Lab Themes
RUB » Department of Biophysics » X-ray structure analysis of proteins

Lab Themes

What is protein crystallography all about?

The determination of whole genomes of several organisms was a milestone in our attempts to understand key processes in biologigal systems. Every single gene codes for a specific protein and determins thereby its three dimensional structure. Nevertheless we are still not able to predict protein 3D-structures efficiently based on the genetic information alone. But the knowledge of the exact arrangement of the protein atoms in space in combination with functional data is of major importance for our understanding of proteins as key motors of all biological processes. Protein structures i.e. can allow the rational design of new drugs for a given target protein.

For this reasons we experimentally determine protein 3D-structures with the method of X-ray protein crystallography. The method is able to provide this information at atomic level, but relies on our ability to grow crystals of the target protein. Therefore one focus of our work is on preparative protein production to get sufficient material of highest purity for crystallization screenings. This part of our work relies on standard molecular biological, biochemical and especially column chromatographic methods.

Once we are able to reproducibly grow crystals of sufficient quality, we use them for X-ray diffraction experiments. In these experiments we determine first the internal order and quality of the crystals, and use this information to generate an atomic model of the protein. In this part of the project we use experimental setups in our labs and at synchrotron light sources in Europe, i.e. the Swiss light source (SLS) in Villigen, Switzerland, or the European synchrotron radiation facility (ESRF) in Grenoble, France. For data processing we rely on linux computing clusters and high end stereo graphics workstations.

One focus of our work lies on proteins from the photosynthesis apparatus of algae and bacteria. Another area of interest are membrane proteins involved in active transport across the cytoplasmic membrane.

As a central project in the Protein Research Department of the RUB we are the first contact for groups from within the university (especially from the departments of Biology and Biotechnology, Chemistry and Biochemistry and Medicine), who need to add the structural perspective to current projects.

Our main goal in education is to teach students with a biological background the effective, yet critical use of the protein structural information availible in the public databases.

Structural biology, of which proteincrystallography is a part, is a classical example for interdisciplinarity. The direct interaction of biologists, chemists and physicists is of major importance for the success of our work. During practical work students can aquire expertise in areas requested for work in modern companies in life sciences and biotechnology.

What's Biophysics?

Was sind Membranproteine?

Zellen und Zellorganellen sind von komplexen Membransystemen umgeben, wodurch Kompartimente voneinander bzw. Zellen vom Extrazellularraum abgegrenzt werden. Biologische Membranen bestehen aus Lipiden und Proteinen, wobei man zwischen Transmembranproteinen und membranständigen Proteinen unterscheidet. Membranproteine leisten den Austausch/Transport ausgewählter Substanzen und dienen der Kommunikation durch die Verarbeitung von Signalen. Sie übernehmen ebenfalls enzymatische Aktivität und sind an der biologischen Energiewandlung beteiligt.

Der Transport von Molekülen und Ionen wird beim „passiven Transport“ u.a. von Kanälen, Poren und Permeasen gewährleistet. Desweiteren unterscheidet man zwischen „primär“ und „sekundär aktivem Transport“, der einen direkten Energielieferanten benötigt oder indirekt beispielsweise durch den Aufbau eines Konzentrationsgradienten ermöglicht wird.

Ein Beispiel für Signaltransduktion bei Membranproteinen sind G-Protein gekoppelte Rezeptoren, die bei äußeren Einflüssen wie Lichtreizen einen aktiven bzw. inaktiven Zustand einnehmen können und dann, je nach Funktion, eine Signalkaskade in Gang setzen bzw. unterbrechen.

Durch die Aktivität von Membranproteinen können elektrochemische Gradienten entstehen. So wird etwa bei der Zellatmung ein Protonengradient erzeugt, der dazu genutzt wird um den Energielieferanten ATP zu synthetisieren.

What are Structures?

Proteins are atomic machines. Each protein has a specific 3-dimensional form - its structure - in order to be able to fulfill its function in the most optimal way. The order of aminoacids is important and imminently determine a protein's structure. They form a so called secondary structure, alpha-helices and b-strands that then assemble into the teriary structure which is the final 3-dimensional form of the protein. Often, the structure changes dramatically during the catalytic process of a protein, and it is this change in form that we are interested in the most.
Protein structures can grouped into classes of similarily folded proteins. Suprisingly research has reached some sort of end point in that respect. Since 2008 no new protein fold has been discovered and all newly determined protein structures resemble a known fold.
This however does not indicate that structure determination of proteins is obsolete. Each new protein structure tells a new story about the atomic nature of its chemistry.