One focus of our research is structure-function investigations of integral membrane proteins. To date, the atomic structures of just over 1,100 membrane proteins are known (vs. over 90,000 soluble protein structures). This imbalance is in stark contrast to the fact that most genomes contain 20-30% membrane proteins.
In recent years, we have solved the atomic resolution structure of the light-driven ion pump bacteriorhodopsin (BR) in the resting state at very high resolution (1.4 Å). Together with the structures of several photocycle intermediates "frozen in mid-stroke", we have been able to develop a detailed atomic mechanism of light-driven ion pumping. In addition, the structures of a related membrane protein that serves as the primary receptor in archaeal phototaxis (sensory rhodopsin II), that of a photoreceptor from Anabaena, the first eubacterial rhodopsin structure, and that of xanthorhodopsin, a light-driven ion pump with a dual chromophore (primary & antenna), have been determined.
We have determined the structure of the proton-gated urea channel from the human pathogen H. pylori (Nature, Dec 2012). Six channels form a hexameric ring, and the channel pore has a novel architecture. This channel is essential for H. pylori survival in the low-pH medium of the stomach and is thus an attractive cancer target.
We have identified compounds that inhibit the channel at submicromolar concentrations. Thus, the second general area of interest is structure-based drug discovery.
Current research focus
- The acid-gated urea channel from Helicobacter pylori, a bacterium that is estimated to chronically infect about half of all humans, leading to ulcers and stomach cancer
- Annexin A2, metastasin (S100A4) and p11 (S100A10) are cancer and cardiovascular targets
- Reactivation of cancer mutants of p53, the well-known tumor suppressor
- Terminal uridylyl transferases involved in RNA-editing in trypanosomatids
- Inosine-5'-monophosphate dehydrogenase from the parasites P. falciparum and T. foetus
- Nuclear receptors, in particular PPAR-alpha (obesity)
We are studying annexins, a family of proteins which interact with phospholipid bilayers in a Ca2+-dependent manner. Annexins have been reported to mediate membrane aggregation and fusion events; they also modulate actin polymerization. Detailed structural studies of annexins are essential for understanding their properties and interaction with other proteins, such as S100 proteins, at the atomic level. We have determined several structures of a large subclass of annexins called alpha-giardins from the human pathogen, Giardia lamblia.
We have also solved the structure of a key enzyme in purine metabolism, inosine-5'-monophosphate dehydrogenase (IMPDH). IMPDH catalyzes the NAD-dependent conversion of IMP to XMP, which in turn is converted to GMP, an essential building block of DNA. The IMPDH-reaction is the rate-limiting step in GMP synthesis and is thus a promising target for anti-parasitic and anti-bacterial drugs.
3'-Uridylyltion of RNA is emerging as a phylogenetically widespread phenomenon, involved in processing events as diverse as uridine insertion/deletion RNA editing in mitochondria of trypanosomes and small nuclear RNA maturation in humans. This reaction is catalyzed by terminal uridylyltransferases (TUTases), which are template-independent RNA nucleotidyltransferases that specifically recognize UTP and belong to a large enzyme superfamily typified by DNA polymerase beta. Multiple TUTases, recently identified in trypanosomes, as well as a U6 snRNA-specific TUTase enzyme in humans, are highly divergent at the protein sequence level.
However, they all possess conserved catalytic and UTP recognition domains, often accompanied by various auxiliary modules present at the termini or between conserved domains. We have determined the x-ray structure of a novel trypanosomal TUTase, TbTUT4, which represents a minimal catalytically active RNA uridylyltransferase.
A further interest of my group is ultra-high resolution (1.0 Å or better) structures of phosphate binding protein and certain annexins. These studies require synchrotron-generated X-rays of very high brilliance. Atomic structures at this resolution are able to reveal details of hydrogen bonding and anisotropic motion that cannot be obtained by other methods.