Publications related to The importance of dynamics in integrative modeling of supramolecular assemblies

Advancements in Nanomechanical Characterization and Biomolecular Imaging with Atomic force Microscopy

Atomic force microscopy (AFM) is a widely used imaging tool for obtaining a variety of information for a range of samples. Although it was initially intended to serve as a method of observing very flat solid surfaces, its use expanded into several other fi ...

EPFL2024

Fractal Analysis of Four Xerogels Based on TEGylated Phenothiazine and Chitosan

Maria-Alexandra Paun

The present article describes novel massive materials (in the solid phase) based on TEGylated phenothiazine and chitosan that possess great capability to recover mercury ions from constituent aqueous solutions. These were produced by chitosan hydrogelation ...

MDPI2023

Half-clathrochelate Complexes as Versatile Links in Supramolecular Chemistry

Erica Giraldi

Clathrochelate complexes have been widely investigated with different size and shape and used as building blocks for the obtainment of discrete supramolecular architectures. These clathrochelate complexes are very stable and kinetically inert complexes. A ...

EPFL2021

The role of xanthophylls in the supramolecular organization of the photosynthetic complex LHCII in lipid membranes studied by high-resolution imaging and nanospectroscopy

Giovanni Dietler, Serguei Sekatski, Jiangtao Zhou

The xanthophyll cycle is a regulatory mechanism operating in the photosynthetic apparatus of plants. It consists of the conversion of the xanthophyll pigment violaxanthin to zeaxanthin, and vice versa, in response to light intensity. According to the curre ...

ELSEVIER2020

Soft matter probed by nonlinear scattering: self-assembly, interfaces, hydration, and long-range order

Jan Dedic

All organisms are made to a large extent of soft matter - macromolecules such as proteins and polysaccharides, or assemblies of small molecules such as lipids embedded in an aqueous environment. Understanding the role of order in soft matter presents a cha ...

EPFL2020

Boronate Ester-Capped Helicates

Kay Severin, Rosario Scopelliti, Daniel Ortiz Trujillo, Farzaneh Fadaei Tirani, Adrien Bryan Depallens, Erica Giraldi

Triple‐stranded helicates were obtained by metal‐templated multicomponent reactions of bispyridyloxime ligands with arylboronic acids. The helicates feature two hexa‐coordinated MII ions (M=Fe, Zn, or Mn), which are embedded in a macrobicyclic ligand frame ...

2020

Identifying and Tracking Defects in Dynamic Supramolecular Polymers

Michele Ceriotti, Piero Gasparotto

A central paradigm of self-assembly is to create ordered structures starting from molecular monomers that spontaneously recognize and interact with each other via noncovalent interactions. In recent years, great efforts have been directed toward perfecting ...

AMER CHEMICAL SOC2020

Electrochemical Assay for Extremely Selective Recognition of Fructose Based on 4-Ferrocene-Phenylboronic Acid Probe and beta-Cyclodextrins Supramolecular Complex

Sandro Carrara, Irene Taurino, Maria Antonietta Casulli

The aim of the present paper is to highlight a novel electrochemical assay for an extremely-selective detection of fructose thanks to the use of a supramolecular complex between beta-cyclodextrins (beta-CDs) and a chemically modified ferrocene with boronic ...

2020

Synthesis and Characterization of Coordination Cages Based on Clathrochelate Metalloligands

Giacomo Cecot

The work presented in this thesis focused on the synthesis and characterization of new metalloligands based on iron(II) clathrochelate complexes. Clathrochelates can be functionalized peripherally with donor groups capable of coordinating metal ions. The s ...

EPFL2019

Quantifying Guest-Host Dynamics in Supramolecular Assemblies to Analyze Their Robustness

Maartje Martina Cornelia Bastings, Eva Eugene Kurisinkal

The most basic function of synthetic microenvironments for tissue engineering is to act as a physical substrate for cell attachment, migration, and proliferation, similar to the natural cell environment. Functionalization of supramolecular materials with g ...

WILEY-V C H VERLAG GMBH2019

Excitonic channels from bio-inspired templated supramolecular assembly of J-aggregate nanowirest

Frank Nüesch, Surendra Babu Anantharaman, Jakob Heier

Supramolecular assemblies with controlled morphology are of paramount importance for energy transport in organic semiconductors. Despite considerable freedom in molecular design, the preparation of dyes that form one dimensional J-aggregates is challenging ...

2019

Molecular nanostructures based on polyfunctional clathrochelate complexes

Suzanne Maria Jansze

This thesis describes the design and synthesis of clathrochelate metalloligands for the construction of molecular nanostructures. The low synthetic effort, versatility and stability of the clathrochelate metalloligands makes them particularly suited to the ...

EPFL2019

Photons in - numbers out: perspectives in quantitative fluorescence microscopy for in situ protein counting

Kristin Stefanie Grussmayer

The full understanding of cellular functions requires information about protein numbers for various biomolecular assemblies and their dynamics, which can be partly accessed by super-resolution fluorescence microscopy. Yet, many protein assemblies and cellu ...

2019

High-speed photothermal off-resonance atomic force microscopy reveals assembly routes of centriolar scaffold protein SAS-6

Pierre Gönczy, Santiago Harald Andany, Georg Fantner, Adrian Pascal Nievergelt, Niccolo Banterle

The self-assembly of protein complexes is at the core of many fundamental biological processes1, ranging from the polymerization of cytoskeletal elements, such as microtubules2, to viral capsid formation and organelle assembly3. To reach a comprehensive un ...

2018

In situ Studies of Peptide and Protein Assemblies at the Solid-Liquid Interface : Hierarchical Self-Assembly, Dynamics and Functional Properties

Bart Willem Stel

At the interface between science and engineering, there is the field of biomimicry: Innovations inspired by the observation of natural, evolutionary optimized biological structures and processes. To understand the challenges of biomimicry, the concept of â ...

EPFL2018

PdII2L4-type coordination cages up to three nanometers in size

Kay Severin, Rosario Scopelliti, Matthew David Wise, Suzanne Maria Jansze

The utilization of large ligands in coordination-based self-assembly represents an attractive strategy for the construction of supramolecular assemblies more than two nanometers in size. However, the implementation of this strategy is hampered by the fact ...

2017

Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies

Dario Floreano, Matteo Thomas Degiacomi, Matteo Dal Peraro, Sylvain Träger, Andrea Maesani, Giorgio Elikem Tamo

Predicting the structure of large molecular assemblies remains a challenging task in structural biology when using integrative modeling approaches. One of the main issues stems from the treatment of heterogeneous experimental data used to predict the archi ...

Nature Research2017

AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species

Giovanni Dietler, Andrea Cerreta, Francesco Simone Ruggeri

Background: A wide class of human diseases and neurodegenerative disorders, such as Alzheimer's disease, is due to the failure of a specific peptide or protein to keep its native functional conformational state and to undergo a conformational change into a ...

Bentham Science Publishers2016

Facile synthesis of oligoyne amphiphiles and their rotaxanes

Holger Frauenrath, Stephen Schrettl, Tobias Hoheisel, Ruth Szilluweit, Martin Fritzsche, Emmanuel Romaric Contal

Carbon-rich organic compounds containing a series of conjugated triple bonds (oligoynes) are relevant synthetic targets, but an improved access to oligoynes bearing functional groups would be desirable. Here, we report the straightforward synthesis of two ...

Royal Soc Chemistry2015

New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly

Matteo Thomas Degiacomi, Matteo Dal Peraro, Enrico Spiga

Data reporting on structure and dynamics of cellular constituents are growing with increasing pace enabling, as never before, the understanding of fine mechanistic aspects of biological systems and providing the possibility to affect them in controlled way ...

Elsevier Academic Press Inc2014