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School of Biological and Biomedical Sciences

All Staff

Dr Ehmke Pohl


Researcher ID profile
Telephone: +44 (0) 191 33 43619
Member of the Durham X-ray Centre
Telephone: +44 (0) 191 33 43619

(email at ehmke.pohl@durham.ac.uk)

Research Interests

The major goal of the laboratory is to unravel the three-dimensional structures of proteins associated with virulence and disease. The results will be used to elucidate structure-function relationships with the ultimate goal of exploiting this information whenever feasible to improve existing or design novel ligands that possess the potential to become medically relevant. Although X-ray crystallography will be the dominant technique employed, complementary methods, including microPIXE, X-ray absorption spectroscopy, Isothermal calorimetry (ITC), are utilized.

Bacterial DNA-binding proteins and regulatory networks

The viability of all (pathogenic) bacteria depends greatly on adaption to the changing environment. Therefore, the regulation of gene expression in response of external signal and the regulatory networks governing these processes are of significant importance.  In our on-going effort to unravel the molecular basis of bacterial gene control we have solved the structures of a number of DNA-binding protein from Corynebacteria and Mycobacteria (Lucarelli et al. 2007, 2008). More recently we have determined the crystal of ClgR (Clp gene regulator) one of the central transcriptional activator in the stress response of Corynebacterium diphtheria (Russo et al. 2009).

Figure 1. Crystal structure of the ClgR dimer with the putative DNA-recognition helices shown in red (Russo et al. 2009) 

The protein adopts an all-helical dimeric structure with the putative DNA-recognition helices in an almost perfect position to bind to slightly bent B-DNA. Computer models depicted in Figure 2 suggest a way how pseudo-palindromic DNA is recognized.

Figure: Model of ClgR bound to DNA.


Glycolytic enzymes from T. tenax.

The anaerobic, facultative heterotrophic crenarchaeote Thermoproteus tenax was one of the first hyperthermophilic Archaea described and today serves as a model organism to study the many basic physiological processes including the central carbohydrate metabolism. Over the last years we have solved crystal structures of a number of enzymes from T. tenax in order to elucidate the structural basis of catalysis, enzymatic mechanism and regulation. The most recent example shown here is the crystal structure of KD(P)G aldolase solved in a covalent complex with pyruvate which helped to explain substrate promiscuity in this enzyme.
Figure 2 (Right): Ribbon diagram of KDPG Aldolase from T. Tenax (Pauluhn et al. 2008)

Protein crystallography laboratory

Our laboratory is affiliated to the Center for Bioactive Chemistry and has thus access to all molecular biology techniques for cloning, protein overexpression and purification. In addition, particular emphasis is given to the biochemical and biophysical characterization (for example ITC, ultra-centrifugation, mass spectrometry). These techniques are used to characterize the sample and hence to increase the crystallization success rate. The laboratory is equipped with an Akta Explorer FPLC for protein purification and an Innovadyne Screenmaker for high-throughput crystallization in nL scale. Diffraction
data will be collected on a Bruker MicroStar H rotating anode equipped with a Proteum 135 CCD detector. Nevertheless, a significant part of our diffraction experiments is carried out at third-generation synchrotron sources, including the Swiss Light Source (SLS), the European Synchrotron Radiation Facility (ESRF) grenoble, and the Diamond Light Source (DLS), Didcot, UK.

Collaborators and funding

We collaborate with many colleagues in the Department of Chemistry as well as the School of Biological and Biomedical Sciences.  The Biophysical Sciences Institute is of particular importance to support our cross-disciplinary research projects

Our external collaborators include microbiologists (Dr. M.L. Vasil, University of Denver, Colorado, and Dr. B. Siebers, Dr. R. Hensel from the University of Duisburg-Essen), biophysicists/protein crystallographers (Dr. E. Garman, University of Oxford), protein crystallographer and chemists (Dr. J. Yeh and Dr. C. Achim, Pittsburgh) and synchrotron scientists (Dr. A. Pauluhn, Swiss Light Source).

The work has been or is currently supported by the Royal Society, the BBSRC,  EPSRC and the Wellcome Trust.

References

  • Russo, S., Schweizer, J., Polen, T., Bott, M., Pohl, E. "Crystal Structure of the Caseinolytic Protease Gene Regulator, a Transcriptional Activator in Actinomycetes ", J. Biol. Chem. (2009) 284: 5208-5216.
  • Yeh, J.I., Pohl, E., Truan, D., He, W., Sheldrick, G.M., Du, S., Achim, C. "The crystal structure of non-modified and bipyridine modified PNA-duplexes. Chemistry - A European Journal. (2010) 16:11867-75.
  • Landsbury, A. Der Perng, M., Pohl, E., Roy A. Quinlan, R.A. "Functional symbiosis between the intermediate filament cytoskeleton and small heat shock proteins" in "Small Stress Proteins and human Diseases", ed. Simon, S., Arigo A.P. Nova Publisher (2010).
  • Lucarelli, D, Vasil, M.L., Meyer-Klaucke, Pohl E. "The metal-dependent regulator FurA and FurB from Mycobacterium tuberculosis". Int. J. Mol. Sci. (2008) 9:1548-1560.
  • Truan,D., Vasil, A., Stonehouse, M., Vasil, M.L., Pohl, E. "High-level over-expression, purification, and crystallization of a novel phospholipase C/sphingomyelinase from Pseudomonas aeruginos" (2013) Protein Expression and Purification, in press.
  • Quinlan, R.A., Zhang, Y., Lansbury, A., Williamson, I., Pohl, E., Sun, F., "Changes in the quaternary structure and function of MjHSP16.5 attributable to deletion of the I–X–I motif and introduction of the substitution, R107G in the a-crystallin domain", (2013), Phil Trans R Soc B in press.

Research Groups

School of Biological and Biomedical Sciences

Department of Chemistry

  • Materials: Synthesis and Structure

Research Interests

  • Protein Crystallography
  • DNA-Binding Proteins

Publications

Journal papers: academic