Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
[HTML][HTML] Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations
Highlights•The accuracy of physical models used in protein-folding simulations is
assessed.•This assessment is based on data from very long molecular dynamics …
assessed.•This assessment is based on data from very long molecular dynamics …
[HTML][HTML] Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins
Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study
of biomolecular structure and dynamics in vitro and in vivo. We performed an international …
of biomolecular structure and dynamics in vitro and in vivo. We performed an international …
[HTML][HTML] Roadmap for optical tweezers
Optical tweezers are tools made of light that enable contactless pushing, trapping, and
manipulation of objects, ranging from atoms to space light sails. Since the pioneering work …
manipulation of objects, ranging from atoms to space light sails. Since the pioneering work …
Nuclear magnetic resonance detection and spectroscopy of single proteins using quantum logic
Nuclear magnetic resonance spectroscopy is a powerful tool for the structural analysis of
organic compounds and biomolecules but typically requires macroscopic sample quantities …
organic compounds and biomolecules but typically requires macroscopic sample quantities …
Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
Protein–protein association is fundamental to many life processes. However, a microscopic
model describing the structures and kinetics during association and dissociation is lacking …
model describing the structures and kinetics during association and dissociation is lacking …
Non-Markovian modeling of protein folding
C Ayaz, L Tepper, FN Brünig… - Proceedings of the …, 2021 - National Acad Sciences
We extract the folding free energy landscape and the time-dependent friction function, the
two ingredients of the generalized Langevin equation (GLE), from explicit-water molecular …
two ingredients of the generalized Langevin equation (GLE), from explicit-water molecular …
Identification of slow molecular order parameters for Markov model construction
G Pérez-Hernández, F Paul, T Giorgino… - The Journal of …, 2013 - pubs.aip.org
A goal in the kinetic characterization of a macromolecular system is the description of its
slow relaxation processes via (i) identification of the structural changes involved in these …
slow relaxation processes via (i) identification of the structural changes involved in these …
Fluorescence enhancement at docking sites of DNA-directed self-assembled nanoantennas
GP Acuna, FM Möller, P Holzmeister, S Beater… - Science, 2012 - science.org
We introduce self-assembled nanoantennas to enhance the fluorescence intensity in a
plasmonic hotspot of zeptoliter volume. The nanoantennas are prepared by attaching one or …
plasmonic hotspot of zeptoliter volume. The nanoantennas are prepared by attaching one or …
Single-molecule FRET spectroscopy and the polymer physics of unfolded and intrinsically disordered proteins
The properties of unfolded proteins have long been of interest because of their importance
to the protein folding process. Recently, the surprising prevalence of unstructured regions or …
to the protein folding process. Recently, the surprising prevalence of unstructured regions or …