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

The elastic network (EN) is a prime model that describes the long-timedynamics of biomolecules. However, the use of harmonic potentials renders thismodel insufficient for studying large conformational changes of proteins (e.g.stretching of proteins, folding and thermal unfolding). Here, we extend thecapabilities of the EN model by using a harmonic approximation described byLennard-Jones (LJ) interactions for far contacts and native contacts obtainedfrom the standard overlap criterion as in the case of Go-like models. While ourmodel is validated against the EN model by reproducing the equilibriumproperties for a number of proteins, we also show that the model is suitablefor the study of large conformation changes by providing various examples. Inparticular, this is illustrated on the basis of pulling simulations thatpredict with high accuracy the experimental data on the rupture force of thestudied proteins. Furthermore, in the case of DDFLN4 protein, our pullingsimulations highlight the advantages of our model with respect to Go-likeapproaches, where the latter fail to reproduce previous results obtained byall-atom simulations that predict an additional characteristic peak for thisprotein. In addition, folding simulations of small peptides yield differentfolding times for alpha-helix and beta-hairpin, in agreement with experiment,in this way providing further opportunities for the application of our model instudying large conformational changes of proteins. In contrast to the EN model,our model is suitable for both normal mode analysis and molecular dynamicssimulation. We anticipate that the proposed model will find applications in abroad range of problems in biology, including, among others, protein foldingand thermal unfolding.

Generalization of the Elastic Network model for the study of large conformational changes in biomolecules