Title
Generalization of the elastic network model for the study of large conformational changes in biomolecules
Date Issued
01 January 2018
Access level
open access
Resource Type
journal article
Author(s)
Li M.S.
Theodorakis P.E.
Academia Polaca de Ciencias
Publisher(s)
Royal Society of Chemistry
Abstract
The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching of proteins, folding and thermal unfolding). Here, we extend the capabilities of the EN model by using a harmonic approximation described by Lennard-Jones (LJ) interactions for far contacts and native contacts obtained from the standard overlap criterion as in the case of Go-like models. While our model is validated against the EN model by reproducing the equilibrium properties for a number of proteins, we also show that the model is suitable for the study of large conformation changes by providing various examples. In particular, this is illustrated on the basis of pulling simulations that predict with high accuracy the experimental data on the rupture force of the studied proteins. Furthermore, in the case of DDFLN4 protein, our pulling simulations highlight the advantages of our model with respect to Go-like approaches, where the latter fail to reproduce previous results obtained by all-atom simulations that predict an additional characteristic peak for this protein. In addition, folding simulations of small peptides yield different folding times for α-helix and β-hairpin, in agreement with experiment, in this way providing further opportunities for the application of our model in studying large conformational changes of proteins. In contrast to the EN model, our model is suitable for both normal mode analysis and molecular dynamics simulation. We anticipate that the proposed model will find applications in a broad range of problems in biology, including, among others, protein folding and thermal unfolding.
Start page
17020
End page
17028
Volume
20
Issue
25
Language
English
OCDE Knowledge area
Bioquímica, Biología molecular
Scopus EID
2-s2.0-85049207450
PubMed ID
Source
Physical Chemistry Chemical Physics
ISSN of the container
14639076
Sources of information: Directorio de Producción Científica Scopus