Journal of Physical Chemistry B, Vol.115, No.4, 749-757, 2011
Simulation of the Amide I Absorption of Stacked beta-Sheets
Aggregated beta-sheet structures are associated with amyloid and prion diseases. Techniques capable of revealing detailed structural and dynamical information on beta-sheet structure are thus of great biomedical and biophysical interest. In this work, the infrared (IR) amide I spectral characteristics of stacked beta-sheets were modeled using the transition dipole coupling model. For a test set of beta-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 beta-sheets decreases from 20 to 5 angstrom. Rotation around the normal of one of the sheets relative to the other results in maximum intersheet coupling near 0 degrees and 180 degrees. Upon of rotation from 0 degrees to 90 at an intersheet distance of 9 angstrom, the amide I maximum shifts about 3 cm(-1). Tilting of one of the sheets by 30 degrees from the normal results in a shift of the amide I maximum by less than 1 cm(-1). When stacking several beta-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 angstrom. The study provides an aid in the interpretation of the IR amide I region for experiments involving beta-sheets and creates awareness of the many effects that determine the spectrum of beta-sheet structures.