Molecular Dynamics

Course with Participations of Group Members

Offers for Theses in the Group

Computer simulation of the binding of peptides to RNA

RNA molecules are involved in many processes in cells. Typically, these processes involve the interaction with proteins and peptides. There are specific short peptide segments that often mediate the interaction between proteins and RNA. In the BSc thesis project the binding of short tripeptides with a central Arginine residue (often part of RNA binding peptides) and RNA will be studied using Molecular Dynamics simulations. Aim is to identify and characterize the preferred binding sites on the RNA molecules. It is hoped that it will allow the prediction of how and where larger proteins (that contain such short RNA binding motifs) bind to RNA molecules.

suitable as

• Bachelor’s Thesis Physics

Supervisor: Martin Zacharias

Molecular simulation of amyloid structure folding

Natural proteins typically form stable globular structures. However, approximately 30% of natural proteins do not adopt a single stable structure but adopt a so called disordered state. Disordered proteins but also mutated globular proteins can aggregate to form regular amyloid structures. Such structures are involved in many diseases. In the BSc-project a computational methodologyto predict the amyloid structure of protein sequences will be developed and tested. The method is based on including information extracted from known amyloid structures to guide molecular dynamyics simulations.

suitable as

• Bachelor’s Thesis Physics

Supervisor: Martin Zacharias

Studying amyloid flexibility using MD simulations

Amyloid structures can form by aggregation of misfolded protein molecules or peptides. These aggregates are involved in several diseases. The various amyloid structures differ in the conformational flexibility and stability. Very flexibile amyloid structures are more likely to disaggregate and can be recognized and eliminated by proteases and immune molecules. Aim of the BSc thesis is to investigate the conformational flexibility and dynamics of different amyloid structures using computer simulations and to understand the physical origin of the dynamics of amyloid structures.

suitable as

• Master’s Thesis Biophysics

Supervisor: Martin Zacharias

Current and Finished Theses in the Group