Publications related to Alpha sheet

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

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

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

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

Beyond 8 THz Displacement-field Nano-switches for 5G and 6G Communications

Mihai Adrian Ionescu, Elison de Nazareth Matioli, Mohammad Samizadeh Nikooytabalvandani, Riyaz Mohammed Abdul Khadar, Pirouz Sohi

The rapid progress in high capacity communication systems is reaching extremely high data rates of 100 Gb s−1, which demands electronic switches with cut-off frequencies well above 1 THz. The excellent electron transport properties of III-V heterojunctions ...

IEEE2022

Structure-Property Relationships in Complex Materials by Combining Supervised and Unsupervised Machine Learning

Benjamin Aaron Helfrecht

The work presented in this thesis combines supervised and unsupervised machine learning to examine structure-property relationships in databases of materials. While either supervised learning or unsupervised learning alone can be a powerful tool for assess ...

EPFL2021

Repair or Degrade: the Thermodynamic Dilemma of Cellular Protein Quality-Control

Paolo De Los Rios, Bruno Claude Daniel Fauvet, Pierre Goloubinoff, Satyam Tiwari, Mathieu Rebeaud

Life is a non-equilibrium phenomenon. Owing to their high free energy content, the macromolecules of life tend to spontaneously react with ambient oxygen and water and turn into more stable inorganic molecules. A similar thermodynamic picture applies to th ...

FRONTIERS MEDIA SA2021

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

Jaume Bonet Martinez

Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. We present RADI/raDIMod, a variation of the original DCA algorithm that grou ...

OXFORD UNIV PRESS2021

Capture system adapted to capture orbital objects, in particular for deorbiting purposes

Muriel Richard, Pierre-Alain Mäusli, Michaël Pellet

There is described a capture system (100) adapted to capture orbital objects (2000), in particular for deorbiting purposes. The capture system (110) comprises (i) a deployable capture structure (110) designed to be deployable between a standby configuratio ...

2020

Atomistic Simulations of The Structure of Calcium Silicate Hydrates: Interlayer Positions, Water Content And A General Structural Brick Model

Aslam Kunhi Mohamed

Portland cement has been in use by human civilization for over a century. Yet, we do not fully understand its hydration reaction mechanisms due to the complexity of the system and its continued reaction over time making it hard to study it experimentally. ...

EPFL2018

Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold

Kai Johnsson, Alberto Schena

Attempts to create novel ligand-binding proteins often focus on formation of a binding pocket with shape complementarity against the desired ligand (particularly for compounds that lack distinct polar moieties). Although designed proteins often exhibit bin ...

OXFORD UNIV PRESS2018

Synthesis and structure-activity relationship of 2,6-disubstituted pyridine derivatives as inhibitors of beta-amyloid-42 aggregation

Andrea Pfeifer, Andreas Muhs, Paolo Paganetti

It is assumed that amyloid-beta aggregation is a crucial event in the pathogenesis of Alzheimer's disease. Novel 2,6-disubstituted pyridine derivatives were designed to interact with the beta-sheet conformation of A beta via donor-acceptor-donor hydrogen b ...

Pergamon-Elsevier Science Ltd2016

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

Bruno Emanuel Ferreira De Sousa Correia, Stefano Zamuner

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based ...

Wiley-Blackwell2016

Discriminative adsorption of amphiphilic monolayer protected gold nanoparticles on amyloid fibers

Paulo Henrique Jacob Silva

This thesis presents a systematic study of how different types monolayer-protected AuNPs interact with amyloid fibers. We report a class of amphiphilic gold nanoparticles capable of adsorbing onto specific surface features on these types of protein fibers. ...

EPFL2016

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

Structure and Biophysical Properties of a Triple-Stranded Beta-Helix Comprising the Central Spike of Bacteriophage T4

Laure Menin, Petr Leiman, Sergii Buth

Gene product 5 (gp5) of bacteriophage T4 is a spike-shaped protein that functions to disrupt the membrane of the target cell during phage infection. Its C-terminal domain is a long and slender -helix that is formed by three polypeptide chains wrapped aroun ...

Mdpi Ag2015

The centriolar protein CPAP G-box: an amyloid fibril in a single domain

Georgios Hatzopoulos

Centrioles are evolutionarily conserved cylindrical cell organelleswith characteristic radial symmetry. Despite their considerable size (400 nm x 200 nm, in humans), genetic studies suggest that relatively few protein components are involved in their assem ...

Portland Press Ltd2015

Damping Materials from Hierarchically Structured Oligopeptide-Modified Polymer Blends

Su Liang

Certain natural materials such as bones not only show high stiffness and high damping performance but also exhibit other superior properties as the result of complex hierarchical structure formation. Synthetic polymer materials have demonstrated a great ve ...

EPFL2015

The Crystal Structures of Apo and cAMP-Bound GlxR from Corynebacterium glutamicum Reveal Structural and Dynamic Changes upon cAMP Binding in CRP/FNR Family Transcription Factors

Stewart Cole, Florence Pojer

The cyclic AMP-dependent transcriptional regulator GlxR from Corynebacterium glutamicum is a member of the super-family of CRP/FNR (cyclic AMP receptor protein/fumarate and nitrate reduction regulator) transcriptional regulators that play central roles in ...

Public Library of Science2014

Development of bicyclic peptide Her2 binders and phage selection of alpha-helical peptide ligands

Philippe Diderich

Conformationally constrained peptide ligands offer an attractive format for the development of therapeutics. They can bind with high affinity and selectivity to protein targets, they are small enough to diffuse into tissues, they can be synthesized chemica ...

EPFL2014

Structure and properties of the C-terminal beta-helical domain of VgrG protein from Escherichia coli O157

Petr Leiman

The bacterial Type 6 secretion system (T6SS) translocates protein toxins (also called effectors) from the cytosol of a T6SS-carrying cell to a target cell by a syringe-like supramolecular complex resembling a contractile tail of bacteriophages. Valine-glyc ...

Oxford University Press2014