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CIC04_Master_Origins of protein misfolding from structural propensities of small peptides

Protein misfolding and aggregation diseases like Alzheimer’s, Parkinson’s or diabetes are not caused by bacteria or viruses, but by proteins that do not fold correctly. Current research indicates that the binding of healthy proteins on the surface of fibrils triggers misfolding. Hence a pre-existing fibril may seem necessary. Here we attempt to make a connection between this mechanism and the intrinsic propensities of short polypeptide sequences that are pathogenic.

We tackle this problem using atomistic molecular dynamics simulations of the short peptides tuning their intrinsic conformational propensities. This can be easily done by using different force-fields that result in different degrees of helix or beta sheet content. The calculations will be performed using well established software packages and will require learning shell scripting and computer programming. Although prior knowledge of these tools is not essential, we are seeking for highly motivated candidates for acquiring these skills.


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