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Concept

Macromolecular crowding

Related publications (19)

Information Theory in Transmembrane Transport

Solange Marie Flatt

The past decades have seen the advent of information theory in various fields, from quantum physics to cosmology. At an intermediary scale between atomic and cosmological scales are biological systems and in particular the cell, as a constitutive element o ...

EPFL2023

Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities

Vassily Hatzimanikatis, Liliana Angeles Martinez

The metabolic capabilities of the species and the local environment shape the microbial interactions in a community either through the exchange of metabolic products or the competition for the resources. Cells are often arranged in close proximity to each ...

2021

The influence of the crowding assumptions in biofilm simulations

Vassily Hatzimanikatis, Liliana Angeles Martinez

Author summary In nature, many organisms grow in crowded biofilms that protect against stressful conditions, making their control/eradication a challenge. Modeling these microbial systems is a valuable tool for studying the interactions among cells and exp ...

2021

Modeling biochemical reaction networks in complex intracellular environments

Daniel Robert Weilandt

Whether one aims to design treatments for diseases such as cancer or diabetes, engineer cells to produce valuable biochemicals sustainably, or to grasp the behavior of living organisms, it is essential to understand how cells react to genetic, environmenta ...

EPFL2020

Allostery in Its Many Disguises: From Theory to Applications

Matthieu Wyart, Giulia Palermo, Jingshi Li, Riccardo Ravasio

Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, andmetabolism. Allostery is rooted in the fundamental physical properties of macromolecular systems, but its underlying mec ...

CELL PRESS2019

Structural and functional analysis of host attachment proteins from contractile injection systems

Michel Plattner

Bacteriophages of the myoviridae family, R-type pyocin, Photorhabus virulence cassette (PVC), Serratia antifeeding prophage (Afp) and type 6 secretion system (T6SS) form a class of contractile injection systems that share common structural and functional c ...

EPFL2018

Tandem affinity purification of AtTERT reveals putative interaction partners of plant telomerase in vivo

Jana Majerská

The life cycle of telomerase involves dynamic and complex interactions between proteins within multiple macromolecular networks. Elucidation of these associations is a key to understanding the regulation of telomerase under diverse physiological and pathol ...

Springer Wien2017

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics

Matteo Dal Peraro, Luciano Andres Abriata, Enrico Spiga

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known e ...

Cell Press2016

Quantification of the neurochemical profile using simulated macromolecule resonances at 3 T

Rolf Gruetter, Cristina Ramona Cudalbu Moldovan, Lijing Xin, Benoît Schaller

The broad resonances underlying the entire (1) H NMR spectrum of the brain, ascribed to macromolecules, can influence metabolite quantification. At the intermediate field strength of 3 T, distinct approaches for the determination of the macromolecule signa ...

Wiley-Blackwell2013

All-atom simulations of crowding effects on ubiquitin dynamics

Matteo Dal Peraro, Luciano Andres Abriata, Enrico Spiga

It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to pro ...

Iop Publishing Ltd2013

Predicting Fish Acute Toxicity Using a Fish Gill Cell Line-Based Toxicity Assay

Kristin Schirmer

The OECD test guideline 203 for determination of fish acute toxicity requires substantial numbers of fish and uses death as an apical end point. One potential alternative are fish cell lines; however, several studies indicated that these appear up to sever ...

Amer Chemical Soc2013

Multiscale simulations of protein dynamics

Enrico Spiga

Characteristic timescales associated with the function of biomolecules, like proteins, range from femtoseconds up to minutes, whereas their corresponding spatial extent ranges from few ̊A to μm when associating in large macromolecular complexes. Moreover, ...

EPFL2013

Molecular Modeling of Bacterial Nanomachineries

Matteo Thomas Degiacomi

Proteins have the ability to assemble in multimeric states to perform their specific biological function. Unfortunately, characterizing experimentally these structures at atomistic resolution is usually difficult. For this reason, in silico methodologies a ...

EPFL2012

Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging

Suliana Manley, Christian Sieben

Simultaneous tracking of many thousands of individual particles in live cells is possible now with the advent of high-density superresolution imaging methods. We present an approach to extract local biophysical properties of cell-particle interaction from ...

Natl Acad Sciences2012

Assembly Mechanisms and Cellular Effects of Bacterial Pore-Forming Toxins

Mirko Bischofberger

The correct assembly of macromolecular protein complexes such as ribosomes or multisubunit membrane channels is essential for their function. Alterations in the process can lead to disease either by loss of function or by acquisition of toxic function. How ...

EPFL2011

Redundancy and specificity of multiple Trigger Factor chaperones in Desulfitobacteria

Christof Holliger, Julien Maillard

The ribosome-bound Trigger Factor (TF) chaperone assists folding of newly synthesized polypeptides and participates in the assembly of macromolecular complexes. In the present study we showed that multiple distinct TF paralogues are present in genomes of D ...

2011

Excluded Volume Effects on Semiflexible Ring Polymers

Giovanni Dietler, Guillaume Witz

Two-dimensional semiflexible polymer rings are studied both by imaging circular DNA adsorbed on a mica surface and by Monte Carlo simulations of phantom polymers as well as of polymers with finite thickness. Comparison of size and shape of the different mo ...

American Chemical Society (ACS)2010

Salt Removal During Off-GelTM Electrophoresis of Protein Samples

Hubert Girault, Christophe Roussel, Niels Erik Lion

The Off-Gel™ technology was recently described for protein fractionation in a solution placed on top of an immobilized pH gradient gel. In addition, this process was found to remove salts from the biological samples to analyze. This desalting effect is stu ...

2005

Quantifying Pb and Cd complexation by alginates and the role of metal binding on macromolecular aggregation

Cristina Lamelas, Fabrice Avaltroni

The Pb and Cd binding capacity of alginates were quantified by the determination of their complex stability constants and the concentration of complexing sites using H+,Pb 2+,orCd2+ selective electrodes in both static and dynamic titrations. Centrifugation ...

American Chemical Society2005