α-Helix stability in proteins: I. Empirical correlations concerning substitution of side-chains at the N and C-caps and the replacement of alanine by glycine or serine at solvent-exposed surfaces

Abstract

The importance of amino acid side-chains in helix stability has been investigated by making a series of mutations at the N-caps, C-caps and internal positions of the solvent-exposed faces of the two α-helices of barnase. There is a strong positional and context dependence of the effect of a particular amino acid on stability. Correlations have been found that provide insight into the physical basis of helix stabilization. The relative effects of Ala and Gly (or Ser) may be rationalized on the basis of solvent-accessible surface areas: burial of hydrophobic surface stabilizes the protein as does exposure to solvent of unpaired hydrogen bond donors or acceptors in the protein. There is a good correlation between the relative stabilizing effects of Ala and Gly at internal positions with the total change in solvent-accessible hydrophobic surface area of the folded protein on mutation of Ala → Gly. The relationship may be extended to the N and C-caps by including an extra term in hydrophilic surface area for the solvent exposure of the non-intramolecularly hydrogen-bonded mainchain CO, NH or protein side-chain hydrogen bonding groups. The requirement for solvent exposure of the C-cap main-chain CO groups may account for the strong preference for residues having positive φ and ψ angles at this position, since this α L -conformation results in the largest solvent exposure of the C-terminal CO groups. Glycine in an α L -conformation results in the greatest exposure of these CO groups. Further, the side-chains of His, Asn, Arg and Lys may, with positive φ and ψ-angles, form a hydrogen bond with the backbone CO of residue in position C − 3 (residues are numbered relative to the C-cap). The preferences at the C-cap are Gly ⪢ His > Asn > Arg > Lys > Ala ~ Ser ~ > Asp. The preferences at the N-cap are determined by hydrogen bonding of side-chains or solvent to the exposed backbone NH groups and are: Thr ~ Asp ~ Ser > Gly ~ Asn > Gln ~ Glu ~ His > Ala > Val ⪢ Pro. These general trends may be obscured when mutation allows another side-chain to become a surrogate cap. There is another empirical correlation between the relative stabilizing effects of Ala and Ser at internal positions in α-helices with the exposure of the Ser side-chain O γ group. The general trend in preference at internal positions is: Ala > Ser > Gly. The empirical correlations predict quantitatively the experimental results for the substitution of Ala by Gly or Ser found by other investigators in model systems. The simple correlations do not extend to substitutions by larger side-chains, since other physical principles, summarized in the accompanying paper, are invoked.