Energy evaluation of β-strand packing in a fibril-forming SH3 domain.

We examine the energetics of β-strand packing in a fibril-forming SH3 domain using a simple sequence-based energy model. First, we describe this packing energy function and then apply it to three model systems: Aβ, HET-s prion, and SH3 domain. The packing results of Aβ and HET-s are compared to and are consistent with available experimental and computational results. Moreover, our results show that a native β-strand in SH3 is strongly disfavored to pack with any other strand, in accord with recent NMR data. Finally, based on packing energy calculations, several SH3 models of β-strand packing are proposed that fit well with known electron microscopy maps.