Berlin 2012 – scientific programme
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BP: Fachverband Biologische Physik
BP 7: Posters: Proteins
BP 7.11: Poster
Monday, March 26, 2012, 17:30–19:30, Poster A
A method to construct the free energy landscape of peptide aggregation from molecular dynamics simulations. — •Laura Riccardi, Phuong H. Nguyen, and Gerhard Stock — Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
A broad range of diseases are associated with the conversion of polypeptide chains from their normally soluble form to insoluble fibrillar aggregates. One of the most studied pathogenic peptides is the Alzheimer β-amyloid peptide, and its fragment Aβ16−22 appears to be a perfect model system as it is among the shortest fragments which are able to form fibrils [1]. We propose a new method to identify and characterize the different conformational states occurring during the aggregation process. This method is general as no a priori knowledge of the dynamics of the process or the structure of the encounter complex is required. In the different steps, intramolecular and intermolecular interactions are considered as well as the degeneracy of the multi-molecule system. The obtained states are used to construct a network which reflects the free energy landscape of the process and helps to identify the aggregation pathways.
[1] P.H. Nguyen et al, Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock-lock mechanism. PNAS 104, 111 (2007)