DESIGN OF HELIX ENDS - AMINO-ACID PREFERENCES, HYDROGEN-BONDING AND ELECTROSTATIC INTERACTIONS

The amino acid sequence and chemical interactions at the ends of 163 helices were surveyed so as better to understand amino acid preferences previously observed [Richardson, J.S. & Richardson, D.C. (1988) Science 240, 1648-1652]. Amino acid preferences differed from the previous survey in some significant details and in ways that might affect the choice of amino acids during the design of a protein helix. The following major conclusions about helix ends were deduced from additional patterns of amino acid occurrence and interactions that were observed. (1) A specific pair of hydrogen bonds is often observed between a glutamic acid (or glutamine) side chain at the N3 position and the N-cap amide hydrogen, and between the N-cap side chain (often threonine) and the N3 amide hydrogen. This reciprocal interaction may be an important means of stabilizing the N-terminal end of a helix. (2) Negatively charged amino acids (aspartic acid and glutamic acid) at the N-terminal end of helices may be more important in stabilizing protein helices than positively charged residues (chiefly lysine) at the C-terminal end. (3) The identity of the residue at the N-cap position is correlated with the backbone conformation at that position. (4) Aspartic acid (or asparagine) at the N2 or N3 position may adopt a conformation that suggests a hydrogen-bonding interaction with the end of the helix, especially when the N-cap side chain does not form a hydrogen bond with the end of the helix.