Structural Biology Group

Structure determination of unstable reaction intermediates

p21_caged_reaction.jpgMany (bio)chemical reactions are complex, often involving several reaction intermediates. For a thorough understanding of the reaction mechanism it is necessary to know all steps occurring along the reaction coordinate the kinetics of their interconversion, their equilibrium constants, and the three-dimensional structures of the intermediates. Crystallography, NMR, and electron microscopy are excellent tools for determining three-dimensional structures to atomic resolution, but are generally regarded as static methods, averaging over space and data collection time.

p21_reaction_flow.jpgBecause data acquisition is generally lengthy and intermediates are usually short-lived, their structures cannot normally be determined by conventional approaches. Thus, transition state or substrate analogues, inhibitors and mutants are traditionally used to obtain mechanistic information. In the last two decades, however, crystallographic structure determination of species that are short-lived has become feasible either on ultra-fast time scales ("time-resolved crystallography") or by slowing reactions via manipulation of, for example, temperature, pH, or slow substrates ("kinetic crystallography", "trapping"). Both approaches require rapid and efficient initiation of the reaction in the crystal. We have developed protocols for handling caged compounds in crystallographic studies which opened up investigations of enzymatic systems operating on phosphate-containing substances.

Vesicular Protein Transport



The biogenesis of membranes, the delivery of proteins to specific cellular compartments, protein secretion and endocytosis are mediated by vesicular intermediates. The formation of transport vesicles, their correct targeting and the specificity of membrane fusion events require multicomponent transport machineries. Many of their components are highly conserved from the unicellular yeast to human brain cells. Our current research is focused on so-called Ypt/Rab-proteins and their interacting effector proteins for complex formation.

Structure-Activity Studies on DNA Methyltransferases




In cooperation with Professor Elmar Weinhold (RWTH Aachen) we are investigating the structure-function- relationship of DNA methyltransferases (MTases). DNA methylation has many biological functions, including protection against endogenous restriction endonucleases, directing DNA mismatch repair after replication and regulation of gene expression. Whereas the transfer of the activated methyl group of the cofactor S-adenosyl-L-methionine (AdoMet) to the extracyclic amino group of adenine (N6-DNA MTases) is well investigated, the removal of methylgroups from nucleotide bases is less well understood.

Protein chemistry and chemical tools

p21_caged_nbd_xsticks2.jpgThis work is concerned with the development and application of derivatives of natural products as tools for modifying of proteins and nucleic acids for studying structure-function relationships of biomacromolecules. For time-resolved and kinetic crystallography as well as for biophysical characterization of proteins and protein complexes the modification of proteins and their ligands is frequently needed. The main applications are the incorporation of heavy atom into biomacromolecules useful for solving the phase problem in X-ray crystallography and the site-directed incorporation of chromophor labeled amino acids for spectroscopic detection systems.

Redox proteins involved in sulfur oxidation and carbohydrate modification

sox_reaction_cycle.jpgThe sox (sulfur oxidizing system) gene cluster in Paracoccus pantotrophus consists of 15 genes. The 7 essential proteins build the 4 protein complexes SoxXA, SoxYZ, SoxB and SoxCD. These proteins are quite different in their type and their proposed catalytic reaction. In cooperation with Prof. C. Friedrich (University Dortmund) we determine the structure of selected members of this sox gene cluster.

gatdh_tetramer_ribbon.jpgIn cooperation with Prof. F. Giffhorn (University Saarland) we are working on the structure-function characterization of different dehydrogenases converting carbohydrates as their major substrates. These projects have some relation to biotechnology and protein design.

Proteins as targets for new antibiotics



In cooperation with Prof. Ch. Klein (University Heidelberg) we investigate different proteins in complex with putative pharmaceutical inhibitor leads.