2019Jimenez SAXS

Citation

Jimenez, A.; Jonic, S.; Majtner, T.; Oton, J.; Vilas, J. L.; Maluenda, D.; Mota, J.; Ramirez-Aportela, E.; Martinez, M.; Rancel, Y.; Segura, J.; Sanchez-Garcia, R.; Melero, R.; Del Cano, L.; Conesa, P.; Skjaerven, L.; Marabini, R.; Carazo, J. M. & Sorzano, C. O. S. Validation of Electron Microscopy Initial Models via Small Angle X-Ray Scattering Curves. Bioinformatics, 2019 , 35 , 2427-2433

Abstract

Cryo Electron Microscopy (EM) is currently one of the main tools to reveal the structural information of biological macromolecules. The reconstruction of three-dimensional (3D) maps is typically carried out following an iterative process that requires an initial estimation of the 3D map to be refined in subsequent steps. Therefore, its determination is key in the quality of the final results, and there are cases in which it is still an open issue in single particle analysis (SPA). Small angle X-ray scattering (SAXS) is a well-known technique applied to structural biology. It is useful from small nanostructures up to macromolecular ensembles for its ability to obtain low resolution information of the biological sample measuring its X-ray scattering curve. These curves, together with further analysis, are able to yield information on the sizes, shapes, and structures of the analyzed particles. In this paper, we show how the low resolution structural information revealed by SAXS is very useful for the validation of EM initial 3D models in SPA, helping the following refinement process to obtain more accurate 3D structures. For this purpose, we approximate the initial map by pseudo-atoms, and predict the SAXS curve expected for this pseudo-atomic structure. The match between the predicted and experimental SAXS curves is considered as a good sign of the correctness of the EM initial map. The algorithm is freely available as part of the Scipion 1.2 software at http://scipion.i2pc.es/.

Links

https://academic.oup.com/bioinformatics/article/35/14/2427/5221010