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Deeper Insight of the Conformational Ensemble of Intrinsically Disordered Proteins

Svensson, Oskar LU ; Bakker, Michael J. LU and Skepö, Marie LU (2024) In Journal of Chemical Information and Modeling 64(15). p.6105-6114
Abstract

It is generally known that, unlike structured proteins, intrinsically disordered proteins, IDPs, exhibit various structures and conformers, the so-called conformational ensemble, CoE. This study aims to better understand the conformers that make up the IDP ensemble by decomposing the CoE into groups separated by their radius of gyration, Rg. A common approach to studying CoE for IDPs is to use low-resolution techniques, such as small-angle scattering, and combine those with computer simulations on different length scales. Herein, the well-studied antimicrobial saliva protein histatin 5 was utilized as a model peptide for an IDP; the average intensity curves were obtained from small-angle X-ray scattering; and compared with... (More)

It is generally known that, unlike structured proteins, intrinsically disordered proteins, IDPs, exhibit various structures and conformers, the so-called conformational ensemble, CoE. This study aims to better understand the conformers that make up the IDP ensemble by decomposing the CoE into groups separated by their radius of gyration, Rg. A common approach to studying CoE for IDPs is to use low-resolution techniques, such as small-angle scattering, and combine those with computer simulations on different length scales. Herein, the well-studied antimicrobial saliva protein histatin 5 was utilized as a model peptide for an IDP; the average intensity curves were obtained from small-angle X-ray scattering; and compared with fully atomistic, explicit water, molecular dynamics simulations; then, the intensity curve was decomposed with respect to the different Rg values; and their secondary structure propensities were investigated. We foresee that this approach can provide important information on the CoE and the individual conformers within; in that case, it will serve as an additional tool for understanding the IDP structure-function relationship on a more detailed level.

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organization
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type
Contribution to journal
publication status
published
subject
in
Journal of Chemical Information and Modeling
volume
64
issue
15
pages
10 pages
publisher
The American Chemical Society (ACS)
external identifiers
  • scopus:85199498779
  • pmid:39056166
ISSN
1549-9596
DOI
10.1021/acs.jcim.4c00941
language
English
LU publication?
yes
id
9b6be4bc-2713-411f-a40f-13a648dfafb4
date added to LUP
2024-09-10 15:34:14
date last changed
2024-10-08 20:29:24
@article{9b6be4bc-2713-411f-a40f-13a648dfafb4,
  abstract     = {{<p>It is generally known that, unlike structured proteins, intrinsically disordered proteins, IDPs, exhibit various structures and conformers, the so-called conformational ensemble, CoE. This study aims to better understand the conformers that make up the IDP ensemble by decomposing the CoE into groups separated by their radius of gyration, R<sub>g</sub>. A common approach to studying CoE for IDPs is to use low-resolution techniques, such as small-angle scattering, and combine those with computer simulations on different length scales. Herein, the well-studied antimicrobial saliva protein histatin 5 was utilized as a model peptide for an IDP; the average intensity curves were obtained from small-angle X-ray scattering; and compared with fully atomistic, explicit water, molecular dynamics simulations; then, the intensity curve was decomposed with respect to the different R<sub>g</sub> values; and their secondary structure propensities were investigated. We foresee that this approach can provide important information on the CoE and the individual conformers within; in that case, it will serve as an additional tool for understanding the IDP structure-function relationship on a more detailed level.</p>}},
  author       = {{Svensson, Oskar and Bakker, Michael J. and Skepö, Marie}},
  issn         = {{1549-9596}},
  language     = {{eng}},
  number       = {{15}},
  pages        = {{6105--6114}},
  publisher    = {{The American Chemical Society (ACS)}},
  series       = {{Journal of Chemical Information and Modeling}},
  title        = {{Deeper Insight of the Conformational Ensemble of Intrinsically Disordered Proteins}},
  url          = {{http://dx.doi.org/10.1021/acs.jcim.4c00941}},
  doi          = {{10.1021/acs.jcim.4c00941}},
  volume       = {{64}},
  year         = {{2024}},
}