Issue 1, 2018

Unfolding dynamics of small peptides biased by constant mechanical forces

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

Article information

Article type
Paper
Submitted
29 Aug. 2017
Accepted
26 Okt. 2017
First published
30 Okt. 2017

Mol. Syst. Des. Eng., 2018,3, 204-213

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

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements