Molecular Dynamics Studies of Atomistically Determined Fibrillar Assemblies: Comparison of the Rippled β-Sheet, Pleated β-Sheet, and Herringbone Structures

Pauling and Corey expected that a racemic mixture would result in a rippled β-sheet, however, it has been known from experiments that the racemic mixtures of triphenylalanine lead to a herringbone structure. Because of the theoretical limitations concerning crystal structures such as rippled β-sheet, it is inevitable to understand how the interplay of the amino acids prefers a specific structural motif. In this paper we use molecular dynamics to understand the sequence- and enantiomer-dependent structures by comparisons between rippled β-sheet and pleated β-sheet, solvated and anhydrous rippled β-sheet, and rippled β-sheet and the herringbone structure, based on thermodynamics and structures at the atomic level. The tripeptides select the favored structure that can be stabilized through aromatic or hydrogen bonding interactions between tripeptides. Furthermore, the solubility is determined by the environment of space that is created around the side chains. Our findings provide comprehensive insight into the crystallized fibril motif of the polypeptide.