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Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions

Cragnell, Carolina LU ; Rieloff, Ellen LU and Skepö, Marie LU orcid (2018) In Journal of Molecular Biology 430(16). p.2478-2492
Abstract

In this study, we have used the coarse-grained model developed for the intrinsically disordered saliva protein (IDP) Histatin 5, on an experimental selection of monomeric IDPs, and we show that the model is generally applicable when electrostatic interactions dominate the intra-molecular interactions. Experimental and theoretically calculated small-angle X-ray scattering data are presented in the form of Kratky plots, and discussions are made with respect to polymer theory and the self-avoiding walk model. Furthermore, the impact of electrostatic interactions is shown and related to estimations of the conformational ensembles obtained from computer simulations and “Flexible-meccano.” Special attention is given to the form factor and how... (More)

In this study, we have used the coarse-grained model developed for the intrinsically disordered saliva protein (IDP) Histatin 5, on an experimental selection of monomeric IDPs, and we show that the model is generally applicable when electrostatic interactions dominate the intra-molecular interactions. Experimental and theoretically calculated small-angle X-ray scattering data are presented in the form of Kratky plots, and discussions are made with respect to polymer theory and the self-avoiding walk model. Furthermore, the impact of electrostatic interactions is shown and related to estimations of the conformational ensembles obtained from computer simulations and “Flexible-meccano.” Special attention is given to the form factor and how it is affected by the salt concentration, as well as the approximation of using the form factor obtained under physiological conditions to obtain the structure factor.

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author
; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
coarse-grained modeling, electrostatic interactions, intrinsically disordered proteins, Monte Carlo simulations, small-angle X-ray scattering
in
Journal of Molecular Biology
volume
430
issue
16
pages
2478 - 2492
publisher
Elsevier
external identifiers
  • pmid:29573987
  • scopus:85044773582
ISSN
0022-2836
DOI
10.1016/j.jmb.2018.03.006
language
English
LU publication?
yes
id
4427b0e7-f806-4a3e-b80b-eae7d22f7ac2
date added to LUP
2018-04-12 13:37:28
date last changed
2025-02-04 10:43:06
@article{4427b0e7-f806-4a3e-b80b-eae7d22f7ac2,
  abstract     = {{<p>In this study, we have used the coarse-grained model developed for the intrinsically disordered saliva protein (IDP) Histatin 5, on an experimental selection of monomeric IDPs, and we show that the model is generally applicable when electrostatic interactions dominate the intra-molecular interactions. Experimental and theoretically calculated small-angle X-ray scattering data are presented in the form of Kratky plots, and discussions are made with respect to polymer theory and the self-avoiding walk model. Furthermore, the impact of electrostatic interactions is shown and related to estimations of the conformational ensembles obtained from computer simulations and “Flexible-meccano.” Special attention is given to the form factor and how it is affected by the salt concentration, as well as the approximation of using the form factor obtained under physiological conditions to obtain the structure factor.</p>}},
  author       = {{Cragnell, Carolina and Rieloff, Ellen and Skepö, Marie}},
  issn         = {{0022-2836}},
  keywords     = {{coarse-grained modeling; electrostatic interactions; intrinsically disordered proteins; Monte Carlo simulations; small-angle X-ray scattering}},
  language     = {{eng}},
  month        = {{03}},
  number       = {{16}},
  pages        = {{2478--2492}},
  publisher    = {{Elsevier}},
  series       = {{Journal of Molecular Biology}},
  title        = {{Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions}},
  url          = {{http://dx.doi.org/10.1016/j.jmb.2018.03.006}},
  doi          = {{10.1016/j.jmb.2018.03.006}},
  volume       = {{430}},
  year         = {{2018}},
}