X-rays reveal L-shape of scaffolding protein

Structural biologists discover unexpected results at PETRA III

Illustration: scaffolding protein PDZK1

Artistic shape interpretation of the scaffolding protein PDZK1. (Credit: Manon Boschard)

An investigation at DESY's X-ray light source PETRA III has revealed a surprising shape of an important scaffolding protein for biological cells. The scaffolding protein PDZK1 is comprised of four so-called PDZ domains, three linkers and a C-terminal tail. While bioinformatics tools had suggested that PDZK1’s PDZ domains and linkers would behave like beads on a string moving around in a highly flexible manner, the X-ray experiments showed that PDZK1 has a relatively defined L-shaped conformation with only moderate flexibility. The team led by Christian Löw from the Centre for Structural Systems Biology CSSB  at DESY and Dmitri Svergun from the Hamburg branch of the European Molecular Biology Laboratory EMBL report their results in the journal Structure.

Similar to metal scaffolding which provides construction workers with access points to a building, scaffolding proteins mediate interactions between proteins situated on the membrane of the human cell. While the molecular structure of each of PDZK1's four individual PDZ domains has been solved using X-ray crystallography and NMR spectroscopy, the overall arrangement of the domains in the protein as well as their interactions was not yet understood.

Löw, a group leader at CSSB and EMBL, teamed up with his EMBL colleague Dmitri Svergun, who runs the P12 beamline at PETRA III, for his help in performing a systematic study of PDZK1 using small-angle X-ray scattering (SAXS). SAXS is an X-ray based technique that allows the analysis of proteins and other molecules in solution. “SAXS is a powerful method to obtain shape information of molecules,” explains Svergun.

The SAXS experiments with PDZK1 held some surprises for the scientists like the unexpected L-shape of the protein. They also revealed that PDZK1's linker regions are not simply disordered spacers but actively contribute to the proteins L-shaped conformation. “Taking a closer look at these intermediate regions will ultimately help us to fully understand the function and dynamics of PDZK1 as well that of other scaffolding proteins,” notes Nelly Hajizadeh, one of the first authors of the study.

Löw and Svergun’s collaboration not only resulted in the publishing of a structural model of PDZK1 but also demonstrates the power of using an integrated approach to solve complex structural biology questions. For the future, Löw and his group plan to examine PDZK1 in complex with binding partners using electron cryo-microscopy. “Only by integrating a range of techniques and collaborating with colleagues, will we be able to fully understand complex proteins like PDZK1,” states Löw.


Reference : 
Probing the Architecture of a Multi-PDZ Domain Protein: Structure of PDZK1 in Solution; Nelly R. Hajizadeh, Joanna Pieprzyk, Petr Skopintsev, Ali Flayhan, Dmitri I. Svergun, Christian Löw; Structure, 2018; DOI: 10.1016/j.str.2018.07.016