Side Chain Geometry Determines the Fibrillation Propensity of a Minimal Two-Beads-per-Residue Peptide Model

The molecular mechanism of fibrillation is an important issue for understanding peptide aggregation. In our previous work, we demonstrated that the interchain attraction and intrachain bending stiffness control the aggregation kinetics and transient aggregate morphologies of a one-bead-per-residue implicit solvent peptide model. However, that model did not lead to fibrillation. In this work, we study the molecular origin of fibril formation using a two-beads-per-residue model, where one bead represents the backbone residue atoms and the other the side chain atoms. We show that the side chain geometry determines the fibrillation propensity that is further modulated by the modified terminal beads. This allows us to bring out the effects of side chain geometry and terminal capping on the fibrillation propensity. Our model does not assume a secondary structure and is, perhaps, the simplest bead-based chain model leading to fibrillation.