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Methods. 2017 Apr 15;118-119:146-162. doi: 10.1016/j.ymeth.2016.12.002. Epub 2016 Dec 8.

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods.

Author information

1
Alberta RNA Research and Training Institute, Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta T1K 3M4, Canada. Electronic address: trushar.patel@uleth.ca.
2
European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22607, Germany. Electronic address: gchojnowski@gmail.com.
3
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland. Electronic address: abhu@genesilico.pl.
4
Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada. Electronic address: koula@myumanitoba.ca.
5
Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada; Manitoba Institute for Materials, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada. Electronic address: sean.mckenna@umanitoba.ca.
6
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland; Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland. Electronic address: iamb@genesilico.pl.

Abstract

The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes.

KEYWORDS:

Analytical ultracentrifugation; Computational modeling; Disordered and flexible systems; Dynamic light scattering; Size exclusion chromatography; Size exclusion chromatography coupled to multi-angle laser light scattering; Small angle X-ray scattering; Small angle neutron scattering

PMID:
27939506
DOI:
10.1016/j.ymeth.2016.12.002
[Indexed for MEDLINE]
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