ALPHA-HELIX STABILITY AND THE NATIVE-STATE OF MYOGLOBIN

Native proteins fold to form structures that contain secondary-structu re regular patterns in the peptide backbone, such as alpha-helix, beta -structure, and turns with high frequency. The role of this secondary structure in stabilizing the native folded state is presently unclear. Alanine substitutions at helical sites in myoglobin show no correlati on with the helical propensity of the side chains involved. In an effo rt to demonstrate a relationship between the effect of a side chain on stabilizing secondary structure and the native structure, we have car ried out site-directed changes in the sequence of the helical protein sperm whale myoglobin. Fully buried hydrophobic side chains were excha nged for similar side chains at sites corresponding to midhelical posi tions in the native state. The results show a positive correlation bet ween the alpha-helix-forming ability of the substituted side chain and the stability of the mutant proteins, when differences between the si ze of the side chains are taken into account. If in addition, each typ e of amino acid substitution is averaged over different sites, the hel ix propensities of the amino acids account for much of the residual va riation. This implies that the stability of the native state of a prot ein is coupled to that of secondary structural elements in the structu re. In magnitude, the net contribution of propensity differences is sm aller than hydrophobic effects, but not negligible in terms of the net free energy of unfolding.