Peptides in Lipid Bilayers: Determination of Location by Absolute-Scale X-ray Refinement

Abstract

The amphipathic α-helix structural motif is frequently encountered in membrane proteins [1,2] and membrane-active peptides such as toxins [3–5] and antimicrobial peptides [6–8]. Its structural utility apparently arises from the thermodynamic advantage gained by matching its polar/non-polar surfaces to those of the water/lipid interfaces of micelles and bilayers. Despite the simplicity of this general idea and a large amount of empirical data [9,10], quantitative predictions about the interaction of a specific peptide sequence with a particular lipid system are problematic because of the lack of structure-based quantitative principles. Such principles are most likely to emerge from coordinated, systematic studies of peptide-bilayer interactions using thermodynamic and direct structural methods [11–14]. Recently, we have obtained the first direct views of an amphipathic α-helix in fluid lipid bilayers using a novel x-ray diffraction method [15]. The method, referred to as absolute-scale refinement, is derived from so-called liquid crystallography [16–18]. In this chapter we show how absolute-scale refinement can be used to obtain quantitative information about the position, orientation, and conformation of a helical peptide in a fluid lipid bilayer and about the perturbations of the bilayer structure caused by the peptide. The ability to obtain such information is essential for testing theories and algorithms that have been developed for predicting the orientation and the penetration depth of peptides and proteins in lipid bilayers based upon amino acid sequence [19–23].