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Related publications (30)

Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes

Matteo Dal Peraro, Luciano Andres Abriata, Alexander Mayorov

A recent analysis of evolutionary rates in >500 globular soluble enzymes revealed pervasive conservation gradients toward catalytic residues. By looking at amino acid preference profiles rather than evolutionary rates in the same data set, we quantified th ...

OXFORD UNIV PRESS2019

Advanced Computational Methods for NMR Crystallography

Albert Hofstetter

Knowledge of the atomic-level structure is key to understanding and predicting properties of materials. X-ray diffraction (XRD) is the methods of choice for structures containing well-defined long-range order. However, many materials contain various degree ...

EPFL2019

Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank

Michele Ceriotti, Piero Gasparotto, Benjamin Aaron Helfrecht, Federico Giberti

Rationalizing the structure and structure–property relations for complex materials such as polymers or biomolecules relies heavily on the identification of local atomic motifs, e.g., hydrogen bonds and secondary structure patterns, that are seen as buildin ...

2019

The yeast C/D box snoRNA U14 adopts a "weak" K-turn like conformation recognized by the Snu13 core protein in solution

Benjamin Marcel Daniel Rothé

Non-coding RNAs associate with proteins to form ribonucleoproteins (RNPs), such as ribosome, box C/D snoRNPs, H/ACA snoRNPs, ribonuclease P, telomerase and spliceosome to ensure cell viability. The assembly of these RNA-protein complexes relies on the abil ...

ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER2019

Transmembrane Prolines Mediate Signal Sensing and Decoding in Bacillus subtilis DesK Histidine Kinase

Matteo Dal Peraro, Luciano Andres Abriata

Environmental awareness is an essential attribute of all organisms. The homeoviscous adaptation system of Bacillus subtilis provides a powerful experimental model for the investigation of stimulus detection and signaling mechanisms at the molecular level. ...

2019

CnoX Is a Chaperedoxin: A Holdase that Protects Its Substrates from Irreversible Oxidation

Camille Véronique Bernadette Goemans

Bleach (HOCl) is a powerful oxidant that kills bacteria in part by causing protein aggregation. It inactivates ATP-dependent chaperones, rendering cellular proteins mostly dependent on holdases. Here we identified Escherichia coli CnoX (YbbN) as a folding ...

2018

Molecular Imaging of Biopolymers Enabled by Electrospray-Ion Beam Deposition

Sabine Abb

Biomolecular functional complexes often serve as inspiration for the development of artificial molecular nanostructures. The functionality of the biomolecular structures is based on complex and adaptable binding motifs that have evolved over billions of ye ...

EPFL2017

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis

Paolo De Los Rios, Alessandro Barducci, Duccio Malinverni

The interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of the interaction are still elusive and contrasting models hav ...

Elife Sciences Publications Ltd2017

Gas-phase probes of kinetically trapped peptides

Liudmila Voronina

Gas-phase techniques are promising for studying intrinsically disordered peptides and proteins, as they can be implemented in a conformer-selective way. One of the issues that prevent them from finding a broader use is the question of to which extent the s ...

EPFL2016

Structural, Dynamical, and Electronic Properties of Liquid Water: A Hybrid Functional Study

Alfredo Pasquarello, Giacomo Francesco Leonardo Miceli, Francesco Ambrosio

We study structural, dynamical, and electronic properties of liquid water through ab initio molecular dynamics (MD) simulations based on a hybrid functional which includes nonlocal van der Waals (vdW) interactions. The water dimer, the water hexamer, and t ...

Amer Chemical Soc2016

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