Pioneering SAXS: Using X-rays to make the invisible visible in biological solutions

Small-angle X-ray scattering (SAXS) is a powerful technique for studying the size, shape, and dynamics of large biological molecules to help unveil their function.

SAXS is one of few structural biology technologies that can provide essential information about molecules directly in solution without the need to crystallise or flashfreeze samples. This opens up the possibility of probing proteins and nucleic acids in a variety of experimental conditions and of addressing biological questions relevant to applications ranging from drug discovery to synthetic biology.

Dmitri Svergun, Group Leader at EMBL Hamburg, has made exceptional contributions to SAXS instrumentation and has developed new methods, analysis tools, and software over the past two decades to bring SAXS into the mainstream for the structural biology research community worldwide.

The Svergun Group developed (and now operates) EMBL's SAXS beamline, which is powered by one of the world's brightest X-ray radiation sources, PETRA III at the German Electron Synchrotron Radiation Facility (DESY) in Hamburg. In conjunction, improvements in associated software tools have unlocked the potential of using high-throughput SAXS data to derive models of 3D molecular structures. ATSAS, developed at EMBL, is one of the most popular and comprehensive software packages for analysing and modelling SAXS data. The software has been downloaded more than 100,000 times by over 18,000 unique users from over 50 countries. Svergun also coordinated an initiative to improve sharing of SAXS resources and the unification of data standards and guidelines across SAXS facilities and communities in Europe. SAXS data from various research groups using beamlines around the world can now be easily shared and re-used in dedicated open-source databases such as SASBDB, which is maintained by EMBL. SASBDB contains over 2,400 experimental data sets (30% produced by EMBL's SAXS beamline), which have been used to generate over 3,500 models (80% of which used the ATSAS software).

beamline P12 instruments
The beamline P12 at EMBL Hamburg Credit: Svergun group/EMBL

Advancing scientific discoveries

Today, SAXS is accessible to even novice users and has become an invaluable tool for structural biologists to determine nanoscale structures and their dynamic changes over time. Since EMBL's newest SAXS beamline became available to the scientific community in 2012, an average of 250 users from around the world have taken advantage of this service every year.

One area where SAXS has been transformative is in synthetic biology. Recently, a team of Slovenian researchers led by Roman Jerala from the National Institute of Chemistry, Ljubljana, determined the molecular structure of artificial proteins using SAXS, in collaboration with EMBL scientists. This work builds on previous research where Jerala's group invented a method to design new protein structures named 'coiled-coil protein origami' after the Japanese art of paper folding. By using EMBL experimental services, the researchers were able to determine the molecular structures of synthetic proteins, show that they folded into the desired shape, and study the self-assembly process. This collaboration demonstrates EMBL's strength in taking an integrative structural biology approach: the molecular structures were verified and probed by combining SAXS data with data obtained from multiple other techniques at EMBL, such as electron microscopy, calorimetry, and computational modelling. Such an approach can have wide-reaching potential, according to Jerala: "We can tailor designed proteins to make new materials, deliver drugs and vaccines, and much more." Scientists at EMBL provided not only their expertise in SAXS but also the "tools to help make sense of the SAXS experimental data and create 3D models". Fabio Lapenta, a postdoctoral researcher working on the project, highlighted the importance of working with EMBL: "SAXS analysis was crucial in identifying which design leads to the desired shapes, and the superb tools developed at EMBL allowed us to detect unique features of our designed cages [proteins]." The results of the study were published in the leading scientific journal Nature.

EMBL Hamburg's reputation for the application of SAXS in complex research projects has led to growing interest from and collaborations with industry. In late 2015, EMBL launched BIOSAXS, a spin-off company offering SAXS services to industry for medical and material sciences research. Projects are planned in close consultation with industry users and carried out by the expert team at EMBL, ensuring high-quality results.

In 2020, BioNTech, a biotech company working with Pfizer, used BIOSAXS for Project Lightspeed, a groundbreaking programme to develop a vaccine against COVID-19. In the words of Ugur Sahin, Chief Executive Officer of BioNTech:

Our aim is clear: Making a potential vaccine available to the public as quickly as possible -- worldwide.

To realise this mission, BioNTech, together with researchers at Johannes Gutenberg University Mainz, Tel Aviv University, Leiden University, and Forschungszentrum Jülich, published the results of several studies using SAXS to show how to improve the packaging and delivery of RNA into human cells. These studies paved the way for the development of a new class of vaccines that use lipid nanoparticles to deliver messenger RNA (mRNA) into cells. In less than a year, this research resulted in a pioneering mRNA vaccine against COVID-19, which is now available in over 116 countries worldwide. The work showcases EMBL's important role in supporting industry and academic collaborations to accelerate innovation in technology and medicine. Scientists at EMBL are also using SAXS to model the structure of coronavirus to develop new tests and treatments in collaboration with other researchers.

EMBL Hamburg’s practical and lecture courses allow young scientists to gain hands-on experience and explore various aspects of SAXS in studying biomolecules.
Using EMBL Hamburg’s world-class beamline P12 at DESY’s PETRA III synchrotron, researchers directed powerful X-ray beams at artificial proteins called coiled-coil origami proteins. Credit: Fabio Lapenta

What the future holds

EMBL continues to push boundaries, expanding its offer of new applications and its role as a 'onestop shop' for integrative structural biology services for the scientific community. The future arrival of PETRA IV, an even more powerful X-ray source, at EMBL Hamburg in 2025 "will offer a unique opportunity to start an entirely new era of services in structural biology", said Matthias Wilmanns, Head of EMBL Hamburg. Integrated with other techniques, SAXS will continue to play an important role in the comprehensive structural analysis of biological molecules in solution.

EMBL’s experimental services deliver substantial value to Europe by delivering scientific services and thereby enabling researchers to conduct novel and demanding experiments that could not be easily achieved at a purely national level, an independent review found.

The global consultancy Technopolis Group, specialising in research and innovation policy, conducted a survey and analysis of external (non-EMBL) users of EMBL’s experimental services. The survey aimed to identify whether users perceived scientific, technological, societal and economic benefits as a result of utilising the experimental services at EMBL Barcelona, Grenoble, Hamburg, Heidelberg, and Rome.