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From dilute to concentrated solutions of intrinsically disordered proteins : Interpretation and analysis of collected data

Lenton, Samuel LU ; Fagerberg, Eric LU ; Tully, Mark and Skepö, Marie LU (2023) In Methods in Enzymology 678. p.299-330
Abstract

Intrinsically disordered proteins (IDPs) have a broad energy landscape and consequently sample many different conformations in solution. The innate flexibility of IDPs is exploited in their biological function, and in many instances allows a single IDP to regulate a range of processes in vivo. Due to their highly flexible nature, characterizing the structural properties of IDPs is not straightforward. Often solution-based methods such as Nuclear Magnetic Resonance (NMR), Förster Resonance Energy Transfer (FRET), and Small-Angle X-ray Scattering (SAXS) are used. SAXS is indeed a powerful technique to study the structural and conformational properties of IDPs in solution, and from the obtained SAXS spectra, information about the average... (More)

Intrinsically disordered proteins (IDPs) have a broad energy landscape and consequently sample many different conformations in solution. The innate flexibility of IDPs is exploited in their biological function, and in many instances allows a single IDP to regulate a range of processes in vivo. Due to their highly flexible nature, characterizing the structural properties of IDPs is not straightforward. Often solution-based methods such as Nuclear Magnetic Resonance (NMR), Förster Resonance Energy Transfer (FRET), and Small-Angle X-ray Scattering (SAXS) are used. SAXS is indeed a powerful technique to study the structural and conformational properties of IDPs in solution, and from the obtained SAXS spectra, information about the average size, shape, and extent of oligomerization can be determined. In this chapter, we will introduce model-free methods that can be used to interpret SAXS data and introduce methods that can be used to interpret SAXS data beyond analytical models, for example, by using atomistic and different levels of coarse-grained models in combination with molecular dynamics (MD) and Monte Carlo simulations.

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Please use this url to cite or link to this publication:
author
; ; and
organization
publishing date
type
Chapter in Book/Report/Conference proceeding
publication status
published
subject
keywords
All-atom, BioSAXS, Coarse-grained, Computer simulations, Ensemble optimization method, IDPs, Intrinsically disordered proteins, Molecular dynamics, Monte Carlo, Proteins, Radius of gyration
host publication
Small Angle Scattering Part B: Methods for Structural Interpretation
series title
Methods in Enzymology
editor
Tainer, John A.
volume
678
pages
32 pages
publisher
Academic Press
external identifiers
  • pmid:36641212
  • scopus:85143511205
ISSN
0076-6879
1557-7988
ISBN
978-0-323-99181-0
DOI
10.1016/bs.mie.2022.09.021
language
English
LU publication?
yes
id
686ca054-accc-4aa7-937f-8af8f16526e9
date added to LUP
2023-01-30 10:53:48
date last changed
2024-06-23 12:25:40
@inbook{686ca054-accc-4aa7-937f-8af8f16526e9,
  abstract     = {{<p>Intrinsically disordered proteins (IDPs) have a broad energy landscape and consequently sample many different conformations in solution. The innate flexibility of IDPs is exploited in their biological function, and in many instances allows a single IDP to regulate a range of processes in vivo. Due to their highly flexible nature, characterizing the structural properties of IDPs is not straightforward. Often solution-based methods such as Nuclear Magnetic Resonance (NMR), Förster Resonance Energy Transfer (FRET), and Small-Angle X-ray Scattering (SAXS) are used. SAXS is indeed a powerful technique to study the structural and conformational properties of IDPs in solution, and from the obtained SAXS spectra, information about the average size, shape, and extent of oligomerization can be determined. In this chapter, we will introduce model-free methods that can be used to interpret SAXS data and introduce methods that can be used to interpret SAXS data beyond analytical models, for example, by using atomistic and different levels of coarse-grained models in combination with molecular dynamics (MD) and Monte Carlo simulations.</p>}},
  author       = {{Lenton, Samuel and Fagerberg, Eric and Tully, Mark and Skepö, Marie}},
  booktitle    = {{Small Angle Scattering Part B: Methods for Structural Interpretation}},
  editor       = {{Tainer, John A.}},
  isbn         = {{978-0-323-99181-0}},
  issn         = {{0076-6879}},
  keywords     = {{All-atom; BioSAXS; Coarse-grained; Computer simulations; Ensemble optimization method; IDPs; Intrinsically disordered proteins; Molecular dynamics; Monte Carlo; Proteins; Radius of gyration}},
  language     = {{eng}},
  pages        = {{299--330}},
  publisher    = {{Academic Press}},
  series       = {{Methods in Enzymology}},
  title        = {{From dilute to concentrated solutions of intrinsically disordered proteins : Interpretation and analysis of collected data}},
  url          = {{http://dx.doi.org/10.1016/bs.mie.2022.09.021}},
  doi          = {{10.1016/bs.mie.2022.09.021}},
  volume       = {{678}},
  year         = {{2023}},
}