(571r) Understanding the Role of Secondary Structure In Protein Aggregation

Understanding protein aggregation is key to solving problems both in bioprocessing where aggregation of partially folded proteins leads to reduced yields and in biomedicine where many diseases have been linked to the formation of fibrillar protein aggregates. However, studying the early steps in the aggregation is difficult as the process occur quickly and irreversibly. Consequently, computer simulation provides an attractive alternative or complementary method to experimental studies. However, accessing the time and length scales of interest in the aggregation requires using coarse grained models. One of the key ingredients of these models is that they are able to capture secondary structure formation. In this work we study a simple beta-sheet forming model which consists of overlapping beads with fixed bond lengths and angles interacting through directional bonds, a model which is based on the Kemp and Chen helical forming model.1 The directional bonds are meant to mimic the hydrogen bonding interactions found in beta sheets. As such we first find the directionality which is required so that only one hydrogen bond can be formed per bead and determine the phase behaviour for this model. We then compare the thermodynamics of the sheet-globule transition to that of the helix-globule elucidating the role of secondary structure in aggregation.

1. J. P. Kemp and J. Z. Y. Chen, ?Helical structures in proteins?, Biomacromolecules 2, 389 (2001).