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

J Phys Chem B. 2013 Oct 24;117(42):13051-7. doi: 10.1021/jp402442p. Epub 2013 Jul 25.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amyloid beta-Peptides / chemistry*
  • Amyloid beta-Peptides / metabolism
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Phosphatidylinositol 3-Kinases / chemistry
  • Phosphatidylinositol 3-Kinases / metabolism
  • Prions / chemistry*
  • Prions / metabolism
  • Protein Structure, Secondary
  • Thermodynamics
  • src Homology Domains

Substances

  • Amyloid beta-Peptides
  • Prions
  • Phosphatidylinositol 3-Kinases