Jump to main content
Jump to site search
PLANNED MAINTENANCE Close the message box

Scheduled maintenance work on Wednesday 21st October 2020 from 07:00 AM to 07:00 PM (BST).

During this time our website performance may be temporarily affected. We apologise for any inconvenience this might cause and thank you for your patience.


Issue 1, 2018
Previous Article Next Article

Unfolding dynamics of small peptides biased by constant mechanical forces

Author affiliations

Abstract

We show how multi-ensemble Markov state models can be combined with constant-force equilibrium simulations. Besides obtaining the unfolding/folding rates, Markov state models allow gaining detailed insights into the folding dynamics and pathways through identifying folding intermediates and misfolded structures. For two specific peptides, we demonstrate that the end-to-end distance is an insufficient reaction coordinate. This problem is alleviated through constructing models with multiple collective variables, for which we employ the time-lagged independent component analysis requiring only minimal prior knowledge. Our results show that combining Markov state models with constant-force simulations is a promising strategy to bridge the gap between simulation and experiments even for medium-sized biomolecules.

Graphical abstract: Unfolding dynamics of small peptides biased by constant mechanical forces

Back to tab navigation

Article information


Submitted
29 Aug 2017
Accepted
26 Oct 2017
First published
30 Oct 2017

Mol. Syst. Des. Eng., 2018,3, 204-213
Article type
Paper

Unfolding dynamics of small peptides biased by constant mechanical forces

F. Knoch and T. Speck, Mol. Syst. Des. Eng., 2018, 3, 204
DOI: 10.1039/C7ME00080D

Social activity

Search articles by author

Spotlight

Advertisements