Who Interacts With Whom and Why?

The word “protein” derives from the Ancient Greek word “protos” and essentially means “the most important” or “first”. And these building materials of life are exactly that, particularly so for Professor Juri Rappsilber, head of the Chair of Bioanalytics at TU Berlin. “They are the most diverse and variable building blocks of life. Nothing happens without proteins – they are key molecules in all living cells and are responsible for tissue and organ structure, function, and regulation in the human body,” he says. The Rappsilber Laboratory’s primary aim is to understand how proteins fold in their natural environment, what they interact with, and how they arrange themselves into larger structures.

One of the most advanced and modern mass spectrometers on the market

To achieve this, the researchers analyze the proteins in two main different processes that were further developed in the academic chair. Both processes are based on the creative computational inquiry of mass spectrometric data. The researchers acquire this data using one of the most advanced and modern spectrometers available on the market.

This liquid chromatography mass spectrometer (LC-MS) is the heart of the analysis conducted in Rappsilber’s labs. The 1.5 million-euro device, well-protected in its own temperature-controlled and shaded room, does not look like anything special. From the outside, you only see a smooth metal shell with an injection device on one side and a large screen on the other. The advanced technology remains hidden behind the metal facade.

How does a mass spectrometer work?

A mass spectrometer ionizes the injected sample by giving it an electric charge and brings it into the gaseous phase. The samples are the proteins to be analyzed, which were previously digested with a special enzyme into peptides - fragments of proteins. These ions are then separated in an electric field according to their mass-to-charge ratio. The resulting mass spectrum of peptides is compared with special protein databases to reconstruct the protein sequence. In a liquid chromatography mass spectrometer (LC-MS), mixtures of substances are separated by molecule size during chromatography before entering the mass spectrometer. This allows even the smallest quantities of substances to be analyzed.

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Crosslinking processes and data visualization

“We are not only interested in the pure protein sequence but also the dynamic 3D structure of a protein and its interactions within its natural environment, the cell,” explains Rappsilber. “We use a wide range of interdisciplinary techniques in our investigation.” His laboratory developed special expertise in the so-called crosslinking procedure as well as in data merging and visualization, the latter developed by a team from the Rappsilber group at the University of Edinburgh.

Crosslinking is a process in which functional groups of amino acids within a protein or between two proteins within a protein complex are joined together using a special “glue”. Afterwards, these proteins are analyzed in the mass spectrometer as described above. “Knowing which building blocks of a protein were close enough to be joined together by the crosslinking substances allows us to glean valuable information about the 3D structure of the proteins or protein complexes,” says Rappsilber. The Rappsilber group makes all of its published results and data freely accessible online. “My vision is to eventually be able to visualize the 3D structure of every single protein in every cell together with its interactions in a time-resolved manner,” says Rappsilber.

Professor Juri Rappsilber, head of the Chair of Bioanalytics

“Proteins are the building blocks of life and have always fascinated me,” says Juri Rappsilber. Rappsilber acquired his Diplom degree at TU Berlin in 1995, receiving the Erwin-Stephan-Preis for his excellent grades and completing his studies quickly. After several study and research stays abroad, including at Harvard Medical School, he was appointed professor of proteomics at the University of Edinburgh in 2010. He returned to TU Berlin as an Einstein professor in 2011, establishing the bioanalytics lab.

Swantje Lenz, research associate at the Chair of Bioanalytics

“I am from northern Germany and first came to Technische Universität Berlin to study biotechnology. During my master’s thesis in Professor Rappsilber’s group, I worked on optimizing a crucial step in our data processing pipeline. I then had the opportunity to remain in the group as a doctoral candidate. Currently, I am developing our special software further. It helps identify crosslinks, the bonds linking several peptides or proteins together. I am also working on integrating these crosslinks into protein structure modeling.”

Francis O’Reilly, research associate at the Chair of Bioanalytics

“I’m originally from a small village on the border of Northern Ireland and the Republic of Ireland. I studied in Edinburgh before moving to Heidelberg for my doctorate. I am interested in how proteins assemble into small molecular machines within a cell and which proteins are involved. In our research we are developing special new procedures to stabilize these molecular machines in the cell in such a way that we can then analyze them in the mass spectrometer. If we succeed, this would be a huge step forward in understanding how cells function.”

Ana Pérez-López, IPODI fellow in the Chair of Bioanalytics

“I did my doctorate in medical chemistry in Spain. From the beginning, I was obsessed with working at the interface between chemistry and biology, with the enormous potential to bring about life-improving changes. My interest in cancer research and my experience with intercellular metal catalysis led me to develop a gold-based catalytic chemistry for targeted cancer therapy during a research stay in Edinburgh. I transfered to the Rappsilber Laboratory upon receiving the IPODI scholarship. My goal is to produce better biocompatable catalyst systems.”