Concept

Conformational ensembles

Related publications (51)

Structural Insights into Electrophiles and Electrophilic Metabolites Sensing and Signaling: The Missing Information

Native reactive electrophilic species (RES) are long-recognized regulators of pathophysiology; yet, knowledge surrounding how RES regulate context-specific biology remains limited. The latest technological advances in profiling and precision decoding of RE ...

WILEY-V C H VERLAG GMBH2023

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

Patrick Daniel Barth, 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

New Methods for the Integrative Dynamic Modeling of Biomolecular Structures

Sylvain Träger

The true understanding of most cellular functions is only really achievable through the structural determination of their underlying macromolecular assemblies. However, their size, large number of individual components and metastable states make their eluc ...

EPFL2021

Low-energy electron holography imaging of conformational variability of single-antibody molecules from electrospray ion beam deposition

Klaus Kern, Stephan Rauschenbach, Sabine Abb, Sven Alexander Szilagyi, Hannah Julia Ochner

Imaging of proteins at the single-molecule level can reveal conformational variability, which is essential for the understanding of biomolecules. To this end, a biologically relevant state of the sample must be retained during both sample preparation and i ...

NATL ACAD SCIENCES2021

Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization

Matteo Dal Peraro, Luciano Andres Abriata

Continuous assessment of transferable forcefields for molecular simulations is essential to identify their weaknesses and direct improvement efforts. The latest efforts focused on better describing disordered proteins while retaining proper description of ...

2021

Exploring the Molecular Conformation Space by Soft Molecule- Surface Collision

Klaus Kern, Stephan Rauschenbach, Sabine Abb

Biomolecules function by adopting multiple conformations. Such dynamics are governed by the conformation landscape whose study requires characterization of the ground and excited conformation states. Here, the conformational landscape of a molecule is samp ...

AMER CHEMICAL SOC2020

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

Majed Chergui, Malte Oppermann, Benjamin Bauer

The far-UV spectral window widely used for the conformational analysis of biomolecules is not easily covered with broad-band lasers. This has made it difficult to use circular dichroism (CD) spectroscopy to directly follow fast structure changes. By combin ...

AMER CHEMICAL SOC2019

Can Mutational Analysis Be Used To Assist Structure Determination of Peptides?

Thomas Rizzo, Valeriu Scutelnic, Chiara Masellis, Liudmila Voronina

Mutational analysis is widely used to study the relationship between sequence and structure of proteins and peptides. It is often assumed that substituting a proline with another amino acid "locks" the peptide bond in the trans conformation, allowing only ...

2018

An Automatic, Data-Driven Definition of Atomic-Scale Structural Motifs

Piero Gasparotto

Structure-property relationships at the atomic scale are usually understood in terms of recurrent structural motifs formed by atoms and molecules, and how they transform and interact with each other. We introduce with this thesis a novel analysis approach, ...

EPFL2018

Nanoplasmonic mid-infrared biosensor for in vitro protein secondary structure detection

Giovanni Dietler, Hilal Lashuel, Hatice Altug, Francesco Simone Ruggeri, Dordaneh Etezadi, John Blaine Warner IV

Plasmonic nanoantennas offer new applications in mid-infrared (mid-IR) absorption spectroscopy with ultrasensitive detection of structural signatures of biomolecules, such as proteins, due to their strong resonant near-fields. The amide I fingerprint of a ...

Springer Nature2017

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