Publications associées à Biomolecular structure

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

Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero, Mohan Vamsi Nallapareddy

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

Bioengineered Tubular Biliary Organoids

Matthias Lütolf, Mikhail Nikolaev, Bilge Sen Elçi, Saba Rezakhani

Liver organoids have emerged as promising in vitro models for toxicology, drug discovery, and disease modeling. However, conventional 3D epithelial organoid culture systems suffer from significant drawbacks, including limited culture duration, a nonphysiol ...

Wiley2024

Searching for the Thinnest Metallic Wire

Nicola Marzari, Davide Campi

One-dimensional materials have gained much attention in the last decades: from carbon nanotubes to ultrathin nanowires to few-atom atomic chains, these can all display unique electronic properties and great potential for next-generation applications. Exfol ...

Amer Chemical Soc2024

Secondary structure of the human mitochondrial genome affects formation of deletions

Jacques Fellay, Konstantin Popadin

BackgroundAging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain ...

BMC2023

Nanopore-based scanning system and method

Aleksandra Radenovic, Georg Fantner, Vytautas Navikas, Samuel Mendes Leitão

Nanopore-based scanning system including a probe structure comprising a nanopore; suction means configured to draw an end of a (bio)molecule inside the nanopore and inside the probe structure, single or multiple times; and displacement means configured to ...

2023

Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy

Marta Di Fabrizio

All coronaviruses are characterized by spike glycoproteins whose S1 subunits contain the receptor binding domain (RBD). The RBD anchors the virus to the host cellular membrane to regulate the virus transmissibility and infectious process. Although the prot ...

MDPI2023

Computational conceptual design — typological exploration of spatial truss systems through optimization

Corentin Jean Dominique Fivet, Jonas Warmuth, Pierluigi D'Acunto

Exploring a wide range of design options is crucial for every sound conceptual design process. In the conventional structural design workflow, optimization techniques are generally employed to generate well-performing design options. However, focusing only ...

International Association for Shell and Spatial Structures (IASS)2023

Advancing Glycan Analysis: Cryogenic Ion Spectroscopy for Database-Driven Identification

Ali H Abikhodr

Glycans play a pivotal role in both physiological processes; however, the field of glycobiology remains relatively understudied within biochemistry. The intricate complexity of glycans, coupled with their abundance of isomeric forms, presents formidable ch ...

EPFL2023

Ultra-tunable bistable structures for universal robotic applications

Jamie Paik, Lei Wang, Ke Liu, Hongying Zhang, Yongkang Jiang, Xin Tong

Bistable structures in nature are unparalleled for their fast response and force amplification even with the most minute physical stimula-tion. However, current works on bistable structures mainly focus on their stable states, while promising intermediate ...

CELL PRESS2023

Combining ion mobility spectrometry and cryogenic ion spectroscopy with enzymatic digestion/synthesis for the study of N-linked glycans

Irina Märki

Glycans play an essential role in numerous physiological and pathological processes of living organisms. Despite their significant biological relevance, glycobiology remains one of the least explored fields of biochemistry. The intrinsic isomeric complexit ...

EPFL2023

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

De novo designed proteins: a study in engineering novel folds and functions

Alexandra Krina Van Hall-Beauvais

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

EPFL2023

A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers

Christoph Bostedt, Camila Bacellar Cases Da Silveira

Serial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we ...

Nature Portfolio2023

Recombinant Full-Length TDP-43 Oligomers Retain Their Ability to Bind RNAs, Are Not Toxic, and Do Not Seed TDP-43 Aggregation in Vitro

Hilal Lashuel, Yllza Jasiqi, Lixin Yang

TAR DNA-binding protein with 43 kD (TDP-43) is a partially disordered protein that misfolds and accumulates in the brains of patients affected by several neurodegenerative diseases. TDP-43 oligomers have been reported to form due to aberrant misfolding or ...

Amer Chemical Soc2023

De novo protein design by inversion of the AlphaFold structure prediction network

Bruno Emanuel Ferreira De Sousa Correia, Hamed Khakzad, Casper Alexander Goverde, Stéphane Rosset, Benedict Dieter Gregor Wolf

De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in comp ...

2023

Crystalline or amorphous? A critical evaluation of phenomenological phase selection rules

Johann Michler, Caroline Hain, Ashish Sharma

In this work, we reviewed the available phase selection rules comprising atomic size and topological aspects, entropies, enthalpies, melting points, valence and itinerant electron concentrations, as well as electronegativity, and validated them using a car ...

ELSEVIER SCI LTD2023

NMR Crystallography in the Big Data Era: New Methods and Applications Powered by Machine Learning

Manuel Cordova

Structure determination of materials is key to understanding their physical properties. While single-crystal X-ray diffraction is the gold standard for structures displaying long-range order, many materials of interest are polycrystalline and/or disordered ...

EPFL2023

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

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

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

The Height of Chitinous Ridges Alone Produces the Entire Structural Color Palette

Hemant Kumar Raut

The colorful wings of butterflies result from the interaction between light and the intricate chitinous nanostructures on butterflies’ scales. This study demonstrates that just by reproducing the chitinous ridges present in butterfly scales (i.e., without ...

2022

Scaffolding protein functional sites using deep learning

Bruno Emanuel Ferreira De Sousa Correia, Wayne Yang Wen Wei, Karla Montserrat Castro Gilabert, Basile Isidore Martin Wicky, Jue Wang

The binding and catalytic functions of proteins are generally mediated by a small number of functional residues held in place by the overall protein structure. Here, we describe deep learning approaches for scaffolding such functional sites without needing ...

American Association for the Advancement of Science2022