Helix capping


In 1988, Richardson and Richardson observed that certain amino acid residues are stastically favored as the amino-terminal caps for the alpha helices in 45 globular proteins. The introduction of a negatively charged side chain at the N-cap, which can neutralize the partial dipole created by the unpaired amide protons, has been shown to increase stability in T4 lysozyme.In particular, Gly is often observed at the C-cap position , Asn at the N-cap position, Pro at the Ncap+1 and Asp and Glu at N2 and N3. The increased frequency of glycine residues at the C termini of seven helices in thermophilic citrate synthases was attributed to the capacity of glycine to adopt the alphaL conformation at the C cap without strain. A related analysis of the N and C capping preferencds for all 20 aminoacids in alpha helical peptides found that the N cap preferences of peptides and protein are retained, but that glycine was not preferred in the C cap of peptide helices. This may reflect a greater need for correct helix termination in proteins and its role in structure stabilization.

Graphs of preferences values for individual amino acids

Stereo images of N cap and C cap