Intermolecular anti-parallel beta sheet: Comparison of predicted and observed conformations of gramicidin S

Abstract

A recently determined x-ray structure of the hydrated gramicidin S-urea complex is compared with a structure predicted by conformational energy minimization. It is shown that the two structures are in good general agreement, including the prediction of a hydrogen bond between the side-chain amino group of ornithine and the backbone carbonyl of phenylalanine. This agreement demonstrates the power of empirical potential energy methods in conformational analysis and illustrates one method for solution of the multiple-minimum problem for small peptides. It is noted that, in the crystal, gramicidin S is a dimer that forms an intermolecular antiparallel four-stranded beta sheet and that differences between the predicted and x-ray structures can be explained by this intermolecular interaction. The residual conformational asymmetry of the x-ray structure is shown to be due to the formation of the complex with urea.