Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W Xi, R Nussinov, B Ma - Chemical reviews, 2016 - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
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

S Piana, JL Klepeis, DE Shaw - Current opinion in structural biology, 2014 - Elsevier
Highlights•The accuracy of physical models used in protein-folding simulations is
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

G Agam, C Gebhardt, M Popara, R Mächtel, J Folz… - Nature …, 2023 - nature.com
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 …

[HTML][HTML] Roadmap for optical tweezers

G Volpe, OM Maragò… - Journal of Physics …, 2023 - iopscience.iop.org
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 …

Nuclear magnetic resonance detection and spectroscopy of single proteins using quantum logic

I Lovchinsky, AO Sushkov, E Urbach, NP de Leon… - Science, 2016 - science.org
Nuclear magnetic resonance spectroscopy is a powerful tool for the structural analysis of
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

N Plattner, S Doerr, G De Fabritiis, F Noé - Nature chemistry, 2017 - nature.com
Protein–protein association is fundamental to many life processes. However, a microscopic
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 …

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 …

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 …

Single-molecule FRET spectroscopy and the polymer physics of unfolded and intrinsically disordered proteins

B Schuler, A Soranno, H Hofmann… - Annual Review of …, 2016 - annualreviews.org
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 …