Evaluation of interactions between residues in α-helices by exhaustive conformational search

Exhaustive conformational search is a simple and practical way to explore the entire conformational space available to a peptide (or molecular segment) with fewer than a dozen rotatable bonds. This chapter discusses the exhaustive conformational searches to evaluate interactions between pairs of hydrophobic side chains in mid-helix positions and to understand the motifs adopted by glycine-terminated helices. Hydrophobic interactions between residue side chains in an α-helix are thought to be helix-stabilizing. The chapter explains that exhaustive search techniques can be used to successfully model the interactions and small motifs that are characteristic of protein structure. It has been shown that small, stabilizing interactions can occur between two hydrophobic residues at appropriate spacings in the middle positions of an α-helix, in agreement with experimental findings. The two motifs adopted by glycine-terminated helices have also been rationalized and shown to be authentic helix stop signals.