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

Intrinsically Disordered Proteins / chemistry Protein Conformation Scattering, Small Angle X-Ray Diffraction Molecular Dynamics Simulation
All-atom BioSAXS Coarse-grained Computer simulations Ensemble optimization method IDPs Intrinsically disordered proteins Molecular dynamics Monte Carlo Proteins Radius of gyration

Journal

Methods in enzymology
ISSN: 1557-7988
Titre abrégé: Methods Enzymol
Pays: United States
ID NLM: 0212271

Informations de publication

Date de publication:
2023
Historique:
entrez: 14 1 2023
pubmed: 15 1 2023
medline: 18 1 2023
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1016/bs.mie.2022.09.021 PMID: 36641212
pubmed: 36641212
pii: S0076-6879(22)00402-5
doi: 10.1016/bs.mie.2022.09.021
pii:
doi:

Substances chimiques

Intrinsically Disordered Proteins 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

299-330

Informations de copyright

Copyright © 2023 Elsevier Inc. All rights reserved.

Auteurs

Samuel Lenton (S)

Drug Delivery and Biophysics of Biopharmaceuticals, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark; Division of Theoretical Chemistry, Lund University, Lund, Sweden.

Eric Fagerberg (E)

Division of Theoretical Chemistry, Lund University, Lund, Sweden.

Mark Tully (M)

BioSAXS beamline, BM29, European Synchrotron Radiation Facility, ESRF, Grenoble, France.

Marie Skepö (M)

Division of Theoretical Chemistry, Lund University, Lund, Sweden; LINXS-Institute of Advanced Neutron and X-ray Science, Lund, Sweden. Electronic address: marie.skepo@teokem.lu.se.

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Classifications MeSH

questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines intrinsèquement désordonnées › From dilute to concentrated solutions of...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Conformation moléculaire › Conformation des protéines › From dilute to concentrated solutions of...
questionsmedicales.fr › Phénomènes physiques › Diffusion de rayonnements › Diffusion aux petits angles › From dilute to concentrated solutions of...
questionsmedicales.fr › Phénomènes chimiques › Diffraction des rayons X › From dilute to concentrated solutions of...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Simulation numérique › Simulation de dynamique moléculaire › From dilute to concentrated solutions of...