bacellar Cases Da Silveira

Chirality is a structural property of molecules lacking mirror symmetry that has strong implications in diverse fields, ranging from life sciences to materials science. Chirality-sensitive spectroscopic methods, such as circular dichroism, exhibit weak sig ...

Nature Publishing Group2022

Amplitude and phase reconstruction for Low-Energy Electron Holography of individual proteins

Hannah Julia Ochner

Single-molecule imaging methods are of importance in structural biology, and specifically in the imaging of proteins, since they can elucidate conformational variability and structural changes that might be lost in imaging methods relying on averaging proc ...

EPFL2022

Molten globule-like transition state of protein barnase measured with calorimetric force spectroscopy

Sebastian James Davis

Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native conformation of glob ...

National Academy of Sciences2022

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

Stefano Zamuner

Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference ...

PUBLIC LIBRARY SCIENCE2022

Plasmonic nanobar-on-mirror antenna with giant local chirality: a new platform for ultrafast chiral single-photon emission

Wen Chen, Kai Wang

Providing an additional degree of freedom for binary information encoding and nonreciprocal information transmission, chiral single photons have become a new research frontier in quantum optics. Without using complex external conditions (e.g., magnetic fie ...

ROYAL SOC CHEMISTRY2022

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

Zander Harteveld

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 ...

EPFL2022

Magneto-optical study of metamagnetic transitions in the antiferromagnetic phase of alpha-RuCl3

Zhe Wang

alpha-RuCl3 is a promising candidate material to realize the so far elusive quantum spin liquid ground state. However, at low temperatures, the coexistence of different exchange interactions couple the effective pseudospins into an antiferromagnetically zi ...

NATURE PORTFOLIO2022

Binding affinity of p-PD-based schiff-bases towards human serum albumin; in-vitro and in-silico assessment

Kurt Schenk

The Schiff-bases [N,N'-Bis(2-hydroxybenzylidene)-benzene-1,4-diamine (L-1), N,N'-Bis(5-bromo-2-hydroxybenzylidene)-benzene-1,4-diamine (L-2), N,N'-Bis(2-hydroxy-3-methoxy-benzylidene)-benzene-1,4-diamine (L-3), and N,N'-Bis(2-hydroxynaphthylidene)-benzene- ...

ELSEVIER2022

Optical metasurfaces: synthesis, nanofabrication, and colorful applications

Hsiang-Chu Wang

In this thesis, we mainly utilize silver to construct the meta-atoms. Although suffering from easily oxidized, its excellent lossless property throughout the visible range makes it suitable for study. When preserved properly, silver-made metasurfaces can s ...

EPFL2022

Ultrafast carrier and quasiparticle dynamics in strongly confined perovskite nanoplatelets

Etienne Christophe Socie

Over the past decade, lead halide perovskites (LHPs) have received considerable attention thanks to their impressive optoelectronic properties. Today, LHP-based devices are one of the most efficient single-junction solar cells, with power-conversion effici ...

EPFL2022

Computationally designed GPCR quaternary structures bias signaling pathway activation

Patrick Daniel Barth, Robert Everett Jefferson

Communication across membranes controls critical cellular processes and is achieved by receptors translating extracellular signals into selective cytoplasmic responses. While receptor tertiary structures can be readily characterized, receptor associations ...

Nature Research2022