Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy

A Soranno, B Buchli, D Nettels… - Proceedings of the …, 2012 - National Acad Sciences
Internal friction, which reflects the “roughness” of the energy landscape, plays an important
role for proteins by modulating the dynamics of their folding and other conformational …

Peptide chain dynamics in light and heavy water: zooming in on internal friction

JCF Schulz, L Schmidt, RB Best… - Journal of the …, 2012 - ACS Publications
Frictional effects due to the chain itself, rather than the solvent, may have a significant effect
on protein dynamics. Experimentally, such “internal friction” has been investigated by …

Aggregation of α-synuclein is kinetically controlled by intramolecular diffusion

B Ahmad, Y Chen, LJ Lapidus - Proceedings of the …, 2012 - National Acad Sciences
We hypothesize that the first step of aggregation of disordered proteins, such as α-synuclein,
is controlled by the rate of backbone reconfiguration. When reconfiguration is fast …

Nonexponential kinetics of loop formation in proteins and peptides: a signature of rugged free energy landscapes?

J Gowdy, M Batchelor, I Neelov… - The Journal of Physical …, 2017 - ACS Publications
The kinetics of loop formation, ie, the occurrence of contact between two atoms of a
polypeptide, remains the focus of continuing interest. One of the reasons is that contact …

Activated barrier crossing dynamics in the non-radiative decay of NADH and NADPH

TS Blacker, RJ Marsh, MR Duchen, AJ Bain - Chemical Physics, 2013 - Elsevier
In live tissue, alterations in metabolism induce changes in the fluorescence decay of the
biological coenzyme NAD (P) H, the mechanism of which is not well understood. In this …

Effect of donor–acceptor coupling on TICT dynamics in the excited states of two dimethylamine substituted chalcones

R Ghosh, DK Palit - The Journal of Physical Chemistry A, 2015 - ACS Publications
Significant effect of coupling between the electron donor and acceptor groups in
intramolecular charge transfer (ICT) dynamics has been demonstrated by comparing the …

Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models

RR Cheng, AT Hawk, DE Makarov - The Journal of Chemical Physics, 2013 - pubs.aip.org
Recent experiments showed that the reconfiguration dynamics of unfolded proteins are often
adequately described by simple polymer models. In particular, the Rouse model with …

[HTML][HTML] Non-Markov models of single-molecule dynamics from information-theoretical analysis of trajectories

K Song, R Park, A Das, DE Makarov… - The Journal of Chemical …, 2023 - pubs.aip.org
Whether single-molecule trajectories, observed experimentally or in molecular simulations,
can be described using simple models such as biased diffusion is a subject of considerable …

Conformational dynamics modulating electron transfer

DV Matyushov - The Journal of chemical physics, 2022 - pubs.aip.org
Diffusional dynamics of the donor–acceptor distance are responsible for the appearance of
a new time scale of diffusion over the distance of electronic tunneling in electron-transfer …

Ultrafast Twisting Dynamics of Thioflavin‐T: Spectroscopy of the Twisted Intramolecular Charge‐Transfer State

R Ghosh, DK Palit - ChemPhysChem, 2014 - Wiley Online Library
Understanding the excited‐state properties of thioflavin‐T (ThT) has been of immense
importance, because of its efficient amyloid‐sensing ability related to neurodegenerative …