Simulation of the amide I absorption of stacked β-sheets

J Phys Chem B. 2011 Feb 3;115(4):749-57. doi: 10.1021/jp109918c. Epub 2010 Dec 17.

Abstract

Aggregated β-sheet structures are associated with amyloid and prion diseases. Techniques capable of revealing detailed structural and dynamical information on β-sheet structure are thus of great biomedical and biophysical interest. In this work, the infrared (IR) amide I spectral characteristics of stacked β-sheets were modeled using the transition dipole coupling model. For a test set of β-sheet stacks, the simulated amide I spectrum was analyzed with respect to the following parameters; intersheet distance, relative rotation of the sheets with respect to each other and the effect of number of sheets stacked. The amide I maximum shifts about 5 cm(-1) to higher wavenumbers when the intersheet distance between two identical β-sheets decreases from 20 to 5 Å. Rotation around the normal of one of the sheets relative to the other results in maximum intersheet coupling near 0° and 180°. Upon of rotation from 0° to 90° at an intersheet distance of 9 Å, the amide I maximum shifts about 3 cm(-1). Tilting of one of the sheets by 30° from the normal results in a shift of the amide I maximum by less than 1 cm(-1). When stacking several β-sheets along the normal, the amide I maximum shifts to higher wavenumbers with increasing stack size. The amide I maximum shifts about 6 cm(-1) when stacking four sheets with an intersheet distance of 9 Å. The study provides an aid in the interpretation of the IR amide I region for experiments involving β-sheets and creates awareness of the many effects that determine the spectrum of β-sheet structures.

MeSH terms

  • Amides / chemistry
  • Amyloid beta-Peptides / chemistry
  • Computer Simulation*
  • Models, Molecular*
  • Peptide Fragments / chemistry
  • Protein Folding
  • Protein Structure, Secondary*
  • Spectroscopy, Fourier Transform Infrared / methods

Substances

  • Amides
  • Amyloid beta-Peptides
  • Peptide Fragments
  • amyloid beta-protein (1-40)