Jump to main content
Jump to site search


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

Publication details

The article was received on 29 Aug 2017, accepted on 26 Oct 2017 and first published on 30 Oct 2017


Article type: Paper
DOI: 10.1039/C7ME00080D
Citation: Mol. Syst. Des. Eng., 2018, Advance Article
  •   Request permissions

    Unfolding dynamics of small peptides biased by constant mechanical forces

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

Search articles by author

Spotlight

Advertisements