English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Plus monthly

Global: Zendy Tools annual

Global: Zendy Tools monthly

Global: Zendy Free Plan

It is important to extract reaction coordinates or order parameters fromprotein simulations in order to investigate the local minimum-energy states andthe transitions between them. The most popular method to obtain such data isprincipal component analysis, which extracts modes of large conformationalfluctuations around an average structure. We recently applied relaxation modeanalysis for protein systems, which approximately estimates the slow relaxationmodes and times from a simulation and enables investigations of the dynamicproperties underlying the structural fluctuations of proteins. In this study,we apply this relaxation mode analysis to extract reaction coordinates for asystem in which there are large conformational changes such as those commonlyobserved in protein folding/unfolding. We performed a 750-ns simulation ofchignolin protein near its folding transition temperature, and observed manytransitions between the most stable, misfolded, intermediate, and unfoldedstates. We then applied principal component analysis and relaxation modeanalysis to the system. In the relaxation mode analysis, we could automaticallyextract good reaction coordinates. The free-energy surfaces provide a clearerunderstanding of the transitions not only between local minimum-energy statesbut also between the folded and unfolded states, even though the simulationinvolved large conformational changes. Moreover, we propose a new analysismethod called Markov state relaxation mode analysis. We applied the new methodto states with slow relaxation, which are defined by the free-energy surfaceobtained in the relaxation mode analysis. Finally, the relaxation times of thestates obtained with a simple Markov state model and the proposed Markov staterelaxation mode analysis are compared and discussed.

Relaxation Mode Analysis and Markov State Relaxation Mode Analysis for Chignolin in Aqueous Solution near a Transition Temperature