The proposed cluster will focus on new, primarily mechanistic and structural developments, the evolution of systems for the folding and transport of proteins and the cooperation of the different machineries, as well as their specificity and the biochemical and molecular basis of the function of individual components. Only an integrated approach covering a vast range of sophisticated techniques including short time spectroscopy and single molecule spectroscopy (area A) will allow us to further understand the underlying mechanisms and their structural requirements. The increasing availability of genome sequences combined with bioinformatics and proteome analyses has led to the emergence of unifying concepts and systems-specific aspects. Single molecule techniques for the involved compounds and imaging in isolated organelles or even the living cell are required. Some of these novel methodologies are now beginning to be exploited to great effect. As a consequence, an increased input from chemistry and physics is required to integrate these with the more traditional approaches.

Most of protein translocation nanomachines are highly sophisticated, comprising multiple receptors, motors, checkpoints, gated channels and complex regulatory circuits. Only an integrated approach covering different protein translocation systems from prokaryotes to eukaryotes and the use of nanomechanical approaches (area A) will allow us to understand underlying principles of translocation mechanisms and their structural requirements. Atomic resolution structures of components of the many protein translocation machines that are being solved will lead to revision and fine-tuning of our mechanistic insights into the way they function. At the same time, new techniques in molecular and cellular biology allow us not only to raise and address new mechanistic questions but also to visualize translocation at the molecular level. Methodologies such as biophysics, bioinformatics, and imaging in living cells, which are new to the field can now be exploited to great effect, call for greater knowledge of core subjects such as chemistry and physics and their greater integration with traditional approaches mainly from biology.

The immense significance of protein trafficking in the overall field of molecular and cellular biology is attractive to researchers from different fields to address key questions concerning these complex systems.

Some of the key issues to be addressed are:

• What are the client protein spectra of the different chaperone machines and what features makes them depend on chaperone function?

• How exactly is the conformation of client proteins affected by chaperones?

• A quantitative and comprehensive analysis of the chaperone network within a cellular compartment.

• What is the structural basis for the different routes of active protein movement in the cell?

• A comprehensive mechanistic understanding of the protein import machinery in chloroplasts and mitochondria.

• The structure-function analysis of the Sec Translocation system

• What is the unique folding space and functional range accessible to fibrous proteins.

• A mechanistic understanding of bacterial type III secretion and the regulatory effects of secreted proteins in receiving host cells.