TY - JOUR

T1 - From dilute to concentrated solutions of intrinsically disordered proteins

T2 - Interpretation and analysis of collected data

AU - Lenton, Samuel

AU - Fagerberg, Eric

AU - Tully, Mark

AU - Skepö, Marie

N1 - Funding Information: We acknowledge financial support from the Crafoord Foundation, Sweden. The authors would like to thank the European Synchrotron Radiation Facility (ESRF) in Grenoble, France, for the use of beamline BM29 and the excellent support over the years.

PY - 2023

Y1 - 2023

N2 - 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.

AB - 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.

KW - All-atom

KW - BioSAXS

KW - Coarse-grained

KW - Computer simulations

KW - Ensemble optimization method

KW - IDPs

KW - Intrinsically disordered proteins

KW - Molecular dynamics

KW - Monte Carlo

KW - Proteins

KW - Radius of gyration

U2 - 10.1016/bs.mie.2022.09.021

DO - 10.1016/bs.mie.2022.09.021

M3 - Journal article

C2 - 36641212

AN - SCOPUS:85143511205

VL - 678

SP - 299

EP - 330

JO - Chemical Tools for Imaging, Manipulating, and Tracking Biological Systems: Diverse Methods Based on Optical Imaging and Fluorescence

JF - Chemical Tools for Imaging, Manipulating, and Tracking Biological Systems: Diverse Methods Based on Optical Imaging and Fluorescence

SN - 0076-6879

ER -