Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities

Abstract

The alanine helix provides a model system for studying the energetics of interaction between water and the helical peptide group, a possible major factor in the energetics of protein folding. Helix formation is enthalpy-driven (-1.0 kcal/mol per residue). Experimental transfer data (vapor phase to aqueous) for amides give the enthalpy of interaction with water of the amide group as approximately -11.5 kcal/mol. The enthalpy of the helical peptide hydrogen bond, computed for the gas phase by quantum mechanics, is -4.9 kcal/mol. These numbers give an enthalpy deficit for helix formation of -7.6 kcal/mol. To study this problem, we calculate the electrostatic solvation free energy (ESF) of the peptide groups in the helical and beta-strand conformations, by using the delphi program and parse parameter set. Experimental data show that the ESF values of amides are almost entirely enthalpic. Two key results are: in the beta-strand conformation, the ESF value of an interior alanine peptide group is -7.9 kcal/mol, substantially less than that of N-methylacetamide (-12.2 kcal/mol), and the helical peptide group is solvated with an ESF of -2.5 kcal/mol. These results reduce the enthalpy deficit to -1.5 kcal/mol, and desolvation of peptide groups through partial burial in the random coil may account for the remainder. Mutant peptides in the helical conformation show ESF differences among nonpolar amino acids that are comparable to observed helix propensity differences, but the ESF differences in the random coil conformation still must be subtracted.

Figure 1

The calculated ESF of the peptide groups in an eight-residue alanine peptide, β-strand conformation are plotted against residue number. With the numbering system used here, the number of peptide groups equals the number of alanine residues because, in a series of peptides with varying numbers of alanine residues, the amide bond created by joining the N-terminal acetyl and C-terminal N-methyl blocking groups (to make N-methylacetamide) is not counted as a peptide bond. The ESFs have been calculated as outlined (13) by using delphi and the parse parameter set (11); the internal dielectric constant is 2, and the external dielectric constant is 80. The peptide geometry is generated by using insight ii with the φ,ψ backbone angles set to −120° and 120°, respectively, for the β-strand.

Figure 2

The calculated ESFs, in kcal/mol, of the peptide groups in two helical alanine peptides are plotted against residue number. The peptides contain either five or 15 alanine residues, plus N-terminal acetyl and C-terminal N-methylamide blocking groups. The backbone φ,ψ angles are −65° and −40° respectively. For other information, see legend to Fig. 1.

Figure 3

The calculated ESF values, in kcal/mol, are plotted against residue number for two blocked alanine peptides in the random coil conformation. The peptides contain either three or five alanine residues. The definition of the random coil conformation is given in the text and in ref. , and the method of calculating the results follows ref. .

Figure 4

Comparison between the measured helix propensity difference (6) (filled bars) and the calculated ESF difference for a mutant peptide versus an alanine host in either the β-strand conformation (empty bars) or the helical conformation (hatched bars). The units are kcal/mol. The comparison is made for Leu, Ile, and Val. The β-strand peptides contain five alanine residues plus N-terminal acetyl and C-terminal N-methylamide blocking groups, and only the central Ala residue is substituted by another amino acid. The ESF values of the five central residues of the mutant β-strand peptide are subtracted from those of the Ala peptide and then summed. The peptide sequence used for calculating ESF values in the helical conformation corresponds to the peptide sequence used for measuring helix propensities (6), which is Ac-K(A)₄X(A)₄KGY-NH₂, where X is either A, L, I, V, or G. In calculating ESF differences between helical peptides, the values for the five central peptide groups (groups 4–8) in the mutant peptide are subtracted from the corresponding values for the Ala peptide and then summed. The side-chain torsion angles are: Leu, χ1–60, χ2 180°; Ile, χ1–60, χ2 180°; Val, χ1 180°; the backbone angles are given in the legends to Figs. 1 and 2.