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Karim Fahmy - Structural Dynamics of Biomolecules

  • 1991: Dr. rer. nat., University Freiburg
  • 1991 - 1994: Postdoctoral work, Howard Hughes Medical Institute at Rockefeller University, New York, USA
  • 1994 - 1999: Habilitation, University Freiburg
  • 1999 - 2002: Research Group Leader, University Freiburg
  • 2002 - present: Head of Biophysics Division, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf (HZDR)
  • 2014 - present: Professor, BIOTEC, TU Dresden

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Previous and Current Research

Our studies address the structural transitions in biomolecules that underlie their respective biological function. We are particularly interested in the influence of the molecular environment on molecular structure, such as hydration-dependent conformations or lipid-dependent structures in membrane proteins. We use spectroscopic methods to follow in real time conformational transitions of membrane proteins in lipidic phases under functional conditions. Combining fluorescence and infrared spectroscopy with site-specific mutagenesis we have revealed crystallographically not resolved details on amino acid ionization states and H-bond networks that control the activation of G-protein-coupled receptors. Studies on transmembrane model peptides complement the data and allow deriving fundamental physical constraints on membrane protein structure. These studies are currently extended to metal-binding proteins using in house time-resolved luminescence spectroscopy of lanthanides as sensors for metal-binding sites.

Future Prospects and Goals

1. Little is known about the role of intra-protein water on structure and dynamics of membrane proteins. We use lipid-mimetic systems such as nanodiscs in order to study the role and mobility of intramembrane protein water in metal-binding membrane proteins.

2. New perspectives in Structural Biology have been opened by X-ray free electron lasers (FELs). we design nanoparticles of metal-binding proteins to derive information on metal coordination using X-ray FEL-induced photodissociation.

Selected Publications

  1. The Role of Phospholipid Headgroup Composition and Trehalose in the Desiccation Tolerance of Caenorhabditis elegans.  Abusharkh SE, Erkut C, Oertel J, Kurzchalia TV, Fahmy K. Langmuir 2014; 30:12897-12906
  2. Paramagnetic decoration of DNA origami nanostructures by Eu3+ coordination. Opherden L, Oertel J, Barkleit A, Fahmy K, Keller A. Langmuir 2014; 30:8152-9
  3. Formic acid interaction with the uranyl(VI) ion: structural and photochemical characterization. Lucks C, Rossberg A, Tsushima S, Foerstendorf H, Fahmy K, Bernhard G. Dalton Transact. 2013; 42:13584-13589
  4. Technical Aspects of Fourier Transform Infrared Spectroscopy for Biophysical Applications; Encyclopedia of Biophysics. Fahmy K. Roberts, Gordon (Ed). 2013; Springer, Germany
  5. 3D profile-based approach to proteome-wide discovery of novel human chemokines. Tomczak A, Sontheimer J, Drechsel D, Hausdorf R, Gentzel M, Shevchenko A, Eichler S, Fahmy K, Buchholz F, Pisabarro MT. PLoS One. 2012;7:e36151
  6. How worms survive desiccation: Trehalose pro water. Erkut C, Penkov S, Fahmy K, Kurzchalia T. Worm 2012; 1;61-65.
  7. Trehalose renders the dauer larva of Caenorhabditis elegans resistant to extreme desiccation. Erkut C, Penkov S, Khesbak H, Vorkel D, Verbavatz JM, Fahmy K, Kurzchalia TV.  Curr Biol. 2011; 21:1331-6
  8. Eu(3+)-mediated.polymerization of benzenetetracarboxylic acid studied by spectroscopy, temperature-dependent calorimetry, and density functional theory. Barkleit A, Tsushima S, Savchuk O, Philipp J, Heim K, Acker M, Taut S, Fahmy K. Inorg Chem 2011; 50:5451-9
  9. The role of water H-bond imbalances in B-DNA substate transitions and peptide recognition revealed by time-resolved FTIR spectroscopy. Khesbak H, Savchuk O, Tsushima S, Fahmy K. J Am Chem Soc 2011; 133:5834-42

Group Members

Tsushima, SatoruSenior Scientist
Oertel, JanaPostdoc
Philipp, JennyTechnician
Lessmann, ElisabethTechnician



Simon Alberti – Organization of cytoplasm across space and time

  • 2016 – present: Honorary Professor of Proteomics, BIOTEC, TU Dresden
  • 2016 – present: Senior Research Group Leader (W2) at the MPI-CBG Dresden
  • 2010 – 2015: Junior Research Group Leader at the MPI-CBG Dresden
  • 2005 – 2009: Post-doctoral Fellow at the Whitehead Institute for Biomedical Research in Cambridge (USA)
  • 2000 – 2004: PhD in Biology, University of Bonn

Previous and Current Research

Stressed cells undergo changes on multiple levels to alter their physiology, metabolism and architecture. Our work shows that many of these changes happen in a controlled manner and involve a reorganization of the cytoplasm and the formation of membrane-free compartments via a process known as phase separation. This challenges an established paradigm in cell biology, which posits that compartmentalization requires containment by membranes.

Our recent findings show that the material properties of the cytoplasm are widely adjustable and can be modified locally and globally along a continuum of physical states from liquid to gel to solid. Such changes in the cytoplasmic state, which on the molecular level are reflected by the formation of nanometer- to micrometer-sized assemblies, endow cells with spatiotemporal control over diffusion-limited biochemical processes. Most importantly, we recently discovered that the initially beneficial ability to change the material properties of the cytoplasm and form membrane-less compartments becomes detrimental with increasing age. This is because many compartment-forming proteins are hypersensitive to changing conditions and have a tendency to form aberrant structures that cause aging-associated diseases. Thus, we propose a new model for many age-related neurodegenerative diseases, where we link the physiological function of compartment-forming proteins with their role in disease.

Future Prospects and Goals

In the future, we will pursue two main research lines. First, we will study the changes in intracellular organization that cells undergo when they are stressed and enter into a protective, dormancy-like state. Second, we aim to understand the crucial link between compartment formation, aging and disease.


  1. Are aberrant phase transitions a driver of cellular aging? S. Alberti and A. A. Hyman. BioEssays, 38, 959-968.

  2. M. Ganassi, D. Mateju, I. Bigi, L. Mediani, I. Poser, H. O. Lee, S. J. Seguin, F. F. Morelli, J. Vinet, G. Leo, O. Pansarasa, C. Cereda, A. Poletti, S. Alberti, S. Carra. A surveillance function of the HSPB8-BAG3-HSP70 chaperone complex ensures stress granule integrity and dynamism. Molecular Cell, 63, 796-810.

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