Finding order in chaos

Scientists determine the structure of glass-shaping protein in sponges.

Sponges are some of the oldest animals on Earth. They live in a wide range of waters, from lakes to deep oceans. Remarkably, the skeleton of some sponges is built out of a network of highly symmetrical glass structures. Researchers from TU Dresden and the Swiss Light Source at the Paul Scherrer Institute in Switzerland are the first to determine the three dimensional (3D) structure of a protein responsible for glass formation in sponges. They explain how the earliest and, in fact, the only known natural protein-mineral crystal is formed. The results were published in the journal “PNAS.”

Glass sponges – as the name suggests – have a glass-based skeleton composed of a network of glass needles, hooks, stars, and spheres. To achieve such a unique architecture they have to manipulate the shape of disordered glass to form highly regular and symmetrical elements. Thin crystalline fibers made of a protein, known as silicatein, are present in channels inside of these glass elements. It is known that silicatein crystals are responsible for glass synthesis in sponges and for shaping the glass skeleton. However, until now efforts to determine the 3D structure of this protein, describe how it assembles into crystals, and how those form the glass skeleton were unsuccessful. Mainly, because nobody was able to reproduce these crystals in the lab.

A team of researchers led by Dr. Igor Zlotnikov from the B CUBE –Center for Molecular Bioengineering at TU Dresden tried an unusual approach. Instead of producing silicatein in the lab and trying to obtain lab-grown crystals to study the structure, the researchers decided to take the glass needles from a sponge skeleton and analyze the tiny crystals that already exist inside.

The Zlotnikov group together with researchers from the Dresden Center for Nanoanalysis (DCN) at the Center for Advancing Electronics Dresden (cfaed) used high-resolution transmission electron microscopy (HRTEM) to take a closer look at silicatein crystals packed inside the glass needles. “We have observed an exceptionally ordered and at the same time complex structure. Analyzing the sample we have seen that it is a mixture of an organic and inorganic matter. Meaning that both proteins and glass form a hybrid superstructure that somehow shapes the skeleton of sponges,” explains Dr. Zlotnikov.

A traditional way of obtaining a 3D structure of a protein is to expose its crystal to a beam of X-rays. Each protein crystal scatters the X-rays in a different way providing a unique snapshot of its internal arrangement. By rotating the crystal and collecting such snapshots from many angles, the researchers can use computational methods to determine the 3D protein structure. Such an approach is widely used and is the basis of modern structural biology. It works well for crystals of at least 10 microns in size. However, the Zlotnikov group wanted to analyze silicatein crystals which were about 10 times smaller. When exposed to X-rays they were almost immediately damaged, making it impossible to collect a complete data set of snapshots from multiple angles.

With support from the team at PSI’s Swiss Light Source (SLS), the researchers used a new emerging method known as serial crystallography. “You combine diffraction images from many crystals,” says Filip Leonarski, beamline scientists at PSI, who was involved in the study. “With the traditional method you shoot a movie. With the new method you get many snapshot which you combine afterwards to decipher the structure.” Each snapshot is taken at a different part of the tiny crystal or even from a different crystal.

In total, the researchers collected more than 3500 individual X-ray diffraction snapshots from 90 glass needles at completely random orientations. Using state-of-the-art computational methods they were able to find order within the chaos and assemble the data to determine the first complete 3D structure of silicatein.

“Before this study, the structure of silicatein was hypothesized based on its similarity to other proteins,” says Dr. Zlotnikov. Using the newly obtained 3D structure of silicatein, the researchers were able to understand its assembly and function inside the glass skeleton of the sponge. They built a computational model of the superstructure within the glass needle and explained the initial complex images of the protein-glass superstructures obtained with the HRTEM.

“We provided detailed information on the existence of a functional 3D protein-glass superstructure in a living organism. In fact, what we describe is the first known naturally occurring hybrid mineral-protein crystalline assembly,” concludes Dr. Zlotnikov.
Dr. Igor Zlotnikov is a leader of a multidisciplinary group at the B CUBE, TU Dresden. The group studies the interplay between physics of materials and cellular control. The Zlotnikov group implements state-of-the-art techniques from a large spectrum of fields in life and physical sciences to address the fundamental question of how the nature uses thermodynamic principles to generate complex structures. The group is funded by the Federal Ministry of Education and Research (BMBF; grant 03Z22EN11).

B CUBE – Center for Molecular Bioengineering was founded as a Center for Innovation Competence within the initiative “Unternehmen Region” of the German Federal Ministry of Education and Research. It is part of the Center for Molecular and Cellular Bioengineering (CMCB). B CUBE research focuses on the investigation of living structures on a molecular level, translating the ensuing knowledge into innovative methods, materials and technologies.
www.tu-dresden.de/bcube

Dresden Center for Nanoanalysis (DCN)
As a technology platform of cfaed, the DCN provides both equipment and know-how for nanoanalytical materials characterization to the entire user community of the TU Dresden and its partner institutions within the DRESDEN-concept science alliance. In a sustainable concept, the central access to high-end equipment, especially in the field of electron, ion and X-ray microscopy, and the provision of a state-of-the-art infrastructure that includes magnetically shielded, highly specialized low-noise laboratories, synergies will be generated and cooperation is stimulated across any scientific boundaries.
https://cfaed.tu-dresden.de/dcn

Wissenschaftliche Ansprechpartner:

Dr. Igor Zlotnikov
Tel.: +49 351 463-43090
Email: igor.zlotnikov@tu-dresden.de
Webpage: www.tu-dresden.de/bcube

Dr. Darius Pohl
Senior Scientist TEM
Tel.: +49 351 463-35452
Email: darius.pohl@tu-dresden.de

Originalpublikation:

Stefan Görlich, Abisheik John Samuel, Richard Johannes Best, Ronald Seidel, Jean Vacelet, Filip Karol Leonarski, Takashi Tomizaki, Bernd Rellinghaus, Darius Pohl and Igor Zlotnikov: Natural hybrid silica/protein superstructure at atomic resolution. PNAS (November 2020)
doi: https://doi.org/10.1073/pnas.2019140117