Driving β‑Strands into Fibrils

Abstract

In this work we study contributions of mainchain and side chain atoms to fibrillization of polyalanine peptides using all-atom molecular dynamics simulations. We show that the total number of hydrogen bonds in the system does not change significantly during aggregation. This emerges from a compensatory mechanism where the formation of one interpeptide hydrogen bond requires rupture of two peptide–water bonds, leading to the formation of one extra water–water bond. Since hydrogen bonds are mostly electrostatic in nature, this mechanism implies that electrostatic energies related to these bonds are not minimized during fibril formation. Therefore, hydrogen bonds do not drive fibrillization in all-atom models. Nevertheless, they play an important role in this process since aggregation without the formation of interpeptide hydrogen bonds accounts for a prohibitively large electrostatic penalty (∼9.4 kJ/mol). Our work also highlights the importance of using accurate models to describe chemical bonds since Lennard-Jones and electrostatic contributions of different chemical groups of the protein and solvent are 1 order of magnitude larger than the overall enthalpy of the system. Thus, small errors in modeling these interactions can produce large errors in the total enthalpy of the system