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

doi:10.1016/0022-2836(92)90906-Z

Journal of Molecular Biology

Volume 227, Issue 2, 20 September 1992, Pages 544-559

https://doi.org/10.1016/0022-2836(92)90906-Z Get rights and content

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.

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^†: Present address: European Molecular Biology Laboratory, Meyerhofstrasse 1, 6900 Heidelberg, Germany.

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Journal of Molecular Biology

Articleα-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

J. Mol. Biol

Cell

J. Mol. Biol

Trends Biochem. Sci

J. Mol Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

Gene

J. Mol. Biol

FEBS Letters

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

Helix-coil stability constants for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly(hydroxybutyl-glutamine-co-l-proline)

Biopolymers

Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr59

Biochemistry

Determination of the three dimensional solution structure of barnase using nuclear magnetic resonance spectroscopy

Biochemistry

Large differences in the helix propensities of Ala and Gly

Nature (London)

Hydrophobic bonding and surface accessible area in proteins

Nature (London)

The nature of the accessible and buried surfaces in proteins

J. Mol. Biol

Solvation energy in protein folding and stability

Nature (London)

Hydrogen bonding and biological specificity analysed by protein engineering

Nature (London)

Thermodynamic group contributions from ion pair extraction equilibrium for use in the prediction of partition coefficients. Correlation of surface area with group contributions

J. Phys. Chem

A two state conformational transition of the extracellular ribonuclease of Bacillus amyloliquefaciens (barnase) induced by sodium dodecyl sulfate

Biochemistry

Stabilization of λ repressor against thermal denaturation by site-directed Gly to Ala changes in α-helix 3

Proteins: Struct. Funct. Genet

Theory of hydrophobic bonding. II. The correlation of hydrocarbon solubility in water with solvent cavity surface area

J. Phys. Chem

Simulations of the static and dynamics properties of the DNA double helix

The role of the α-helix dipole in protein function and structure

Progr. Biophys. Mol. Biol

The alpha-helix dipole and the properties of proteins

Nature (London)

Article
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