Figure 1: User interface of CHROMIXS (CHROMatography Inline X-ray Scattering) for rapid reduction and analysis of SEC-SAXS data, either automatically or interactively (Panjkovich & Svergun, 2018).
Figure 2: Ab initio shape (beads) and a rigid body model (Cα traces) of homotetrametic protein Prp19 constructed from its core crystal structure with added missing portions and peripheral WD40 domains (de Moura et al., 2018).
The Svergun group runs and further enhances the biological small-angle X-ray scattering beamline at the PETRA III storage ring and develops novel approaches for scattering data analysis and hybrid structural modelling.
Previous and current research
Small-angle X-ray scattering (SAXS) reveals low-resolution (1-2 nm) structures of biological macromolecules and functional complexes in solution. The resolution and reliability of SAXS-based structural models have increased significantly over the past decade. Subsequently, biological SAXS revealed a rapid growth of popularity in the scientific community worldwide.
Our group leads the development of novel approaches for SAXS data analysis and interpretation. We have developed methods for ab initio shape reconstruction, rigid body modelling, analysis of flexibility and oligomeric composition from SAXS data, widely employed in the community. Particular attention in our work is given to the joint use of SAXS with other structural and bioinformatics methods for hybrid modelling. The methods are implemented in the world’s most used SAXS program package, ATSAS, presently employed by more than 16,000 users from over 50 countries.
Our group operates and maintains a dedicated high brilliance synchrotron beamline – P12 at DESY’s third generation storage ring, PETRA III. P12 has a robotic sample changer for rapid automated experiments and possesses a data analysis pipeline for building structural models online. The beamline offers options for remote access, as well as an in-line purification setup using size exclusion chromatography with parallel biophysical and SAXS measurements (Figure 1). A high flux multi-layer optics and a fast Eiger-4M detector (Dectris, Switzerland) allow for kinetic studies with sub-millisecond time resolution.
In collaborative projects with the users from the ever-growing SAXS community, group members offer advice on sample preparation and provide help with data collection, analysis and structural modelling. SAXS is employed to study overall structural organisation and conformational transitions of macromolecules or complexes (Figure 2) and also to quantitatively characterise oligomeric mixtures, intrinsically unfolded proteins, hierarchical systems and other objects of high biological and medical importance.
Future projects and goals
The present and future work of the group includes:
- Further methods development for the reconstruction of macromolecular structures from X-ray and neutron scattering data.
- Hybrid applications of SAXS with crystallography, NMR, electron microscopy and bioinformatics to construct and validate structural models.
- Participation in collaborative SAXS projects at the P12 beamline.
- Further extension of P12 capabilities including time-resolved and anomalous scattering techniques.
Panjkovich A, Svergun DI. (2018) CHROMIXS: automatic and interactive analysis of chromatography-coupled small-angle X-ray scattering data. Bioinformatics, 34:1944-1946. doi: 10.1093/bioinformatics/btx846.
de Moura TR, Mozaffari-Jovin S, Szabó CZK, Schmitzová J, Dybkov O, Cretu C, Kachala M, Svergun D, Urlaub H, Lührmann R, Pena V. (2018) Prp19/Pso4 Is an Autoinhibited Ubiquitin Ligase Activated by Stepwise Assembly of Three Splicing Factors. Mol. Cell, 69: 979-992. doi: 10.1016/j.molcel.2018.02.022.