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Photo Marie Skepö

Marie Skepö

Professor

Photo Marie Skepö

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

Author

  • Samuel Lenton
  • Eric Fagerberg
  • Mark Tully
  • Marie Skepö

Editor

  • John A. Tainer

Summary, in English

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.

Department/s

  • Physical Chemistry
  • Computational Chemistry
  • LTH Profile Area: Nanoscience and Semiconductor Technology
  • LINXS - Institute of advanced Neutron and X-ray Science
  • eSSENCE: The e-Science Collaboration

Publishing year

2023

Language

English

Pages

299-330

Publication/Series

Methods in Enzymology

Volume

678

Document type

Book chapter

Publisher

Academic Press

Topic

  • Theoretical Chemistry (including Computational Chemistry)

Keywords

  • All-atom
  • BioSAXS
  • Coarse-grained
  • Computer simulations
  • Ensemble optimization method
  • IDPs
  • Intrinsically disordered proteins
  • Molecular dynamics
  • Monte Carlo
  • Proteins
  • Radius of gyration

Status

Published

ISBN/ISSN/Other

  • ISSN: 1557-7988
  • ISSN: 0076-6879
  • ISBN: 978-0-323-99181-0