How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins

Abstract

To determine how different amino acid sequences form similar protein structures, and how proteins adapt to mutations that change the volume of residues buried in their close-packed interiors, we have analysed and compared the atomic structures of nine different globins. The homology of the sequences in the two most distantly related molecules is only 16%. The principal determinants of three-dimensional structure of these proteins are the approximately 59 residues involved in helix to helix and helix to haem packings. Half of these residues are buried within the molecules. The observed variations in the sequence keep the side-chains of buried residues non-polar, but do not maintain their size: the mean variation of the volume among homologous amino acids is 56 Å 3. Changes in the volumes of buried residues are accompanied by changes in the geometry of the helix packings. The relative positions and orientations of homologous pairs of helices in the globins differ by rigid body shifts of up to 7 Å and 30 °. In order to retain functional activity these shifts are coupled so that the geometry of the residues forming the haem pocket is very similar in all the globins. We discuss the implications of these results for the mechanism of protein evolution.