Emeritus Group, Physical Biochemistry
Structural, kinetic and thermodynamic analysis of simplified interaction systems
As a synthesis of the approaches and techniques adopted by the groups of the department, we are interested in understanding how such systems or modules operate and how they are integrated into the overall intracellular network. The word module is used flexibly to adapt to the particular level of organization addressed.
One of the main interests in the department is a system that has been evaluated at the molecular level with the range of molecular biological, biochemical, biophysical and chemical techniques available concerns the role of the Rab family of small guanosine nucleotide binding proteins in the regulation of intracellular vesicular transport. The particular aspects which have been focused on are the post-translational modification of Rab proteins with geranylgeranyl residues, insertion of these residues into membranes and retrieval from membranes ("Rab recycling"). The figure below gives an overview of Rab cycling and indicates structures which have been determined in the work of the department (see Alexandrov and Rak pages for details).
If we include several structures from other groups (not shown), we have the situation that in this "mini-system" most key structures are known and form an important basis for understanding the action of Rab. Our current work is concentrated on establishing a complete quantitative understanding of this cycle and has led to an accepted description of the events involved with, for example, extraction of Rabs from membranes by GDI and explains several differences between GDI and REP that were not previously understood. Future work will extend this type of analysis to other events in the cycle and will transfer knowledge and reagents arising from in vitro studies to cellular studies using new fluorescence microscopy techniques, largely in collaboration with the group of Philippe Bastiaens. These will, for example, address questions concerning timing and location of significant steps, including prenylation, delivery of Rabs to specific membranes, interaction of Rabs with effectors, including those which provide links to actin or microtubule based motor systems and those involved in initial recognition between transport vesicles or related structures and target membranes.