However, SANS has a clear advantage over SAXS when applied to RNP complexes. In SANS, hydrogen
(or deuterons) nuclei are responsible for the scattering of the neutrons, as opposed to electrons that scatter X-ray radiation in SAXS. The biological particle under investigation is usually dissolved in aqueous solvent; this has its own scattering density in dependence of the percentage of D2O contained in the H2O-based buffer. Similarly, proteins have on average a different scattering density from nucleic acids and 2H-labelled RNAs or proteins scatter at higher density than their 1H-counterparts (Fig. 5). Thus, if the SANS scattering curve is recorded for an RNP complex in 42% D2O buffer, the average scattering Enzalutamide cell line density of the proteins is matched by the solvent, and therefore subtracted with the measurement of the reference buffer, while the scattering density of the RNA component of the complex dominates the curve. In this experiment it is possible to gain selective information on the shape of the RNA molecule(s) in the context of the complete RNP complex. Similarly if the SANS scattering curve is recorded in 70% D2O,
the average scattering density of the RNA is matched by the solvent while the proteins dominate the (negative) scattering density. This technique, called “contrast matching”, allows investigating the shape of single components of a complex in the context of the complete assembled particle [56]. The protein and RNA components can be further separated from each other using selective 2H-labelling of one protein Androgen Receptor Antagonist clinical trial or RNA species. In multi-component complexes a number of samples can be prepared with different labeling schemes, for each of which SANS data report on the shape of single components in the complex or on the relative position of two components. In early years, the SANS
contrast matching approach was used to study the ribosome particle and to generate a model of the complex, including the position of the tRNA [57], [58] and [59]; this model has been proven largely correct on the basis of crystal structures obtained years later. Others [60] Nintedanib (BIBF 1120) and we find it very useful to complement NMR data with SANS data in the calculation of the structure of RNP complexes. The SANS data can be used to derive distances between multiple domains or molecules in the complex (Fig. 5), which can then be imposed as restraints in structure calculation. In alternative, a pool of computer-generated structures can be selected on the basis of their agreement with several SANS curves measured with varied contrast for different 2H-labelled samples. In Fig. 6 we propose a possible workflow to determine the structure of high-molecular-weight RNP complexes by the combined use of NMR data and distance or shape information generated by complementary structure biology techniques.
Related posts:
- After incubating on ice for minutes, the extracts have been clear
- In mammals, clear identification of active and null domains is ev
- When applied to heart tissue, the MTB model involves apparent pas
- The Tyramide Signal Amplification Plus Biotin Kit was applied to
- To date, FISH is the check most often applied in clinical trials