Master projects are available in

• amyloid protein aggregation
• protein-protein interaction
• development of EPR techniques including very-high-field 275 GHz EPR

Projects are available in the group, ranging from 3 to 9 months. Projects are suitable for students with backgrounds in Physics, Chemistry and Life Science and Technology!

Master Project: Investigate intrinsically disordered proteins

Recently discovered proteins use flexibility to perform essential functions, such as regulating protein production in the cell. How can such pieces of nano-spaghetti perform such specific tasks? And how flexible is flexible?

Does the structure and conformation of the protein follow a random chain modelor are there sections that possess residual structure? A special interest derives from the finding that these proteins also occur in neurodegenerative diseases.

The project
Compare random chain models and predict experimental observables. 

Experiment
Measure properties of flexible proteins by electron paramagnetic resonance methods

Theory
Compare results to different model of random chains and derive flexibility parameters of the proteins. Parts of this project can also be done as a bachelor project. 

For details please contact huber@physics.leidenuniv.nl  tel: 071 527 5560

Master Project: Amyloid Oligomer Modeling

In neurodegenerative disease, amyloid oligomers are crucial intermediates that may cause the disease. These oligomers are transient and difficult to study. By Electron Paramagnetic Resonance it was shown that a peptide (green arrow) aggregates to hexameric oligomers that are toxic to cells.

Now we want to find out more about these oligomers: What is their structure, and why only peptide (I) aggregates, whereas (II) and (III) do not. The project is experimentally oriented, but can, in case of interest be combined with theory, such as state of the art molecular dynamics methods in collaboration with a group at the VU Amsterdam. 

Clearly, the bulky residue shown as a sphere must play a role, but which?

For you to find out! For details please contact huber@physics.leidenuniv.nl  tel: 071 527 5560